From 92241aea027cdd0df1c771b56007279a1b04c273 Mon Sep 17 00:00:00 2001 From: Digital Drosophila Archive Date: Wed, 30 Sep 2026 07:23:09 +0800 Subject: [PATCH] Validate isolated author LIF semantics without changing frozen models --- CURRENT.md | 69 +- docs/progress/phase4ad-author-semantics.md | 71 + docs/progress/phase4ad-interpretation.md | 54 + .../author-semantics-lab-v1/PROTOCOL.md | 71 + .../author-semantics-lab-v1/checksums.sha256 | 12 + .../author-semantics-lab-v1/config.json | 36 + .../author-semantics-lab-v1/context.py | 27 + .../author-semantics-lab-v1/finalize.py | 411 ++ .../interface_audit.py | 149 + .../author-semantics-lab-v1/manifest.json | 67 + .../author-semantics-lab-v1/math_lab.py | 70 + .../author-semantics-lab-v1/oracle_runner.py | 346 ++ .../author-semantics-lab-v1/prepare.py | 56 + .../requirements-oracle.txt | 20 + .../author-semantics-lab-v1/run_lab.py | 158 + .../author-semantics-lab-v1/verify_frozen.py | 47 + .../evidence-index.json | 2648 +++++++++++++ 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Phase 4AD -最新结果：**COMPLETE-SEMANTICS-AUDIT / LEARNING-NOT-ACHIEVED**。 -学习可用的总目标尚未达到，不把审计 PASS 当成学习 PASS。 -初始化 README/registry 保留原字节，最新结论从本页进入。 +已按用户授权建立独立分支 `codex/lif-author-semantics-lab`。 +正式状态：**COMPLETE-ORACLE-VALIDATED-LAB-ONLY**。 +学习仍未达到可用标准；不替换任何旧候选，不把实现检查PASS当作学习PASS。 -- [中文机制结论及限制](docs/progress/phase4ac-interpretation.md) -- [完整小回路/单细胞结果](docs/progress/phase4ac-lif-semantics.md) -- [预先声明的诊断方案](models/male-cns-lif/lif-semantics-audit-v1/PROTOCOL.md) -- [新阶段校验清单](registry/phase4ac-lif-semantics/seal-verification.json) -- [上一轮末梢作用范围诊断](docs/progress/phase4ab-terminal-scope.md) -- [小回路与全脑背景的只读复核](docs/progress/feedback-context-review-20260930.md) +- [关键结果、限制与下一步](docs/progress/phase4ad-interpretation.md) +- [完整实验报告](docs/progress/phase4ad-author-semantics.md) +- [实验预声明](models/male-cns-lif/author-semantics-lab-v1/PROTOCOL.md) +- [新产物封存核验](registry/phase4ad-author-semantics/seal-verification.json) +- [此前全脑输入背景复核](docs/progress/feedback-context-review-20260930.md) -## 后续只读复核的重要限制 +## 关键发现 -所选五节点只贡献三个 ALLN 晚期正到达权重的 7.57%–8.99%；达到各自80%正输入需要49–52个来源。 -因此孤立小回路可以自持，不意味着它是全脑唯一原因。回路外输入也可能受该回路反馈影响，不是已证明独立的外源驱动。 -对旧数据的派生分解没有新模拟或训练；正输入比例不能当因果责任比例。 -独立新模型分支尚待用户确认，不把持续目标自动当作改变冻结动力学的许可。 +固定作者代码在Brian2 2.5.1实际运行。16项单元检查、10组真实回路/精度对照及其重复通过；58/58审计项通过。 +恢复作者完整动力学后，五节点真实回路1秒放电从1,483降到610，但后500ms仍有306次。 +因此不能认为“修g reset/不应期就解决学习问题”；持续循环仍存在，低活跃度不是晋级条件。 -## 新增机制证据 +下一步先做独立GPU实现的高入度/累加顺序与短时全图对照，再检验固定DoOR嗅觉输入是否保留区别；尚未开始conditioning。 +输入请求、不应期拒绝和实际放电必须分开统计。后续学习必须执行真实无调制/冻结/随机奖励对照和等待期，而非复用标签。 -只施加一次初始 spike，使用原有冻结动力学： +## 冻结与服务 -| 真实小回路 | 1 s 内总 spike | 500–1,000 ms spike | -|---|---:|---:| -| 2 个 ALLN | 473 | 238 | -| 3 个 ALLN | 1,064 | 535 | -| 3 ALLN + VA6 PN + KC | 1,483 | 747 | -| 真实前向边对照 | 3 | 0 | -| 无初始刺激 | 0 | 0 | +原230,239项以及4AA/4AB/4AC与背景复核封存文件前后校验不变。 +旧deterministic-v2五组全脑参考重新运行，事件、计数、最终电压和g精确一致。 +base CSR、raw counts、W_syn、transmitter signs、APL参数、eligibility-v2、14,232-edge mask未修改。 +只在独立实验环境安装作者版本依赖；未停用或修改ComfyUI。 +没有游戏、RL、decoder、视觉输入或权重训练，没有生成新的learned candidate。 -最小回路：body 11478 → 11620（235 contacts），11620 → 11478（283 contacts），两者为 lLN1_bc / ACh。 -单次输入足以在隔离小回路中产生持续到观察期末的活动；不代表已证明全脑必要性，也不代表真实果蝇该回路必然如此。 - -## 原作者实现与本项目适配差异 - -固定作者代码在 spike 后清零 g，对不应期内 g 更新/输入设限，并有不同积分、阈值和刺激时序。 -本项目冻结版本明确保留 g，继续衰减/接收输入。这是建模语义差异，不是本轮发现的 GPU 回归错误。 -单细胞组件测试证明这些选择会改变响应，但真实连接强度的一次输入下，reset-only 并未改变 spike 数。 -因此 **g reset 不得直接称为学习修复**，也不能仅据放电减少自动选择新模型。 - -## 验证与下一步 - -7 项单元测试、17×4 单细胞 fixture、5 个真实小回路 CPU/GPU 全状态/事件精确对照通过。 -五组 deterministic-v2 全脑冻结参考 trial 精确一致。 -原快照 230,239 项及 Phase 4AA / 4AB 模型与实验前后校验无变化。 -新产物有独立 manifest/SHA-256；未训练、未生成 learned candidate。 -ComfyUI 保持驻留，不停用、不卸载、不升级依赖。 - -后续需要明确授权的独立动力学模型分支：先验证原作者 oracle 和局部机制，再检查输入区别与学习功能。 -仍要求独立 evaluation seeds、A 对 B 的特异性、MBON/downstream readout 和完整 conditioning controls。 -不调整学习率/阈值或扩大 mask，不进入游戏、RL、decoder、视觉；不修改已冻结版本。 - -Git 仅同步代码、小报告、官方小型源代码及校验清单。大数据/完整 spike 输出仍在服务器，不等于完整异机备份。 +代码、小报告、来源和校验清单进入Git；大数据及完整实验轨迹保留服务器，不等于完整异机备份。 diff --git a/docs/progress/phase4ad-author-semantics.md b/docs/progress/phase4ad-author-semantics.md new file mode 100644 index 0000000..38f8de1 --- /dev/null +++ b/docs/progress/phase4ad-author-semantics.md @@ -0,0 +1,71 @@ +# Phase 4AD 作者动力学语义实验室 + +状态：`COMPLETE-ORACLE-VALIDATED-LAB-ONLY`。 + +本轮仅有预声明的小回路与算子实验；没有整脑替代动力学运行、conditioning、学习成功或新学习候选。 +检查以原始事件、状态轨迹和预注册误差界限重算。缺失、失败、非有限值或初始事件丢失均不能通过；放电减少或静默本身不构成成功。 + +核查通过 58/58 项；失败或不完整 0 项。 +冻结历史完整性：通过。 +源码与输入预注册一致性：通过。 + +| 回路 | 语义 | 精度 | 总spikes | late spikes | +|---|---|---|---:|---:| +| pair | frozen | float32 | 473 | 238 | +| pair | reset_g_only | float32 | 223 | 111 | +| pair | refractory_gate_only | float32 | 635 | 321 | +| pair | reset_and_refractory | float32 | 223 | 111 | +| trio | frozen | float32 | 1064 | 535 | +| trio | reset_g_only | float32 | 565 | 283 | +| trio | refractory_gate_only | float32 | 1100 | 552 | +| trio | reset_and_refractory | float32 | 469 | 235 | +| five | frozen | float32 | 1483 | 747 | +| five | reset_g_only | float32 | 868 | 433 | +| five | refractory_gate_only | float32 | 1510 | 763 | +| five | reset_and_refractory | float32 | 634 | 318 | +| feedforward | frozen | float32 | 3 | 0 | +| feedforward | reset_g_only | float32 | 3 | 0 | +| feedforward | refractory_gate_only | float32 | 3 | 0 | +| feedforward | reset_and_refractory | float32 | 3 | 0 | +| no_input | frozen | float32 | 0 | 0 | +| no_input | reset_g_only | float32 | 0 | 0 | +| no_input | refractory_gate_only | float32 | 0 | 0 | +| no_input | reset_and_refractory | float32 | 0 | 0 | +| pair | author_complete | float64 | 213 | 106 | +| pair | author_complete | float32 | 213 | 106 | +| trio | author_complete | float64 | 448 | 224 | +| trio | author_complete | float32 | 448 | 224 | +| five | author_complete | float64 | 610 | 306 | +| five | author_complete | float32 | 610 | 306 | +| feedforward | author_complete | float64 | 3 | 0 | +| feedforward | author_complete | float32 | 3 | 0 | +| no_input | author_complete | float64 | 0 | 0 | +| no_input | author_complete | float32 | 0 | 0 | + +作者Brian2与独立NumPy比较： + +| 实验 | 结果 | 事件一致 | 最大V/g误差 mV | 首次事件分歧step | +|---|---|---|---:|---:| +| author:pair:float64 | 通过 | True | 7.105427357601002e-14 | None | +| author:pair:float32 | 通过 | True | 2.41696834564209e-05 | None | +| author:trio:float64 | 通过 | True | 8.526512829121202e-14 | None | +| author:trio:float32 | 通过 | True | 4.25875186920166e-05 | None | +| author:five:float64 | 通过 | True | 3.836930773104541e-13 | None | +| author:five:float32 | 通过 | True | 0.0002123713493347168 | None | +| author:feedforward:float64 | 通过 | True | 3.765876499528531e-13 | None | +| author:feedforward:float32 | 通过 | True | 0.00020179152488708496 | None | +| author:no_input:float64 | 通过 | True | 7.105427357601002e-15 | None | +| author:no_input:float32 | 通过 | True | 1.0728836059570312e-06 | None | + +float32与float64交叉比较仅记录精度影响，允许保留分歧，不能用于掩盖各自与独立oracle的失败。 +- precision_cross_record:pair：事件一致=True，最大误差=3.733467101341148e-05 mV，首次事件分歧step=None。 +- precision_cross_record:trio：事件一致=True，最大误差=3.733467101341148e-05 mV，首次事件分歧step=None。 +- precision_cross_record:five：事件一致=True，最大误差=0.00019546693161487383 mV，首次事件分歧step=None。 +- precision_cross_record:feedforward：事件一致=True，最大误差=0.0005722045887850413 mV，首次事件分歧step=None。 +- precision_cross_record:no_input：事件一致=True，最大误差=0.0 mV，首次事件分歧step=None。 + +所有失败轨迹和错误文件原样保留；本简报没有选择获胜变体。 +小回路缺少外部整脑输入与graded APL，不能证明整脑因果必要性、生物真实性或信息保持。初始诊断seed也不是作者的感官Poisson接口。 +环境为Linux宿主，作者记录为Windows；Python补丁版本与环境差异见environment记录，不能称为二进制相同或原论文整脑复现。 +后续整脑嗅觉比较仍须核查固定输入、实际送达事件、持续活动和信息保持；可用学习仍需至少5个训练seed、独立评估、MBON/downstream的A对中性B特异性及acquisition/reversal/retention/delayed-reward对照。 +封存排除 .venv 与 __pycache__，保留环境安装报告；manifest列出payload哈希，checksums另含manifest，不存在自哈希循环。 diff --git a/docs/progress/phase4ad-interpretation.md b/docs/progress/phase4ad-interpretation.md new file mode 100644 index 0000000..684bfad --- /dev/null +++ b/docs/progress/phase4ad-interpretation.md @@ -0,0 +1,54 @@ +# 独立模型分支首轮结果：实现正确，不等于学习修复 + +用户明确授权独立新模型分支测试动力学假设。分支为 `codex/lif-author-semantics-lab`， +模型目录 `models/male-cns-lif/author-semantics-lab-v1/`，实验目录 `experiments/phase4ad-author-semantics/`。 +Phase 1–4AC 保持原样；没有替换已有候选、训练、调学习率、扩大mask或连接游戏。 + +## 已验证的结果 + +正式状态 `COMPLETE-ORACLE-VALIDATED-LAB-ONLY`，58/58审计项通过。 +实际运行固定作者代码的 `create_model`，并与独立解析积分实现对照，而非仅比较两份自写程序。 +8项算子/边界fixture各测试float64与float32；5个固定真实motif各测试两种精度，分别重复。 +各精度内的spike事件、计数和不应期逐步一致，重复运行逐数组精确一致。 +五个motif的float32与float64事件也一致，但不能外推到全脑高入度累加。 +float64最大V/g差约3.84e-13 mV；float32独立实现相对Brian2最大差约2.12e-4 mV。 + +| 真实回路 | 旧冻结模型1秒总spike | 完整作者语义总spike | 作者语义后500ms spike | +|---|---:|---:|---:| +| 两个ALLN | 473 | 213 | 106 | +| 三个ALLN | 1,064 | 448 | 224 | +| 三ALLN + VA6 PN + KC | 1,483 | 610 | 306 | +| 前向真实边对照 | 3 | 3 | 0 | +| 无刺激 | 0 | 0 | 0 | + +**持续循环没有因恢复作者语义而消失。** 放电减少不是学习成功，也没有据此挑选获胜参数。 +单独限制不应期内g更新甚至提高了这些回路的放电；不能把单一算子改动当作通用修复。 +小回路省略了大部分全脑输入和graded APL，不能证明全脑问题完全由这些连接引起。 +此前全脑背景复核显示，三个ALLN的晚期正到达权重约91%以上来自所选五节点之外；这也不是因果责任百分比。 + +## 作者参考及边界 + +- 官方代码：`philshiu/Drosophila_brain_model`，commit `91bdd1e7dcf193f3e7ca5a8933497fcef63b7960`，MIT。 +- [原作者论文](https://www.nature.com/articles/s41586-024-07763-9)；[固定代码版本](https://github.com/philshiu/Drosophila_brain_model/tree/91bdd1e7dcf193f3e7ca5a8933497fcef63b7960)。 +- Brian2 2.5.1，独立Linux环境；作者记录为Windows/Python3.10.11，此处Linux/Python3.10.12，不能称为二进制相同。 +- 原始g单位为volt，是加性输入状态，不是电导；reset中的局部`w=0`不会清零真实Synapses权重。 +- 原`poi`接口另做了零时长编译审计：向v加入68.75mV、150Hz、N=1，并将目标不应期置零。它不是本轮共同初始seed，也不是已验证的新嗅觉接口。 +- 安装只发生在新实验`.venv`，保存下载URL与归档SHA-256；MarkupSafe1.1.1使用源归档，其他核心包使用wheel。未改旧科学环境或ComfyUI。 + +## 下一关 + +1. 独立GPU实现须补足高入度、正负抵消、逐边加法顺序、非零初始g、阈值临界值与延迟队列边界测试；禁止用`g+sum(w)`擅自代替作者逐边写入。 +2. 在短时全图上对照事件及状态，再开展固定DoOR嗅觉CAL。保持既有输入请求，不顺手切换为作者的rfc=0输入接口；分别统计请求、因不应期拒绝与实际放电。 +3. CAL通过后才能使用独立seed及新odor验证。不能靠低活跃度或held-out调参授予成功。 +4. 真正conditioning须重新执行D(t)=0、frozen与随机奖励路径，并真正推进retention等待时间；旧脚本中复用基线/新建状态的检查不能替代这些端到端验证。 +5. 全部学习结论仍以MBON/downstream的刺激特异性、acquisition/reversal/retention/delayed reward为准，至少5个training seeds与独立evaluation seeds。 + +## 完整性和保存 + +原快照230,239项及4AA、4AB、4AC、背景复核产物前后SHA-256无变化。 +旧deterministic-v2五个全脑冻结trial重新执行，事件、计数、最终V/g逐数组相同。 +4090回归峰值已分配显存285,994,496字节；这不是新动力学全脑性能benchmark。 +新模型11个payload、新实验565个payload已独立封存，环境目录不纳入payload。 +Git同步代码、小报告和校验清单；大数据及完整状态轨迹仍在服务器，不能称为完整异机备份。 + +详见[完整结果](phase4ad-author-semantics.md)、[封存核验](../../registry/phase4ad-author-semantics/seal-verification.json)。 diff --git a/models/male-cns-lif/author-semantics-lab-v1/PROTOCOL.md b/models/male-cns-lif/author-semantics-lab-v1/PROTOCOL.md new file mode 100644 index 0000000..e15a294 --- /dev/null +++ b/models/male-cns-lif/author-semantics-lab-v1/PROTOCOL.md @@ -0,0 +1,71 @@ +# Phase 4AD — independently authorized author-semantics laboratory + +Human authorization: "允许独立新模型分支测试动力学假设". +Goal remains usable stimulus-specific learning, not reducing spike count or passing an isolated fixture. + +All Phase 1–4AC scientific artifacts, canonical CSR/raw counts, transmitter signs, +W_syn=0.275, APL calibration, eligibility-v2 and the 14,232-edge plastic mask are +read-only. No training, threshold/gain/eta search, decoder, game or visual work in +this prerequisite laboratory. Existing candidate names are not replaced. + +## Fixed comparison before results + +Use the exact five preselected 4AC motifs and the same initial single seed event, +not newly selected cells. Record all five outcomes, including persistent firing. +Preserve true edge IDs, counts and original global neuron_idx/body_id. + +1. Reproduce frozen explicit float32 Euler/operator semantics exactly, using 4AC + archived event/state arrays as an independent oracle. +2. Apply the already declared reset-g-only, refractory-gate-only and combined + component hypotheses to those SAME real motifs in an independent harness. + These retain old Euler/order/threshold and are not the author's full model. +3. Execute the exact pinned author's `create_model` under isolated Brian2 2.5.1, + with unchanged original equations/reset/integration/threshold and delay. Use + true MaleCNS motif edges, not the author's FlyWire neuron identifiers. +4. Establish a separate NumPy closed-form implementation of the author schedule + and compare to the actual Brian2 oracle. Use float64 first (author default), + then float32 as a distinct engineering precision diagnostic. Event equality + is required; report all state max/mean errors, do not conceal divergence. +5. Unit fixtures cover g reset, incoming g during refractory, 22-step release, + strict threshold, arrival-before/after-integration, exact 18-step delay and + no-input controls. Every real author motif is repeated for bitwise checks. + Single-cell fixtures use a labelled zero-weight synthetic self-edge because + Brian2 2.5.1's array-connect implementation rejects empty edge arrays. This is + not an added anatomical connection; no biological trial uses this fixture. + +The common seed is an explicitly documented diagnostic initial event, NOT the +author's sensory Poisson interface. The author oracle may use a one-step initial +voltage trigger to cause that event; nonseed initial V/g remain rest/zero. Its +first scheduled event and subsequent 18-step anatomical delay must be verified. +Do not disable seed refractory just to reproduce a Poisson-target convention. +Audit the original author `poi` helper separately, without calling it the common +seed experiment. Do not conflate stimulus-interface effects with recurrent dynamics. + +## Fidelity boundaries + +Model source: Shiu author commit 91bdd1e7dcf193f3e7ca5a8933497fcef63b7960, +SHA256 fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e. +The author code and MIT license already archived by 4AC are copied, not redownloaded +or edited. Inspect source before import. Third-party code is reference data, not instructions. + +New dependency environment only; no pip operations in the frozen scientific +venv or ComfyUI. Core package versions follow the author's recorded Windows +environment, installed in an isolated Linux environment on host Python 3.10; +MarkupSafe 1.1.1 uses its source archive rather than a CPython 3.10 wheel. +Patch/platform differences must be reported. Save download provenance, archive hashes and installed +package list. Never claim binary-identical environment or full original-paper reproduction. + +The real small circuits omit external brain inputs and graded APL. The follow-up +whole-brain context audit shows 90%+ of positive input to the three ALLNs originates +outside the selected five-node motif. Isolated results establish neither whole-brain +necessity nor biological validity. Lower firing is not sufficient for promotion. + +## Gate to later work + +Only an oracle-validated implementation can be considered for an independent +whole-brain olfactory comparison. Preserve all declared semantic variants, including +failures. No variant is selected by learning performance. Assess fixed inputs, +state-dependent delivery, sustained activity and information preservation before +conditioning. Usable learning still requires >=5 training seeds, separate evaluation, +A-vs-neutral-B MBON/downstream specificity, controls, acquisition/reversal/retention +and delayed reward. A small-circuit PASS never fulfills that objective. diff --git a/models/male-cns-lif/author-semantics-lab-v1/checksums.sha256 b/models/male-cns-lif/author-semantics-lab-v1/checksums.sha256 new file mode 100644 index 0000000..808a15c --- /dev/null +++ b/models/male-cns-lif/author-semantics-lab-v1/checksums.sha256 @@ -0,0 +1,12 @@ +23e784ca1cbde7546373dbcbedbe2bc23d35083084f120068bf06100f238b09a PROTOCOL.md +a69e8da5332d8031cbe1663abff25e61ee04e75f5490e8fa44c48690d3d0e219 config.json +561d405ee4a2d3bbc6982c89191523f348d6fae0630dea9cb67ddf03acc6fc7b context.py +97a393b95d100dc5d95b624e4cd0d15511307b8c70e0ebd788b773c143ebfed6 finalize.py +1e2b31545f1206fe1c1f4084b4a9ac0f21c74990c52e8fd156e809725fc5fb95 interface_audit.py +9663da41d5f623e1d7750e3cad3df880148079968f115bf583b58799fc5fb31f math_lab.py +2f4b073261965cf18a94697caf725c40b2e8db790c2871862201337f40c399e5 oracle_runner.py +49caa9553938f06539ecf282868491f8e1319d8f24220f89ac9e232db2d82e51 prepare.py +a69efc6509b85a5cc00a652caa4820c9c9e1406f6b97c6cc741322728c4d51c3 requirements-oracle.txt +8746e1971c5a40a738e10f8f574a243c29cefa5a8b9f61a2846557ceffd1289a run_lab.py +fe37a48ce804e6c50f93404bfd3c23a7e54cd49061bbdfb4860315879648c73b verify_frozen.py +07a22bade4892adca3a4585656aa3ecce5219790b0dc8a851a12bfd7248d3769 manifest.json diff --git a/models/male-cns-lif/author-semantics-lab-v1/config.json b/models/male-cns-lif/author-semantics-lab-v1/config.json new file mode 100644 index 0000000..dc9699b --- /dev/null +++ b/models/male-cns-lif/author-semantics-lab-v1/config.json @@ -0,0 +1,36 @@ +{ + "name": "author-semantics-lab-v1", + "phase": "4AD", + "root": "/data/digital-drosophila", + "experiment": "experiments/phase4ad-author-semantics", + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "human_authorization": "允许独立新模型分支测试动力学假设", + "dt_ms": 0.1, + "duration_ms": 1000.0, + "seed_margin_mv": 1.0, + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "synaptic_tau_ms": 5.0, + "refractory_ms": 2.2, + "resting_potential_mv": -52.0, + "reset_potential_mv": -52.0, + "threshold_mv": -45.0, + "synaptic_delay_ms": 1.8, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "seed_node": 1381, + "motifs": ["pair", "trio", "five", "feedforward", "no_input"], + "component_policies": ["frozen", "reset_g_only", "refractory_gate_only", "reset_and_refractory"], + "author_precisions": ["float64", "float32"], + "comparison": { + "float64_state_max_abs_tolerance_mv": 0.00000001, + "float32_state_max_abs_tolerance_mv": 0.001, + "exact_spike_events_required_for_oracle_validation": true, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "no_training_or_candidate": true +} diff --git a/models/male-cns-lif/author-semantics-lab-v1/context.py b/models/male-cns-lif/author-semantics-lab-v1/context.py new file mode 100644 index 0000000..65c1654 --- /dev/null +++ b/models/male-cns-lif/author-semantics-lab-v1/context.py @@ -0,0 +1,27 @@ +import hashlib +import json +from pathlib import Path + +MODEL=Path(__file__).resolve().parent +CFG=json.loads((MODEL/'config.json').read_text(encoding='utf-8')) +ROOT=Path(CFG['root']);EXP=ROOT/CFG['experiment'];AC=ROOT/CFG['prior_experiment'] + +def digest(path): + h=hashlib.sha256() + with Path(path).open('rb') as f: + for b in iter(lambda:f.read(8<<20),b''):h.update(b) + return h.hexdigest() + +def save(path,value): + path=Path(path);path.parent.mkdir(parents=True,exist_ok=True) + with path.open('x',encoding='utf-8') as f:json.dump(value,f,indent=2,ensure_ascii=False,allow_nan=False);f.write('\n') + +def source_hashes(): + return {p.name:digest(p) for p in sorted(MODEL.iterdir()) if p.is_file() and p.name not in ('manifest.json','checksums.sha256')} + +def check_prereg(): + pre=json.loads((EXP/'protocol/preregistered.json').read_text()) + assert pre['source_hashes']==source_hashes(),'Source changed after preregistration' + for r in pre['input_hashes']: + assert digest(ROOT/r['path'])==r['sha256'],r['path'] + return pre diff --git a/models/male-cns-lif/author-semantics-lab-v1/finalize.py b/models/male-cns-lif/author-semantics-lab-v1/finalize.py new file mode 100644 index 0000000..fa08966 --- /dev/null +++ b/models/male-cns-lif/author-semantics-lab-v1/finalize.py @@ -0,0 +1,411 @@ +"""Seal a descriptive laboratory audit, including incomplete and failed runs. + +Run this with the frozen scientific environment, not the isolated Brian2 venv. +No simulation, parameter selection, candidate promotion or old-artifact write occurs. +""" +from datetime import datetime, timezone +import json +import math +from pathlib import Path +import sys +import traceback + +import numpy as np +import pandas as pd + +from context import CFG, EXP, MODEL, ROOT, check_prereg, digest, save, source_hashes +from prepare import frozen_integrity + + +UNIT_NAMES = ("zero", "weak_excitation", "inhibition", "refractory_boundary", + "equal_threshold", "above_threshold", "nonzero_g_reset", "delay_18") +EXCLUDED_PARTS = {".venv", "__pycache__"} +SEAL_NAMES = {"manifest.json", "checksums.sha256"} + + +def read_json(path): + with Path(path).open(encoding="utf-8") as stream: + return json.load(stream, parse_constant=lambda value: (_ for _ in ()).throw( + ValueError("Nonfinite JSON number: " + value))) + + +def exception_record(error): + return {"type": type(error).__name__, "message": str(error), + "traceback": traceback.format_exc()} + + +def attempt(records, name, function): + """Never let an earlier failed arm hide subsequent available evidence.""" + try: + detail = function() + if not isinstance(detail, dict) or type(detail.get("pass")) is not bool: + raise ValueError("Check must provide an explicit Boolean pass") + item = {"name": name, **detail} + except Exception as error: + item = {"name": name, "pass": False, "error": exception_record(error)} + records.append(item) + return item + + +def require(condition, message): + if not condition: + raise ValueError(message) + + +def load_trace(directory, expected_nodes, steps, cfg, seed_node, natural_events=False): + events = pd.read_csv(directory / "events.csv", dtype={"step": "int64", "neuron_idx": "int64"}) + require(list(events.columns) == ["step", "neuron_idx"], "Unexpected event columns") + for key in ("step", "neuron_idx"): + values = events[key].to_numpy() + require(np.isfinite(values).all() and np.equal(values, np.floor(values)).all(), + "Nonfinite or nonintegral event field: " + key) + ticks = events.step.to_numpy(np.int64) + nodes = events.neuron_idx.to_numpy(np.int64) + require(bool(np.all((ticks >= 0) & (ticks < steps))), "Event outside trial") + require(bool(np.all(np.diff(ticks) >= 0)), "Events not time ordered") + require(not events.duplicated().any(), "Duplicate event at one neuron/timestep") + require(bool(np.isin(nodes, expected_nodes).all()), "Event identity outside motif") + with np.load(directory / "state.npz", allow_pickle=False) as stored: + state = {key: stored[key].copy() for key in stored.files} + require(np.array_equal(state["nodes"], expected_nodes), "State neuron order differs") + history = state["history"] + require(history.shape == (steps, 3, len(expected_nodes)), "Incomplete state history") + require(all(np.isfinite(value).all() for value in state.values()), "Nonfinite state") + actual_counts = np.array([np.count_nonzero(nodes == node) for node in expected_nodes]) + require(np.array_equal(state["counts"], actual_counts), "Counts disagree with raw events") + for index, key in enumerate(("v", "g", "ref")): + require(np.array_equal(state[key], history[-1, index]), + "Final state disagrees with history: " + key) + if seed_node is None and not natural_events: + require(len(ticks) == 0, "No-input control emitted a spike") + elif seed_node is not None: + require(np.array_equal(nodes[ticks == 0], [seed_node]), + "Declared initial seed event missing or duplicated") + late = ticks >= round(cfg["late_start_ms"] / cfg["dt_ms"]) + per_node = [{"neuron_idx": int(node), "spikes": int(actual_counts[index]), + "late_spikes": int(np.count_nonzero(late & (nodes == node))), + "last_ms": float(ticks[nodes == node][-1] * cfg["dt_ms"]) + if actual_counts[index] else None} + for index, node in enumerate(expected_nodes)] + return {"step": ticks, "neuron_idx": nodes, **state}, per_node + + +def compare_raw(actual, expected, tolerance): + require(math.isfinite(tolerance) and tolerance >= 0, "Invalid preregistered tolerance") + a = np.asarray(actual["history"], np.float64) + b = np.asarray(expected["history"], np.float64) + require(a.shape == b.shape and a.size > 0, "Incomplete comparison trajectories") + require(np.isfinite(a).all() and np.isfinite(b).all(), "Nonfinite comparison trajectory") + error = np.abs(a[:, :2] - b[:, :2]) + exact_events = bool(np.array_equal(actual["step"], expected["step"]) and + np.array_equal(actual["neuron_idx"], expected["neuron_idx"])) + first = None + if not exact_events: + for step in range(len(a)): + aa = actual["neuron_idx"][actual["step"] == step] + bb = expected["neuron_idx"][expected["step"] == step] + if not np.array_equal(aa, bb): + first = step + break + prefix = error if first is None else error[:first] + reference_exact = bool(np.array_equal(a[:, 2], b[:, 2])) + count_exact = bool(np.array_equal(actual["counts"], expected["counts"])) + maximum = float(error.max()) + return {"exact_events": exact_events, "exact_counts": count_exact, + "ref_exact": reference_exact, "max_abs_mv": maximum, + "mean_abs_mv": float(error.mean()), + "same_event_prefix_max_abs_mv": float(prefix.max()) if prefix.size else None, + "first_event_divergence_step": first, "tolerance_mv": tolerance, + "pass_oracle": exact_events and count_exact and reference_exact and maximum <= tolerance} + + +def comparison_record_matches(raw, stored): + """Only descriptive mean reduction may differ between scientific NumPy builds.""" + if set(raw) != set(stored): + return False + return all(math.isclose(raw[key], stored[key], rel_tol=0, abs_tol=1e-12) + if key == "mean_abs_mv" else raw[key] == stored[key] for key in raw) + + +def motif_nodes(cfg, motif): + with np.load(ROOT / cfg["prior_experiment"] / "motifs" / (motif + "-state.npz"), + allow_pickle=False) as prior: + return prior["nodes"].copy() + + +def check_summary_rows(table, motif, policy, precision, per_node): + part = table[(table.motif == motif) & (table.policy == policy) & + (table.precision == precision)] + require(len(part) == len(per_node) and not part.neuron_idx.duplicated().any(), + "Missing/duplicate per-neuron summary rows") + require(set(part.neuron_idx) == {row["neuron_idx"] for row in per_node}, + "Summary neuron identities differ") + indexed = part.set_index("neuron_idx") + for row in per_node: + current = indexed.loc[row["neuron_idx"]] + require(current.spikes == row["spikes"] and current.late_spikes == row["late_spikes"], + "Summary spike counts disagree with raw events") + last = current.last_ms + require(pd.isna(last) if row["last_ms"] is None else last == row["last_ms"], + "Summary last-spike time disagrees with raw events") + + +def seal(root): + require(not any((root / name).exists() for name in SEAL_NAMES), + "Refusing to overwrite an existing seal: " + str(root)) + files = [] + for path in sorted(root.rglob("*")): + relative = path.relative_to(root) + if EXCLUDED_PARTS.intersection(relative.parts): + continue + require(not path.is_symlink(), "Unsealed symlink not permitted: " + str(path)) + if not path.is_file() or (len(relative.parts) == 1 and path.name in SEAL_NAMES): + continue + files.append({"path": relative.as_posix(), "bytes": path.stat().st_size, + "sha256": digest(path)}) + require(bool(files), "Refusing empty artifact manifest") + manifest = {"schema": "sha256-artifact-manifest-v1", "root": str(root), + "created_utc": datetime.now(timezone.utc).isoformat(), + "excluded_directory_names": sorted(EXCLUDED_PARTS), + "self_hash_policy": "Manifest lists payload files; checksums also hashes manifest; neither hashes checksums.", + "files": files} + save(root / "manifest.json", manifest) + checksum_rows = files + [{"path": "manifest.json", "sha256": digest(root / "manifest.json")}] + with (root / "checksums.sha256").open("x", encoding="utf-8", newline="\n") as stream: + for row in checksum_rows: + stream.write(row["sha256"] + " " + row["path"] + "\n") + for row in checksum_rows: + require(digest(root / row["path"]) == row["sha256"], + "Artifact changed while sealing: " + row["path"]) + + +def main(): + outputs = [EXP / "audit/finalize-start.json", EXP / "audit/final-summary.json", + EXP / "regression/old-integrity-after.json", EXP / "regression/preregistration-after.json", + EXP / "REPORT.md"] + [root / name for root in (MODEL, EXP) for name in SEAL_NAMES] + require(not any(path.exists() for path in outputs), "Refusing reused finalization outputs") + save(EXP / "audit/finalize-start.json", {"timestamp_utc": datetime.now(timezone.utc).isoformat(), + "python": sys.version, "executable": sys.executable, "learning": False, + "whole_brain_alternative_run": False}) + checks = [] + prereg = attempt(checks, "preregistration", lambda: {"pass": True, "record": check_prereg()}) + if prereg["pass"]: + cfg = prereg["record"]["config"] + else: + # Read the sealed declaration for descriptive recovery, never bless source drift. + try: + cfg = read_json(EXP / "protocol/preregistered.json")["config"] + except Exception: + cfg = CFG + integrity = attempt(checks, "old_frozen_integrity_after", lambda: { + "pass": True, "results": frozen_integrity()}) + save(EXP / "regression/old-integrity-after.json", integrity) + + def completed(): + record = read_json(EXP / "audit/run-complete.json") + require(record.get("learning_achieved") is False and + record.get("whole_brain_alternative_run") is False, "Run scope inconsistent") + require(record.get("author_original_source_sha256") == digest(EXP / "external-resources/model.py"), + "Author source hash disagrees with run-complete record") + return {"pass": record.get("all_author_oracle_comparisons_pass") is True and + record.get("all_frozen_components_match_archive") is True, "record": record} + run_complete = attempt(checks, "run_complete", completed) + + def frozen_five_check(): + record = read_json(EXP / "regression/frozen-five.json") + trials = record.get("trials", []) + require(len(trials) == 5 and len({row["trial"] for row in trials}) == 5, + "Exactly five distinct frozen reference trials are required") + required = {"step", "neuron_idx", "counts", "v", "g"} + exact = all(set(row.get("exact", {})) == required and + all(value is True for value in row["exact"].values()) for row in trials) + return {"pass": record.get("pass_all") is True and exact, "record": record, + "scope": "Old frozen runtime regression only, not a new-model dynamics gate."} + frozen_five = attempt(checks, "frozen_five_gpu_references", frozen_five_check) + + def interface_check(): + record = read_json(EXP / "oracle/poi-interface/audit.json") + flags = record.get("checks", {}) + require(isinstance(flags, dict) and bool(flags), "Empty Poisson interface audit") + require(record.get("author_sha256") == digest(EXP / "external-resources/model.py"), + "Poisson audit source hash differs") + require(record.get("simulation_duration_ms") == 0 and + record.get("stochastic_time_steps") == 0 and + record.get("random_realization_tested") is False and + record.get("common_seed_experiment") is False, "Poisson audit scope differs") + for name, expected in record.get("input_hashes", {}).items(): + require(digest(EXP / "oracle/poi-interface" / name) == expected, + "Poisson fixture input changed: " + name) + return {"pass": record.get("gate") is True and all(value is True for value in flags.values()), + "record": record, "scope": "Compile-time interface audit; no Poisson realization."} + interface = attempt(checks, "author_poi_compile_only", interface_check) + outcomes = [] + components = [] + steps = round(cfg["duration_ms"] / cfg["dt_ms"]) + for motif in cfg["motifs"]: + for policy in cfg["component_policies"]: + def component_check(motif=motif, policy=policy): + nodes = motif_nodes(cfg, motif) + raw, per_node = load_trace(EXP / "components" / (motif + "-" + policy), nodes, + steps, cfg, None if motif == "no_input" else cfg["seed_node"]) + outcomes.append({"motif": motif, "policy": policy, "precision": "float32", + "neurons": per_node, "activity_is_not_a_validation_gate": True}) + table = pd.read_csv(EXP / "components/summary.csv", float_precision="round_trip") + check_summary_rows(table, motif, policy, "float32", per_node) + if policy == "frozen": + prior_dir = ROOT / cfg["prior_experiment"] / "motifs" + old_events = pd.read_parquet(prior_dir / (motif + "-events.parquet")) + require(np.array_equal(raw["step"], old_events.step) and + np.array_equal(raw["neuron_idx"], old_events.neuron_idx), + "Frozen events disagree with 4AC") + with np.load(prior_dir / (motif + "-state.npz"), allow_pickle=False) as old: + require(all(np.array_equal(old[key], raw[key]) for key in old.files), + "Frozen states disagree with 4AC") + return {"pass": True, "raw_and_summary_consistent": True, + "interpretation": "Artifact/finite/seed checks only; activity is descriptive."} + components.append(attempt(checks, "component:" + motif + ":" + policy, component_check)) + + unit_results = [] + for precision in cfg["author_precisions"]: + for fixture in UNIT_NAMES: + def unit_check(precision=precision, fixture=fixture): + stem = fixture + record = read_json(EXP / "regression" / ("unit-" + stem + "-" + precision + ".json")) + require(record.get("fixture") == fixture and record.get("precision") == precision, + "Unit identity mismatch") + unit_cfg = dict(cfg, duration_ms=20.0) + seeded = fixture in ("refractory_boundary", "above_threshold") + directory = EXP / "oracle" / ("unit-" + stem + "-" + precision) + nodes = np.array([-2, -1]) if fixture == "delay_18" else np.array([-1]) + seed = -2 if fixture == "delay_18" else (-1 if seeded else None) + actual, _ = load_trace(directory / "brian-output", nodes, 200, unit_cfg, seed, + natural_events=fixture == "nonzero_g_reset") + independent, _ = load_trace(directory / "independent-output", nodes, 200, unit_cfg, seed, + natural_events=fixture == "nonzero_g_reset") + raw = compare_raw(actual, independent, float(cfg["comparison"][precision + "_state_max_abs_tolerance_mv"])) + stored = read_json(directory / "comparison.json") + require(comparison_record_matches(raw, stored) and + comparison_record_matches(raw, record["comparison"]), + "Unit comparison differs from raw trajectories") + flags = record.get("checks") + require(isinstance(flags, dict) and bool(flags), "Empty unit checks cannot pass") + return {"pass": raw["pass_oracle"] and all(value is True for value in flags.values()), + "checks": flags, "raw_comparison": raw} + unit_results.append(attempt(checks, "unit:" + fixture + ":" + precision, unit_check)) + + author_results = [] + precision_cross = [] + for motif in cfg["motifs"]: + by_precision = {} + for precision in cfg["author_precisions"]: + def author_check(motif=motif, precision=precision): + nodes = motif_nodes(cfg, motif) + directory = EXP / "oracle" / (motif + "-" + precision) + seed = None if motif == "no_input" else cfg["seed_node"] + actual, per_node = load_trace(directory / "brian-output", nodes, steps, cfg, seed) + independent, _ = load_trace(directory / "independent-output", nodes, steps, cfg, seed) + by_precision[precision] = actual + outcomes.append({"motif": motif, "policy": "author_complete", "precision": precision, + "neurons": per_node, "activity_is_not_a_validation_gate": True}) + raw = compare_raw(actual, independent, float(cfg["comparison"][precision + "_state_max_abs_tolerance_mv"])) + stored = read_json(directory / "comparison.json") + require(comparison_record_matches(raw, stored), "Author comparison differs from raw trajectories") + repeated, _ = load_trace(EXP / "oracle" / (motif + "-" + precision + "-repeat") / + "brian-output", nodes, steps, cfg, seed) + repeat_flags = read_json(EXP / "regression" / (motif + "-" + precision + "-repeat.json")) + require(set(repeat_flags) == set(actual) - {"nodes"}, "Incomplete repeat comparison fields") + repeat_raw = {key: bool(np.array_equal(actual[key], repeated[key])) for key in repeat_flags} + require(repeat_raw == repeat_flags, "Repeat flags disagree with raw arrays") + table = pd.read_csv(EXP / "audit/all-motif-results.csv", float_precision="round_trip") + check_summary_rows(table, motif, "author_complete", precision, per_node) + return {"pass": raw["pass_oracle"] and all(repeat_raw.values()), + "raw_comparison": raw, "repeat_exact": repeat_raw} + author_results.append(attempt(checks, "author:" + motif + ":" + precision, author_check)) + def cross_check(motif=motif): + raw = compare_raw(by_precision["float32"], by_precision["float64"], + float(cfg["comparison"]["float32_state_max_abs_tolerance_mv"])) + stored = read_json(EXP / "regression" / (motif + "-precision-cross-comparison.json")) + require(comparison_record_matches(raw, stored), "Precision cross comparison differs from raw trajectories") + return {"pass": True, "comparison": raw, + "interpretation": "Reporting consistency only; cross-precision divergence is allowed and retained."} + precision_cross.append(attempt(checks, "precision_cross_record:" + motif, cross_check)) + + retained_errors = [] + for path in sorted(EXP.rglob("error.json")): + if EXCLUDED_PARTS.intersection(path.relative_to(EXP).parts): + continue + try: + error = read_json(path) + except Exception as exception: + error = exception_record(exception) + retained_errors.append({"path": path.relative_to(EXP).as_posix(), "error": error}) + checks.append({"name": "no_recorded_oracle_errors", "pass": not retained_errors, + "errors": retained_errors}) + final_prereg = attempt(checks, "preregistration_at_seal", lambda: {"pass": True, "record": check_prereg()}) + save(EXP / "regression/preregistration-after.json", { + "initial": prereg, "at_seal": final_prereg, "observed_source_hashes": source_hashes()}) + passed = bool(checks) and all(item["pass"] for item in checks) + summary = {"phase": cfg.get("phase", "4AD"), + "status": "COMPLETE-ORACLE-VALIDATED-LAB-ONLY" if passed else "INCOMPLETE-OR-FAILED-LAB-VALIDATION", + "laboratory_validation_pass": passed, "checks": checks, + "component_checks": components, "unit_checks": unit_results, + "frozen_five_gpu_check": frozen_five, "author_poi_interface_check": interface, + "author_oracle_checks": author_results, "precision_cross_checks": precision_cross, + "motif_outcomes": outcomes, "run_complete_record": run_complete, + "whole_brain_alternative_run": False, "conditioning_run": False, + "learning_achieved": False, "candidate_generated": False, "selected_variant": None, + "goal_remains_unachieved": True, + "limits": ["No whole-brain or learning experiment in this protocol.", + "No activity-based variant selection; silence is not a success gate.", + "Isolated motifs omit external network input and graded APL.", + "Author equations on MaleCNS motifs do not reproduce the original paper's full brain or sensory interface.", + "Linux host and Python patch differences prevent a binary-identical author-environment claim."]} + save(EXP / "audit/final-summary.json", summary) + failures = [item for item in checks if not item["pass"]] + lines = ["# Phase 4AD 作者动力学语义实验室", "", "状态：`" + summary["status"] + "`。", "", + "本轮仅有预声明的小回路与算子实验；没有整脑替代动力学运行、conditioning、学习成功或新学习候选。", + "检查以原始事件、状态轨迹和预注册误差界限重算。缺失、失败、非有限值或初始事件丢失均不能通过；放电减少或静默本身不构成成功。", "", + f"核查通过 {sum(item['pass'] for item in checks)}/{len(checks)} 项；失败或不完整 {len(failures)} 项。", + "冻结历史完整性：" + ("通过。" if integrity["pass"] else "失败或未完成，详见保存的错误。"), + "源码与输入预注册一致性：" + ("通过。" if prereg["pass"] and final_prereg["pass"] else "失败或未完成；不得授予验证成功。"), "", + "| 回路 | 语义 | 精度 | 总spikes | late spikes |", "|---|---|---|---:|---:|"] + for row in outcomes: + lines.append("| {} | {} | {} | {} | {} |".format(row["motif"], row["policy"], row["precision"], + sum(item["spikes"] for item in row["neurons"]), sum(item["late_spikes"] for item in row["neurons"]))) + if not outcomes: + lines.append("| 无完整可读取结果 | 未执行或缺失 | — | — | — |") + lines.extend(["", "作者Brian2与独立NumPy比较：", "", + "| 实验 | 结果 | 事件一致 | 最大V/g误差 mV | 首次事件分歧step |", "|---|---|---|---:|---:|"]) + for item in author_results: + raw = item.get("raw_comparison", {}) + lines.append("| {} | {} | {} | {} | {} |".format(item["name"], "通过" if item["pass"] else "失败/缺失", + raw.get("exact_events", "未知"), raw.get("max_abs_mv", "未知"), + raw.get("first_event_divergence_step", "无或未取得"))) + lines.extend(["", "float32与float64交叉比较仅记录精度影响，允许保留分歧，不能用于掩盖各自与独立oracle的失败。"]) + for item in precision_cross: + raw = item.get("comparison") + if raw: + lines.append(f"- {item['name']}：事件一致={raw['exact_events']}，最大误差={raw['max_abs_mv']} mV，首次事件分歧step={raw['first_event_divergence_step']}。") + if failures: + lines.extend(["", "失败与未完成项：", ""]) + for item in failures: + detail = item.get("error", {}).get("message") or "原始条件未全部满足；完整字段见 final-summary.json。" + lines.append("- `" + item["name"] + "`：" + str(detail).replace("\n", " ")) + lines.extend(["", "所有失败轨迹和错误文件原样保留；本简报没有选择获胜变体。", + "小回路缺少外部整脑输入与graded APL，不能证明整脑因果必要性、生物真实性或信息保持。初始诊断seed也不是作者的感官Poisson接口。", + "环境为Linux宿主，作者记录为Windows；Python补丁版本与环境差异见environment记录，不能称为二进制相同或原论文整脑复现。", + "后续整脑嗅觉比较仍须核查固定输入、实际送达事件、持续活动和信息保持；可用学习仍需至少5个训练seed、独立评估、MBON/downstream的A对中性B特异性及acquisition/reversal/retention/delayed-reward对照。", + "封存排除 .venv 与 __pycache__，保留环境安装报告；manifest列出payload哈希，checksums另含manifest，不存在自哈希循环。", ""]) + with (EXP / "REPORT.md").open("x", encoding="utf-8") as stream: + stream.write("\n".join(lines)) + seal(MODEL) + seal(EXP) + print(json.dumps({"status": summary["status"], "laboratory_validation_pass": passed, + "failed_checks": len(failures), "learning_achieved": False, + "whole_brain_alternative_run": False, "sealed": [str(MODEL), str(EXP)]}, + ensure_ascii=False), flush=True) + return 0 if passed else 1 + + +if __name__ == "__main__": + raise SystemExit(main()) diff --git a/models/male-cns-lif/author-semantics-lab-v1/interface_audit.py b/models/male-cns-lif/author-semantics-lab-v1/interface_audit.py new file mode 100644 index 0000000..3cac51a --- /dev/null +++ b/models/male-cns-lif/author-semantics-lab-v1/interface_audit.py @@ -0,0 +1,149 @@ +"""Compile-only audit of the pinned author's sensory Poisson interface. + +This is separate from the common single-seed diagnostic. Zero simulation time +is advanced, so this audit does not draw or validate any Poisson realization. +""" +from __future__ import annotations + +import hashlib +import types + +import numpy as np +import pandas as pd + +from context import CFG, EXP, digest, save +from oracle_runner import AUTHOR_COMMIT, AUTHOR_SHA256, _code_records, _environment + + +def audit_author_poi() -> dict: + """Create the original model and poi helper, compile at t=0, and save evidence.""" + author_path = EXP / "external-resources" / "model.py" + author_bytes = author_path.read_bytes() + source_hash = hashlib.sha256(author_bytes).hexdigest() + if source_hash != AUTHOR_SHA256: + raise ValueError("The Poisson audit requires the exact pinned author source") + output = EXP / "oracle" / "poi-interface" + output.mkdir(parents=True, exist_ok=False) + environment = _environment() + save(output / "environment.json", environment) + if environment["packages"]["brian2"]["actual"] != "2.5.1": + raise RuntimeError("The Poisson interface audit requires Brian2 2.5.1") + + import brian2 as b2 + + preferences = {name: b2.prefs[name] for name in ( + "codegen.target", "core.default_float_dtype", "legacy.refractory_timing")} + old_dt = b2.defaultclock.dt + try: + b2.start_scope() + b2.prefs["codegen.target"] = "numpy" + b2.prefs["core.default_float_dtype"] = np.float64 + b2.prefs["legacy.refractory_timing"] = False + b2.defaultclock.dt = float(CFG["dt_ms"]) * b2.ms + author = types.ModuleType("phase4ad_poi_author_" + source_hash[:12]) + author.__file__ = str(author_path) + # Execute exactly the reviewed bytes; create no bytecode beside the source. + exec(compile(author_bytes, str(author_path), "exec"), author.__dict__) + parameters = dict(author.default_params) + + nodes = np.array([-2, -1], dtype=np.int32) + completeness = pd.DataFrame( + {"local_index": np.array([0, 1], dtype=np.int32)}, + index=pd.Index(nodes, name="synthetic_global_neuron_idx")) + connections = pd.DataFrame({ + "Presynaptic_Index": np.array([0], dtype=np.int32), + "Postsynaptic_Index": np.array([1], dtype=np.int32), + "Excitatory x Connectivity": np.array([1], dtype=np.int64), + "raw_count": np.array([1], dtype=np.int64), + "edge_id": np.array([-1], dtype=np.int64), + "source_neuron_idx": nodes[:1], "target_neuron_idx": nodes[1:], + }) + comp_path = output / "completeness.csv" + con_path = output / "connectivity.parquet" + completeness.to_csv(comp_path) + connections.to_parquet(con_path, index=False, engine="pyarrow") + neu, syn, spikes = author.create_model(comp_path, con_path, parameters) + rfc_before = np.asarray(neu.rfc[:] / b2.ms, dtype=np.float64).copy() + # One excited target plus one untouched cell makes the helper's scope + # observable. The optional second-rate class is not exercised here. + inputs, same_neu = author.poi(neu, [0], [], parameters) + if same_neu is not neu: + raise AssertionError("The author poi helper returned a different neuron group") + rfc_after = np.asarray(neu.rfc[:] / b2.ms, dtype=np.float64).copy() + before_v = np.asarray(neu.v_[:], dtype=np.float64).copy() + before_g = np.asarray(neu.g_[:], dtype=np.float64).copy() + before_w = np.asarray(syn.w_[:], dtype=np.float64).copy() + network = b2.Network(neu, syn, spikes, *inputs) + save(output / "schedule.json", { + "schedule": list(network.schedule), + "summary": str(network.scheduling_summary()), + }) + network.run(0 * b2.ms, namespace={}) + save(output / "generated-code.json", _code_records(network)) + + input_records = [] + for item in inputs: + # PoissonInput 2.5.1 retains its on-the-fly subgroup as _group; + # N/rate/weight/target_var are its public read-only properties. + target = item._group + input_records.append({ + "name": item.name, "type": type(item).__name__, + "target_group": target.name, + "target_local_start": int(target.start), + "target_local_stop": int(target.stop), + "target_global_nodes": nodes[int(target.start):int(target.stop)].tolist(), + "target_var": item.target_var, "N": int(item.N), + "rate_hz": float(item.rate / b2.Hz), + "weight_mv": float(item.weight / b2.mV), + "weight_volt": float(item.weight / b2.volt), + "when": item.when, "order": int(item.order), + "dt_ms": float(item.clock.dt / b2.ms), + "abstract_code": str(item.abstract_code), + "generated_code": [str(code.code) for code in item.code_objects], + }) + expected_rfc = float(parameters["t_rfc"] / b2.ms) + expected_weight = float(parameters["w_syn"] * parameters["f_poi"] / b2.mV) + expected_rate = float(parameters["r_poi"] / b2.Hz) + checks = { + "exact_author_source": digest(author_path) == source_hash, + "one_poisson_input": len(input_records) == 1, + "initial_refractory_is_original": bool(np.array_equal(rfc_before, [expected_rfc, expected_rfc])), + "only_excited_target_loses_refractory": bool(np.array_equal(rfc_after, [0., expected_rfc])), + "actual_voltage_interface": all(r["target_var"] == "v" for r in input_records), + "actual_N_one": all(r["N"] == 1 for r in input_records), + "actual_rate_150_hz": bool(expected_rate == 150. and all(r["rate_hz"] == expected_rate for r in input_records)), + "actual_weight_68_75_mv": bool(np.isclose(expected_weight, 68.75, rtol=0, atol=1e-12) + and all(np.isclose(r["weight_mv"], expected_weight, rtol=0, atol=1e-12) for r in input_records)), + "actual_synapses_slot_order_zero": all(r["when"] == "synapses" and r["order"] == 0 for r in input_records), + "zero_elapsed_time": float(network.t / b2.ms) == 0., + "no_recorded_spikes": len(spikes.i[:]) == 0, + "compile_preserves_voltage": bool(np.array_equal(before_v, np.asarray(neu.v_[:]))), + "compile_preserves_g": bool(np.array_equal(before_g, np.asarray(neu.g_[:]))), + "compile_preserves_weights": bool(np.array_equal(before_w, np.asarray(syn.w_[:]))), + "compile_preserves_refractory_configuration": bool(np.array_equal(rfc_after, np.asarray(neu.rfc[:] / b2.ms))), + } + result = { + "gate": bool(all(checks.values())), "checks": checks, + "author_commit": AUTHOR_COMMIT, "author_sha256": source_hash, + "fixture": "two synthetic nodes, one raw_count=1 connection", + "nodes": nodes.tolist(), "exc_local_indices": [0], "exc2_local_indices": [], + "rfc_before_ms": rfc_before.tolist(), "rfc_after_ms": rfc_after.tolist(), + "poisson_inputs": input_records, + "synaptic_weight_mv": np.asarray(syn.w[:] / b2.mV, dtype=np.float64).tolist(), + "input_hashes": {"completeness.csv": digest(comp_path), "connectivity.parquet": digest(con_path)}, + "simulation_duration_ms": 0., "stochastic_time_steps": 0, + "random_realization_tested": False, "common_seed_experiment": False, + "interpretation": "Original poi adds 68.75 mV to voltage at 150 Hz with N=1 in the synapses slot and sets its target rfc to zero. This interface is not the common initial seed experiment.", + "scope": "Compile-time interface audit only; no stochastic trial, learning, or whole-brain simulation. The optional exc2 helper branch is not exercised.", + } + save(output / "audit.json", result) + if not result["gate"]: + raise AssertionError("Author Poisson interface gate failed: " + str(checks)) + return result + except Exception as error: + save(output / "error.json", {"type": type(error).__name__, "message": str(error)}) + raise + finally: + for name, value in preferences.items(): + b2.prefs[name] = value + b2.defaultclock.dt = old_dt diff --git a/models/male-cns-lif/author-semantics-lab-v1/manifest.json b/models/male-cns-lif/author-semantics-lab-v1/manifest.json new file mode 100644 index 0000000..befecb6 --- /dev/null +++ b/models/male-cns-lif/author-semantics-lab-v1/manifest.json @@ -0,0 +1,67 @@ +{ + "schema": "sha256-artifact-manifest-v1", + "root": "/data/digital-drosophila/models/male-cns-lif/author-semantics-lab-v1", + "created_utc": "2026-09-29T23:19:04.144370+00:00", + "excluded_directory_names": [ + ".venv", + "__pycache__" + ], + "self_hash_policy": "Manifest lists payload files; 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sequential arrival writes follow spike detection.""" + f=np.dtype(precision).type;m=config['model'];n=len(nodes);dt=config['dt_ms'] + steps=round(config['duration_ms']/dt);rs=round(m['refractory_ms']/dt);ds=round(m['synaptic_delay_ms']/dt) + ix={int(x):i for i,x in enumerate(nodes)} + src=np.array([ix[int(x)] for x in edges.source_neuron_idx],np.int32) + dst=np.array([ix[int(x)] for x in edges.target_neuron_idx],np.int32) + weights=np.asarray(edges.raw_count.to_numpy(np.float64)*(m['w_syn_mv_per_anatomical_synapse']*.001),dtype=precision) + rest=m['resting_potential_mv']*.001;reset=m['reset_potential_mv']*.001;threshold=m['threshold_mv']*.001 + v=np.full(n,rest,dtype=precision);g=np.zeros(n,dtype=precision) + last=np.full(n,-1000000,np.int64);counts=np.zeros(n,np.int32) + em=np.exp(-dt/m['membrane_tau_ms']);es=np.exp(-dt/m['synaptic_tau_ms']) + drive=m['synaptic_tau_ms']/(m['membrane_tau_ms']-m['synaptic_tau_ms'])*(em-es) + history=np.empty((steps,3,n),np.float64);queue=[[] for _ in range(ds+1)];ts=[];ns=[] + external=np.zeros((steps,n),dtype=precision) if external_arrivals is None else np.asarray(np.asarray(external_arrivals,np.float64)*.001,dtype=precision) + assert external.shape==(steps,n) + for t in range(steps): + available=(t-last)>=rs + # Use previous g for the coupled exact differential update, then cast to variable dtype. + oldg=g.copy() + v[available]=np.asarray(rest+em*(v[available]-rest)+drive*oldg[available],dtype=precision) + g[available]=np.asarray(es*oldg[available],dtype=precision) + if t==0 and seed_node is not None:v[ix[seed_node]]=f(threshold+config['seed_margin_mv']*.001) + fire=available&(v>threshold);last[fire]=t;counts+=fire + active=np.flatnonzero(fire);ts.extend([t]*len(active));ns.extend(nodes[active].tolist()) + accept=available&~fire + due=queue[t%(ds+1)];queue[t%(ds+1)]=[] + for e in due: + if accept[dst[e]]:g[dst[e]]=f(g[dst[e]]+weights[e]) + for j in np.flatnonzero(external[t]): + if accept[j]:g[j]=f(g[j]+external[t,j]) + queue[(t+ds)%(ds+1)].extend(np.flatnonzero(fire[src]).tolist()) + v[fire]=f(reset);g[fire]=f(0) + ref=np.maximum(rs-(t-last),0).astype(np.int32) + history[t]=np.asarray(v,np.float64)*1000,np.asarray(g,np.float64)*1000,ref + return dict(step=np.array(ts,np.int32),neuron_idx=np.array(ns,np.int32),counts=counts, + v=np.asarray(v,np.float64)*1000,g=np.asarray(g,np.float64)*1000,ref=ref,history=history,weights=np.asarray(weights,np.float64)*1000) diff --git a/models/male-cns-lif/author-semantics-lab-v1/oracle_runner.py b/models/male-cns-lif/author-semantics-lab-v1/oracle_runner.py new file mode 100644 index 0000000..b743741 --- /dev/null +++ b/models/male-cns-lif/author-semantics-lab-v1/oracle_runner.py @@ -0,0 +1,346 @@ +"""Run the pinned author's create_model in a dedicated, serial Brian2 process. + +This module never edits the author source or its parameters. The caller supplies +an exclusive output directory and the already validated, signed connectivity +multipliers in ``raw_count``. Global IDs are not FlyWire IDs and are mapped only +for this small-circuit diagnostic. Brian stores voltages in SI volts internally; +the returned state and weights are converted to mV in the selected dtype. +""" +from __future__ import annotations + +import hashlib +import importlib.metadata +import json +import platform +import sys +import types +from pathlib import Path + +import numpy as np +import pandas as pd + + +AUTHOR_SHA256 = "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e" +AUTHOR_COMMIT = "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960" +PACKAGE_PINS = { + "brian2": "2.5.1", "numpy": "1.22.3", "pandas": "1.4.3", + "scipy": "1.8.1", "pyarrow": "11.0.0", "joblib": "1.2.0", + "cython": "0.29.33", "jinja2": "2.11.3", "markupsafe": "1.1.1", + "sympy": "1.12", "mpmath": "1.3.0", "pyparsing": "3.0.9", + "packaging": "23.1", "setuptools": "67.8.0", + "python-dateutil": "2.8.2", "pytz": "2023.3", "six": "1.16.0", + "wheel": "0.38.4", +} + + +def _json(path: Path, value) -> None: + with path.open("x", encoding="utf-8") as output: + json.dump(value, output, indent=2, sort_keys=True, allow_nan=False) + output.write("\n") + + +def _steps(value: float, dt: float, label: str, *, positive=False) -> int: + ratio = float(value) / dt + if not np.isfinite(ratio) or ratio < 0: + raise ValueError(f"{label} must be finite and nonnegative") + result = int(round(ratio)) + if not np.isclose(ratio, result, rtol=0, atol=1e-9): + raise ValueError(f"{label} must be an integer number of dt steps") + if result > np.iinfo(np.int32).max or (positive and result == 0): + raise ValueError(f"{label} is outside the supported step range") + return result + + +def _int_vector(values, label: str, dtype=np.int64) -> np.ndarray: + source = np.asarray(values) + if source.ndim != 1 or source.dtype.kind not in "iu": + raise ValueError(f"{label} must be a one-dimensional integer array") + limits = np.iinfo(dtype) + if np.any(source < limits.min) or np.any(source > limits.max): + raise ValueError(f"{label} is outside {np.dtype(dtype).name} range") + return source.astype(dtype, copy=True) + + +def _environment() -> dict: + packages = {} + for name, expected in PACKAGE_PINS.items(): + try: + actual = importlib.metadata.version(name) + except importlib.metadata.PackageNotFoundError: + actual = None + packages[name] = {"expected": expected, "actual": actual, + "matches": actual == expected} + return { + "python": platform.python_version(), "author_python": "3.10.11", + "python_patch_matches": platform.python_version() == "3.10.11", + "python_executable": sys.executable, "platform": platform.platform(), + "author_platform": "Windows", "packages": packages, + "all_package_pins_match": all(p["matches"] for p in packages.values()), + "binary_identical_author_environment_claimed": False, + } + + +def _code_text(value): + if isinstance(value, dict): + return {str(key): _code_text(item) for key, item in value.items()} + return str(value) + + +def _code_records(network) -> list: + records = [] + for obj in network.sorted_objects: + record = {"name": obj.name, "type": type(obj).__name__, + "when": obj.when, "order": int(obj.order), + "active": bool(obj.active)} + for key in ("abstract_code", "user_code"): + if hasattr(obj, key): + record[key] = _code_text(getattr(obj, key)) + record["code_objects"] = [ + {"name": code.name, "type": type(code).__name__, + "generated_code": _code_text(code.code)} + for code in getattr(obj, "code_objects", ()) + ] + records.append(record) + return records + + +def run_brian(author_path: Path, io_dir: Path, nodes: np.ndarray, + edges: pd.DataFrame, config: dict, precision: str, + seed_node: int | None, external_arrivals=None) -> dict: + """Execute an unchanged author model and return canonical end-of-tick arrays. + + ``external_arrivals`` is either None or a (T, N) array in mV. Every nonzero + entry gets its own SpikeGeneratorGroup source and zero-delay conditional + synaptic write, ordered after the anatomical synapses. It is not direct + Python assignment to g. ``seed_margin_mv`` may be zero for a strict-threshold + fixture; positive margins must remain representably above the threshold. + + This function controls process-global Brian preferences and is not thread + safe. Use only the isolated oracle environment, serially or in subprocesses. + A failed run keeps its exclusive inputs and an error record for diagnosis. + """ + if precision not in ("float64", "float32"): + raise ValueError("precision must be float64 or float32") + dtype = np.dtype(precision) + nodes = _int_vector(nodes, "nodes", np.int32) + if not len(nodes) or np.any(np.diff(nodes.astype(np.int64)) <= 0): + raise ValueError("nodes must be nonempty, sorted, and unique") + required = ["edge_id", "source_neuron_idx", "target_neuron_idx", "raw_count"] + if not set(required).issubset(edges.columns): + raise ValueError(f"edges require columns {required}") + edge_ids = _int_vector(edges.edge_id, "edge_id") + if np.any(np.diff(edge_ids) <= 0): + raise ValueError("edge_id order must be canonical, increasing, and unique") + sources = _int_vector(edges.source_neuron_idx, "source_neuron_idx", np.int32) + targets = _int_vector(edges.target_neuron_idx, "target_neuron_idx", np.int32) + multipliers = _int_vector(edges.raw_count, "raw_count") + if not np.isin(sources, nodes).all() or not np.isin(targets, nodes).all(): + raise ValueError("all edge endpoints must occur in nodes") + lookup = {int(node): i for i, node in enumerate(nodes)} + if seed_node is not None and int(seed_node) not in lookup: + raise ValueError("seed_node must occur in nodes") + + dt_ms = float(config["dt_ms"]) + if not np.isfinite(dt_ms) or dt_ms <= 0: + raise ValueError("dt_ms must be finite and positive") + total_steps = _steps(config["duration_ms"], dt_ms, "duration_ms", positive=True) + model = config["model"] + refractory_steps = _steps(model["refractory_ms"], dt_ms, "refractory_ms") + delay_steps = _steps(model["synaptic_delay_ms"], dt_ms, "synaptic_delay_ms") + margin_mv = float(config["seed_margin_mv"]) + if not np.isfinite(margin_mv) or margin_mv < 0: + raise ValueError("seed_margin_mv must be finite and nonnegative") + if "dt_ms" in model and float(model["dt_ms"]) != dt_ms: + raise ValueError("top-level and model dt_ms disagree") + arrivals = None + if external_arrivals is not None: + arrivals = np.asarray(external_arrivals, dtype=np.float64) + if arrivals.shape != (total_steps, len(nodes)) or not np.isfinite(arrivals).all(): + raise ValueError("external_arrivals must be finite with shape (T, N)") + + author_path = Path(author_path).resolve(strict=True) + author_bytes = author_path.read_bytes() + author_hash = hashlib.sha256(author_bytes).hexdigest() + if author_hash != AUTHOR_SHA256: + raise ValueError(f"Author source hash mismatch: {author_hash}") + io_dir = Path(io_dir).resolve() + io_dir.mkdir(parents=True, exist_ok=False) + environment = _environment() + _json(io_dir / "environment.json", environment) + if environment["packages"]["brian2"]["actual"] != "2.5.1": + raise RuntimeError("The author oracle requires exactly Brian2 2.5.1") + + import brian2 as b2 + + saved_preferences = { + "codegen.target": b2.prefs["codegen.target"], + "core.default_float_dtype": b2.prefs["core.default_float_dtype"], + "legacy.refractory_timing": b2.prefs["legacy.refractory_timing"], + } + saved_dt = b2.defaultclock.dt + try: + b2.start_scope() + b2.prefs["codegen.target"] = "numpy" + b2.prefs["core.default_float_dtype"] = dtype.type + b2.prefs["legacy.refractory_timing"] = False + b2.defaultclock.dt = dt_ms * b2.ms + # Compile the checked bytes themselves: no source rewrite or __pycache__ + # is possible, and a subsequent file change cannot alter imported code. + author = types.ModuleType("phase4ad_pinned_author_" + author_hash[:12]) + author.__file__ = str(author_path) + exec(compile(author_bytes, str(author_path), "exec"), author.__dict__) + parameters = dict(author.default_params) + checks = {} + for config_key, author_key, unit in ( + ("membrane_tau_ms", "t_mbr", b2.ms), + ("synaptic_tau_ms", "tau", b2.ms), + ("refractory_ms", "t_rfc", b2.ms), + ("synaptic_delay_ms", "t_dly", b2.ms), + ("resting_potential_mv", "v_0", b2.mV), + ("reset_potential_mv", "v_rst", b2.mV), + ("threshold_mv", "v_th", b2.mV), + ("w_syn_mv_per_anatomical_synapse", "w_syn", b2.mV), + ): + expected = float(model[config_key]) + actual = float(parameters[author_key] / unit) + if not np.isfinite(expected) or not np.isclose(actual, expected, rtol=0, atol=1e-12): + raise ValueError(f"config {config_key}={expected} differs from author {actual}") + checks[config_key] = {"config": expected, "author": actual} + + completeness = pd.DataFrame({"local_index": np.arange(len(nodes), dtype=np.int32)}, + index=pd.Index(nodes, name="global_neuron_idx")) + connections = pd.DataFrame({ + "Presynaptic_Index": [lookup[int(x)] for x in sources], + "Postsynaptic_Index": [lookup[int(x)] for x in targets], + "Excitatory x Connectivity": multipliers, + "edge_id": edge_ids, + "source_neuron_idx": sources, "target_neuron_idx": targets, + }).astype({"Presynaptic_Index": "int32", "Postsynaptic_Index": "int32"}) + comp_path = io_dir / "completeness.csv" + con_path = io_dir / "connectivity.parquet" + completeness.to_csv(comp_path) + connections.to_parquet(con_path, index=False, engine="pyarrow") + neu, syn, spikes = author.create_model(comp_path, con_path, parameters) + if np.dtype(neu.variables["v"].dtype) != dtype or np.dtype(syn.variables["w"].dtype) != dtype: + raise AssertionError("Brian did not allocate the requested floating-point dtype") + np.testing.assert_array_equal(np.asarray(syn.i[:]), connections.Presynaptic_Index) + np.testing.assert_array_equal(np.asarray(syn.j[:]), connections.Postsynaptic_Index) + + objects = [neu, syn, spikes] + seed_state = {"requested_global_node": None if seed_node is None else int(seed_node), + "margin_mv": margin_mv, "injections": 0} + if seed_node is not None: + seed_local = lookup[int(seed_node)] + + def inject_seed(): + if seed_state["injections"] == 0: + if float(b2.defaultclock.t / b2.ms) != 0: + raise AssertionError("Seed injection must occur at tick zero") + neu.v[seed_local] = parameters["v_th"] + margin_mv * b2.mV + applied = float(neu.v[seed_local] / b2.mV) + if margin_mv > 0 and not applied > float(parameters["v_th"] / b2.mV): + raise ValueError("The positive seed margin rounded away in the selected dtype") + seed_state["applied_mv"] = applied + seed_state["injections"] = 1 + + objects.append(b2.NetworkOperation(inject_seed, clock=neu.clock, + when="before_thresholds", order=0, + name="oracle_seed_injection")) + + external_metadata = {"events": 0, "ordering": "after default_synapses.pre"} + if arrivals is not None: + event_ticks, event_targets = np.nonzero(arrivals) + event_values = arrivals[event_ticks, event_targets] + external_metadata["events"] = int(len(event_ticks)) + if len(event_ticks): + event_ids = np.arange(len(event_ticks), dtype=np.int32) + external_source = b2.SpikeGeneratorGroup( + len(event_ticks), indices=event_ids, + times=event_ticks.astype(np.float64) * dt_ms * b2.ms, + sorted=True, clock=neu.clock, name="zz_external_sources") + external_syn = b2.Synapses( + external_source, neu, model="w : volt", on_pre="g_post += w", + delay=0 * b2.ms, name="zz_external_arrivals") + external_syn.connect(i=event_ids, j=event_targets) + external_syn.w = event_values * b2.mV + external_syn.pre.order = int(syn.pre.order) + 1 + if external_syn.pre.when != syn.pre.when: + raise AssertionError("External and anatomical pathways must share a schedule slot") + objects.extend([external_source, external_syn]) + external_metadata["pathway_order"] = int(external_syn.pre.order) + external_metadata["actual_weights_mv"] = np.asarray(external_syn.w[:] / b2.mV, dtype=dtype).tolist() + pd.DataFrame({"tick": event_ticks, "neuron_idx": nodes[event_targets], + "requested_mv": event_values}).to_csv(io_dir / "external-arrivals.csv", index=False) + + trace = b2.StateMonitor(neu, ["v", "g", "lastspike", "not_refractory"], + record=True, when="end", name="oracle_end_state") + objects.append(trace) + network = b2.Network(*objects) + _json(io_dir / "run-spec.json", { + "author_sha256": author_hash, "author_commit": AUTHOR_COMMIT, + "precision": precision, "config": config, "parameter_checks": checks, + "dt_ms": dt_ms, "steps": total_steps, "refractory_steps": refractory_steps, + "delay_steps": delay_steps, "nodes": nodes.tolist(), "edge_ids": edge_ids.tolist(), + "seed": seed_state.copy(), "external_arrivals": external_metadata, + "preferences": {"codegen.target": "numpy", "legacy.refractory_timing": False, + "core.default_float_dtype": precision}, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference", + "internal_voltage_unit": "volt", "returned_voltage_unit": "mV", + }) + _json(io_dir / "schedule.json", {"schedule": list(network.schedule), + "summary": str(network.scheduling_summary())}) + network.run(float(config["duration_ms"]) * b2.ms, namespace={}) + _json(io_dir / "generated-code.json", _code_records(network)) + + ticks_float = np.asarray(spikes.t[:] / b2.ms, dtype=np.float64) / dt_ms + ticks = np.rint(ticks_float).astype(np.int32) + if not np.allclose(ticks_float, ticks, rtol=0, atol=1e-6): + raise AssertionError("Spike timestamps do not lie on the configured integer clock") + event_nodes = nodes[np.asarray(spikes.i[:], dtype=np.int32)] + order = np.lexsort((event_nodes, ticks)) + ticks, event_nodes = ticks[order], event_nodes[order] + counts = np.asarray(spikes.count[:], dtype=np.int32).copy() + if int(counts.sum()) != len(ticks): + raise AssertionError("SpikeMonitor counts disagree with event records") + trace_ticks = np.asarray(trace.t[:] / b2.ms, dtype=np.float64) / dt_ms + if trace_ticks.shape != (total_steps,) or not np.allclose( + trace_ticks, np.arange(total_steps), rtol=0, atol=1e-6): + raise AssertionError("End-state trace has the wrong tick range") + voltage = np.asarray(trace.v / b2.mV, dtype=dtype).T.copy() + conductance = np.asarray(trace.g / b2.mV, dtype=dtype).T.copy() + last_spike_ms = np.asarray(trace.lastspike / b2.ms, dtype=np.float64).T + seen = np.isfinite(last_spike_ms) & (last_spike_ms >= 0) + # Brian's never-spiked sentinel can be far outside int32. Convert only + # real nonnegative timestamps, then compute an end-of-tick countdown. + last_ticks = np.zeros(last_spike_ms.shape, dtype=np.int64) + last_ticks[seen] = np.rint(last_spike_ms[seen] / dt_ms).astype(np.int64) + elapsed = np.arange(total_steps, dtype=np.int64)[:, None] - last_ticks + ref = np.where(seen, np.maximum(refractory_steps - elapsed, 0), 0).astype(np.int32) + available = np.asarray(trace.not_refractory, dtype=bool).T + if not np.array_equal(available, ref == 0): + raise AssertionError("Recorded refractory flag disagrees with the integer countdown") + history = np.stack([voltage, conductance, ref.astype(dtype)], axis=1) + if not np.isfinite(history).all(): + raise AssertionError("Nonfinite author state") + if seed_node is not None: + seed_state["spiked_at_zero"] = bool(np.any((ticks == 0) & (event_nodes == seed_node))) + if seed_state["injections"] != 1 or (margin_mv > 0 and not seed_state["spiked_at_zero"]): + raise AssertionError("The common initial seed event was not produced exactly once") + _json(io_dir / "seed.json", seed_state) + weights = np.asarray(syn.w[:] / b2.mV, dtype=dtype).copy() + _json(io_dir / "actual-weights.json", { + "edge_id": edge_ids.tolist(), "weights_mv": weights.tolist(), + "weights_volt": np.asarray(syn.w_[:], dtype=np.float64).tolist(), + }) + if hashlib.sha256(author_path.read_bytes()).hexdigest() != author_hash: + raise AssertionError("Author source changed during execution") + return {"step": ticks, "neuron_idx": event_nodes, "counts": counts, + "v": voltage[-1].copy(), "g": conductance[-1].copy(), + "ref": ref[-1].copy(), "history": history, "weights": weights} + except Exception as error: + _json(io_dir / "error.json", {"type": type(error).__name__, "message": str(error)}) + raise + finally: + for name, value in saved_preferences.items(): + b2.prefs[name] = value + b2.defaultclock.dt = saved_dt diff --git a/models/male-cns-lif/author-semantics-lab-v1/prepare.py b/models/male-cns-lif/author-semantics-lab-v1/prepare.py new file mode 100644 index 0000000..bbab487 --- /dev/null +++ b/models/male-cns-lif/author-semantics-lab-v1/prepare.py @@ -0,0 +1,56 @@ +"""Predeclare and verify old inputs before executing any alternative dynamics.""" +import ast +from datetime import datetime, timezone +import importlib.metadata +import json +import platform +from pathlib import Path +import shutil +import subprocess +import sys +from context import CFG,ROOT,EXP,MODEL,AC,digest,save,source_hashes + + +def frozen_integrity(): + sys.path.insert(0,str(ROOT/CFG['prior_model'])) + import audit_semantics as old + result=old.integrity() + for p in (ROOT/CFG['prior_model'],AC,ROOT/'registry/feedback-context-review-20260930'): + result[str(p.relative_to(ROOT))]=old.manifest_check(p,digest) + assert all(x['pass'] for x in result.values()) + return result + + +def main(): + assert (MODEL/'oracle_runner.py').is_file() + assert not (EXP/'protocol').exists(),'Refusing reused experiment protocol' + for d in ('protocol','external-resources','inputs','components','oracle','regression','audit','performance'):(EXP/d).mkdir() + source=AC/'external-resources/model.py' + assert digest(source)=='fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e' + tree=ast.parse(source.read_text()) + assert all(isinstance(x,(ast.Import,ast.ImportFrom,ast.Assign,ast.FunctionDef,ast.Expr)) for x in tree.body) + inputs=[source,AC/'external-resources/LICENSE',AC/'external-resources/environment_full.yml', + AC/'audit/selected-real-edges.csv',AC/'audit/selected-metadata.parquet',ROOT/CFG['prior_model']/'math_reference.py'] + for name in CFG['motifs']: + inputs.extend([AC/'motifs'/f'{name}-edges.csv',AC/'motifs'/f'{name}-events.parquet',AC/'motifs'/f'{name}-state.npz']) + save(EXP/'protocol/preregistered.json',dict(config=CFG,timestamp_utc=datetime.now(timezone.utc).isoformat(), + source_hashes=source_hashes(),input_hashes=[dict(path=str(p.relative_to(ROOT)),sha256=digest(p),bytes=p.stat().st_size) for p in inputs], + parent_commit=subprocess.check_output(['git','-C',str(ROOT),'rev-parse','HEAD'],text=True).strip(), + pre_model_execution=True)) + save(EXP/'regression/old-integrity-before.json',frozen_integrity()) + for name in ('model.py','LICENSE','environment_full.yml'): + dst=EXP/'external-resources'/name + with (AC/'external-resources'/name).open('rb') as src,dst.open('xb') as out:shutil.copyfileobj(src,out) + assert digest(dst)==digest(AC/'external-resources'/name) + versions={n:importlib.metadata.version(n) for n in ('numpy','pandas','pyarrow','torch','scipy')} + save(EXP/'environment/frozen-scientific-environment.json',dict(python=sys.version,executable=sys.executable, + platform=platform.platform(),package_versions=versions)) + save(EXP/'environment/bootstrap-notes.json',dict(isolated_venv_only=True,existing_environments_modified=False, + initial_install_failure='New venv pip22.0.2 lacks --report; upgraded ONLY new venv pip to author-pinned23.0.1 before installing', + MarkupSafe='Author-pinned1.1.1 used PyPI source distribution and legacy setup.py because no CPython3.10 wheel; other requested core packages used wheels', + author_environment='Windows conda CPython3.10.11',actual_environment='Linux CPython3.10.12; not binary-identical', + package_download_provenance='install-report.json contains HTTPS PyPI archive URLs and SHA256 for packages')) + print('PREPARED: old integrity PASS; independent model hypotheses preregistered',flush=True) + + +if __name__=='__main__':main() diff --git a/models/male-cns-lif/author-semantics-lab-v1/requirements-oracle.txt b/models/male-cns-lif/author-semantics-lab-v1/requirements-oracle.txt new file mode 100644 index 0000000..e71c573 --- /dev/null +++ b/models/male-cns-lif/author-semantics-lab-v1/requirements-oracle.txt @@ -0,0 +1,20 @@ +# Package versions in the pinned author's environment_full.yml, Linux wheels. +# The host Python patch is recorded separately; this is not the author's Windows binary environment. +brian2==2.5.1 +numpy==1.22.3 +pandas==1.4.3 +scipy==1.8.1 +pyarrow==11.0.0 +joblib==1.2.0 +cython==0.29.33 +jinja2==2.11.3 +markupsafe==1.1.1 +sympy==1.12 +mpmath==1.3.0 +pyparsing==3.0.9 +packaging==23.1 +setuptools==67.8.0 +python-dateutil==2.8.2 +pytz==2023.3 +six==1.16.0 +wheel==0.38.4 diff --git a/models/male-cns-lif/author-semantics-lab-v1/run_lab.py b/models/male-cns-lif/author-semantics-lab-v1/run_lab.py new file mode 100644 index 0000000..f13d326 --- /dev/null +++ b/models/male-cns-lif/author-semantics-lab-v1/run_lab.py @@ -0,0 +1,158 @@ +"""Run fixed component arms and independent author oracle, preserving divergences.""" +import importlib.metadata +import json +from pathlib import Path +import platform +import sys +import subprocess +import time +import numpy as np +import pandas as pd +from context import CFG,ROOT,EXP,MODEL,AC,digest,save,check_prereg +from math_lab import component,author_numpy +from oracle_runner import run_brian,PACKAGE_PINS + + +def save_result(where,result,nodes): + where.mkdir(parents=True,exist_ok=False) + pd.DataFrame(dict(step=result['step'],neuron_idx=result['neuron_idx'])).to_csv(where/'events.csv',index=False) + np.savez_compressed(where/'state.npz',nodes=nodes,**{k:v for k,v in result.items() if k not in ('step','neuron_idx')}) + + +def compare(actual,expected,precision): + event=bool(np.array_equal(actual['step'],expected['step']) and np.array_equal(actual['neuron_idx'],expected['neuron_idx'])) + a=np.asarray(actual['history'],np.float64);b=np.asarray(expected['history'],np.float64) + assert a.shape==b.shape + errs=np.abs(a[:,:2]-b[:,:2]) + # Describe numerical prefix separately from post-event-divergence trajectories. + first=None + for t in range(len(a)): + aa=actual['neuron_idx'][actual['step']==t];bb=expected['neuron_idx'][expected['step']==t] + if not np.array_equal(aa,bb):first=t;break + prefix=errs[:first] if first is not None else errs + tol=CFG['comparison'][precision+'_state_max_abs_tolerance_mv'] + return dict(exact_events=event,exact_counts=bool(np.array_equal(actual['counts'],expected['counts'])), + ref_exact=bool(np.array_equal(a[:,2],b[:,2])),max_abs_mv=float(errs.max()),mean_abs_mv=float(errs.mean()), + same_event_prefix_max_abs_mv=float(prefix.max()) if prefix.size else None, + first_event_divergence_step=first,tolerance_mv=tol, + pass_oracle=bool(event and errs.max()<=tol and np.array_equal(a[:,2],b[:,2]))) + + +def oracle_trial(name,nodes,edges,cfg,precision,seed,external=None): + io=EXP/'oracle'/(name+'-'+precision) + result=run_brian(EXP/'external-resources/model.py',io,nodes,edges,cfg,precision,seed,external) + independent=author_numpy(nodes,edges,cfg,precision,seed,external) + comparison=compare(result,independent,precision) + save(io/'comparison.json',comparison) + save_result(io/'brian-output',result,nodes);save_result(io/'independent-output',independent,nodes) + assert np.isfinite(result['history']).all() and np.isfinite(independent['history']).all() + return result,comparison + + +def unit_fixtures(): + rows=[];nodes=np.array([-1],np.int32) + # Brian2 2.5.1 calls max/min on connect arrays and rejects zero-length arrays. + # An explicitly synthetic zero-weight self-edge is inert, not an anatomical edge. + inert=pd.DataFrame(dict(edge_id=[-1],source_neuron_idx=[-1],target_neuron_idx=[-1],raw_count=[0]),dtype='int64') + for precision in CFG['author_precisions']: + # Synthetic fixture indices are negative and are not MaleCNS body IDs. + c=dict(CFG,duration_ms=20.0) + cases={} + a=np.zeros((200,1));cases['zero']=(a,None,1.0) + a=np.zeros((200,1));a[0,0]=1.;cases['weak_excitation']=(a,None,1.0) + a=np.zeros((200,1));a[0,0]=-1.;cases['inhibition']=(a,None,1.0) + a=np.zeros((200,1));a[[0,21,22,23],0]=.1;cases['refractory_boundary']=(a,-1,1.0) + a=np.zeros((200,1));cases['equal_threshold']=(a,-1,0.0) + a=np.zeros((200,1));cases['above_threshold']=(a,-1,1.0) + a=np.zeros((200,1));a[0,0]=2000.;cases['nonzero_g_reset']=(a,None,1.0) + for name,(arr,seed,margin) in cases.items(): + cfg=dict(c,seed_margin_mv=margin) + r,cmp=oracle_trial('unit-'+name,nodes,inert,cfg,precision,seed,arr) + h=r['history'];events=r['step'];checks={} + if name=='zero':checks={'no_events':len(events)==0,'g_zero':bool(np.all(h[:,1]==0)), + 'rest_stationary':bool(np.max(np.abs(h[:,0]-CFG['model']['resting_potential_mv']))<1e-3)} + elif name in ('weak_excitation','inhibition'): + checks={'no_events':len(events)==0,'arrival_at_zero':bool(h[0,1,0]>0 if name=='weak_excitation' else h[0,1,0]<0), + 'integration_next_step':bool(h[1,0,0]>h[0,0,0] if name=='weak_excitation' else h[1,0,0]0),'release_at_22':bool(h[21,2,0]==1 and h[22,2,0]==0),'reset_g_at_zero':h[0,1,0]==0} + elif name=='equal_threshold':checks={'strict_threshold_no_event':len(events)==0} + elif name=='nonzero_g_reset':checks={'natural_spike_at_1':np.array_equal(events,[1]), + 'nonzero_g_before_spike':bool(h[0,1,0]>1999),'zero_g_after_spike':bool(np.all(h[1:,1,0]==0))} + else:checks={'single_seed':np.array_equal(events,[0]),'reset_g':bool(h[0,1,0]==0)} + row=dict(fixture=name,precision=precision,checks={k:bool(v) for k,v in checks.items()},comparison=cmp) + rows.append(row);save(EXP/'regression'/('unit-'+name+'-'+precision+'.json'),row) + print(json.dumps(dict(unit=name,precision=precision,checks=all(checks.values()),oracle=cmp)),flush=True) + delay_nodes=np.array([-2,-1],np.int32) + weak_edge=pd.DataFrame(dict(edge_id=[-1],source_neuron_idx=[-2],target_neuron_idx=[-1],raw_count=[1]),dtype='int64') + r,cmp=oracle_trial('unit-delay_18',delay_nodes,weak_edge,c,precision,-2) + h=r['history'];checks=dict(one_seed=np.array_equal(r['step'],[0]), + zero_before_arrival=bool(np.all(h[:18,1,1]==0)),arrival_at_18=bool(h[18,1,1]>0), + first_voltage_effect_at_19=bool(h[19,0,1]>h[18,0,1])) + row=dict(fixture='delay_18',precision=precision,checks=checks,comparison=cmp) + rows.append(row);save(EXP/'regression'/('unit-delay_18-'+precision+'.json'),row) + save(EXP/'regression/unit-fixtures.json',rows) + # Unit oracle failures prevent real author-motif execution; preserve all failed traces. + assert all(all(r['checks'].values()) and r['comparison']['pass_oracle'] for r in rows),'Author operator unit gate failed' + + +def main(): + check_prereg();assert not (EXP/'audit/run-start.json').exists(),'Refusing overwritten run' + assert all(importlib.metadata.version(n)==v for n,v in PACKAGE_PINS.items()),'Dependency-pin mismatch' + save(EXP/'environment/installed-packages.json',json.loads(subprocess.check_output([sys.executable,'-m','pip','list','--format=json'],text=True))) + save(EXP/'audit/run-start.json',dict(python=sys.version,platform=platform.platform(), + packages={n:importlib.metadata.version(n) for n in ('brian2','numpy','pandas','scipy','pyarrow','sympy','cython')}, + codegen='numpy',learning=False,user_authorized_new_model_hypotheses=True)) + t0=time.perf_counter();rows=[];validations=[] + for name in CFG['motifs']: + edges=pd.read_csv(AC/'motifs'/f'{name}-edges.csv').sort_values('edge_id') + old=np.load(AC/'motifs'/f'{name}-state.npz');nodes=old['nodes'];seed=None if name=='no_input' else CFG['seed_node'] + weights=edges.raw_count.to_numpy(np.float32)*np.float32(CFG['model']['w_syn_mv_per_anatomical_synapse']) + for policy in CFG['component_policies']: + r=component(nodes,edges,weights,CFG,policy,seed) + assert np.isfinite(r['history']).all() + if policy=='frozen': + ev=pd.read_parquet(AC/'motifs'/f'{name}-events.parquet') + eq={k:bool(np.array_equal(old[k],r[k])) for k in old.files if k!='nodes'} + eq['events']=bool(np.array_equal(ev.step,r['step']) and np.array_equal(ev.neuron_idx,r['neuron_idx'])) + assert all(eq.values()),eq + validations.append(dict(motif=name,frozen_vs_4AC_exact=eq)) + save_result(EXP/'components'/(name+'-'+policy),r,nodes) + late=r['step']>=round(CFG['late_start_ms']/CFG['dt_ms']) + for node in nodes: + select=r['neuron_idx']==node + rows.append(dict(motif=name,policy=policy,precision='float32',neuron_idx=int(node),spikes=int(select.sum()), + late_spikes=int((select&late).sum()),last_ms=float(r['step'][select][-1]*CFG['dt_ms']) if select.any() else None)) + pd.DataFrame(rows).to_csv(EXP/'components/summary.csv',index=False) + save(EXP/'regression/frozen-components.json',validations) + unit_fixtures() + from interface_audit import audit_author_poi + audit_author_poi() + ors=[] + for name in CFG['motifs']: + edges=pd.read_csv(AC/'motifs'/f'{name}-edges.csv').sort_values('edge_id') + nodes=np.load(AC/'motifs'/f'{name}-state.npz')['nodes'];seed=None if name=='no_input' else CFG['seed_node'];by_precision={} + for precision in CFG['author_precisions']: + r,cmp=oracle_trial(name,nodes,edges,CFG,precision,seed);by_precision[precision]=r + repeat=run_brian(EXP/'external-resources/model.py',EXP/'oracle'/(name+'-'+precision+'-repeat'),nodes,edges,CFG,precision,seed) + exact_repeat={k:bool(np.array_equal(r[k],repeat[k])) for k in r} + save_result(EXP/'oracle'/(name+'-'+precision+'-repeat')/'brian-output',repeat,nodes) + save(EXP/'regression'/(name+'-'+precision+'-repeat.json'),exact_repeat) + assert all(exact_repeat.values()),exact_repeat + late=r['step']>=round(CFG['late_start_ms']/CFG['dt_ms']) + for node in nodes: + chosen=r['neuron_idx']==node + rows.append(dict(motif=name,policy='author_complete',precision=precision,neuron_idx=int(node), + spikes=int(chosen.sum()),late_spikes=int((chosen&late).sum()),last_ms=float(r['step'][chosen][-1]*CFG['dt_ms']) if chosen.any() else None)) + ors.append(dict(motif=name,precision=precision,comparison=cmp)) + print(json.dumps(dict(motif=name,precision=precision,events=len(r['step']),late=int(late.sum()),oracle=cmp)),flush=True) + save(EXP/'regression'/(name+'-precision-cross-comparison.json'),compare(by_precision['float32'],by_precision['float64'],'float32')) + pd.DataFrame(rows).to_csv(EXP/'audit/all-motif-results.csv',index=False) + save(EXP/'regression/author-motifs.json',ors) + save(EXP/'performance/summary.json',dict(wall_seconds=time.perf_counter()-t0,backend='CPU NumPy + Brian2',not_runtime_benchmark=True)) + save(EXP/'audit/run-complete.json',dict(all_author_oracle_comparisons_pass=all(x['comparison']['pass_oracle'] for x in ors), + all_frozen_components_match_archive=True,learning_achieved=False,whole_brain_alternative_run=False, + author_original_source_sha256=digest(EXP/'external-resources/model.py'))) + + +if __name__=='__main__':main() diff --git a/models/male-cns-lif/author-semantics-lab-v1/verify_frozen.py b/models/male-cns-lif/author-semantics-lab-v1/verify_frozen.py new file mode 100644 index 0000000..ef8fa32 --- /dev/null +++ b/models/male-cns-lif/author-semantics-lab-v1/verify_frozen.py @@ -0,0 +1,47 @@ +"""Unchanged deterministic-v2 five-trial regression; old outputs are read only.""" +import os +import sys +import time +import numpy as np +import pandas as pd +import yaml +from context import ROOT,EXP,CFG,save,check_prereg + + +def main(): + check_prereg() + assert not (EXP/'regression/frozen-five.json').exists() + runtime=ROOT/'models/male-cns-lif/runtime-v2-deterministic-candidate' + # Discover the exact prior-audit runtime path from its immutable config. + prior=yaml.safe_load((ROOT/CFG['prior_model']/'config.yaml').read_text()) + runtime=ROOT/prior['runtime'];pc=yaml.safe_load((runtime/'phase4p.yaml').read_text()) + sys.path.insert(0,str(ROOT/'models/male-cns-lif/terminal-scope-diagnostic-v1')) + from diagnostic import queues + queues() + os.environ['CUDA_VISIBLE_DEVICES']=pc['device']['visible_gpu_uuid'] + os.environ['CUDA_HOME']='/usr/local/cuda';os.environ['MAX_JOBS']='2';os.environ['TORCH_CUDA_ARCH_LIST']='8.9' + os.environ['PATH']=str(ROOT/'models/male-cns-lif/.venv/bin')+':/usr/local/cuda/bin:'+os.environ['PATH'] + sys.path.insert(0,str(ROOT/'models/male-cns-lif'));sys.path.insert(0,str(runtime)) + import torch,phase4p + free,total=torch.cuda.mem_get_info();assert free>2*1024**3 + torch.cuda.reset_peak_memory_stats();t0=time.perf_counter() + rt=phase4p.CanonicalRuntime(pc,runtime,EXP) + rows=[] + for spec in pc['reference_trials']: + queues();base=ROOT/'experiments/phase4p-deterministic-runtime/phase4c-v2/reference'/spec['name'] + ev=pd.read_parquet(base/'spike-events.parquet') + expected=dict(step=ev.step.to_numpy(),neuron_idx=ev.neuron_idx.to_numpy(), + counts=np.load(base/'per-neuron-spike-counts.int32.npy'), + v=np.load(base/'final-voltage.float32.npy'),g=np.load(base/'final-g.float32.npy')) + r=rt.run(np.flatnonzero(rt.pops[spec['population']]),spec['rate_hz'],spec['seed'],spec['duration_ms']) + eq={k:bool(np.array_equal(r[k],v)) for k,v in expected.items()} + row=dict(trial=spec['name'],exact=eq,wall_seconds=r['metrics']['wall_seconds']) + rows.append(row);save(EXP/'regression'/('frozen-'+spec['name']+'.json'),row) + print(row,flush=True) + save(EXP/'regression/frozen-five.json',dict(pass_all=all(all(x['exact'].values()) for x in rows),trials=rows, + oracle='frozen deterministic-v2, NOT author Brian2',wall_seconds=time.perf_counter()-t0, + peak_allocated_vram=int(torch.cuda.max_memory_allocated()),gpu=torch.cuda.get_device_name(),comfyui_modified=False)) + assert all(all(x['exact'].values()) for x in rows) + + +if __name__=='__main__':main() diff --git a/registry/phase4ad-author-semantics/evidence-index.json b/registry/phase4ad-author-semantics/evidence-index.json new file mode 100644 index 0000000..678b8fb --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence-index.json @@ -0,0 +1,2648 @@ +[ + { + "source": "experiments/phase4ad-author-semantics/REPORT.md", + "copy": "evidence/REPORT.md", + "sha256": 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/dev/null +++ b/registry/phase4ad-author-semantics/evidence/REPORT.md @@ -0,0 +1,71 @@ +# Phase 4AD 作者动力学语义实验室 + +状态：`COMPLETE-ORACLE-VALIDATED-LAB-ONLY`。 + +本轮仅有预声明的小回路与算子实验；没有整脑替代动力学运行、conditioning、学习成功或新学习候选。 +检查以原始事件、状态轨迹和预注册误差界限重算。缺失、失败、非有限值或初始事件丢失均不能通过；放电减少或静默本身不构成成功。 + +核查通过 58/58 项；失败或不完整 0 项。 +冻结历史完整性：通过。 +源码与输入预注册一致性：通过。 + +| 回路 | 语义 | 精度 | 总spikes | late spikes | +|---|---|---|---:|---:| +| pair | frozen | float32 | 473 | 238 | +| pair | reset_g_only | float32 | 223 | 111 | +| pair | refractory_gate_only | float32 | 635 | 321 | +| pair | reset_and_refractory | float32 | 223 | 111 | +| trio | frozen | float32 | 1064 | 535 | +| trio | reset_g_only | float32 | 565 | 283 | +| trio | refractory_gate_only | float32 | 1100 | 552 | +| trio | reset_and_refractory | float32 | 469 | 235 | +| five | frozen | float32 | 1483 | 747 | +| five | reset_g_only | float32 | 868 | 433 | +| five | refractory_gate_only | float32 | 1510 | 763 | +| five | reset_and_refractory | float32 | 634 | 318 | +| feedforward | frozen | float32 | 3 | 0 | +| feedforward | reset_g_only | float32 | 3 | 0 | +| feedforward | refractory_gate_only | float32 | 3 | 0 | +| feedforward | reset_and_refractory | float32 | 3 | 0 | +| no_input | frozen | float32 | 0 | 0 | +| no_input | reset_g_only | float32 | 0 | 0 | +| no_input | refractory_gate_only | float32 | 0 | 0 | +| no_input | reset_and_refractory | float32 | 0 | 0 | +| pair | author_complete | float64 | 213 | 106 | +| pair | author_complete | float32 | 213 | 106 | +| trio | author_complete | float64 | 448 | 224 | +| trio | author_complete | float32 | 448 | 224 | +| five | author_complete | float64 | 610 | 306 | +| five | author_complete | float32 | 610 | 306 | +| feedforward | author_complete | float64 | 3 | 0 | +| feedforward | author_complete | float32 | 3 | 0 | +| no_input | author_complete | float64 | 0 | 0 | +| no_input | author_complete | float32 | 0 | 0 | + +作者Brian2与独立NumPy比较： + +| 实验 | 结果 | 事件一致 | 最大V/g误差 mV | 首次事件分歧step | +|---|---|---|---:|---:| +| author:pair:float64 | 通过 | True | 7.105427357601002e-14 | None | +| author:pair:float32 | 通过 | True | 2.41696834564209e-05 | None | +| author:trio:float64 | 通过 | True | 8.526512829121202e-14 | None | +| author:trio:float32 | 通过 | True | 4.25875186920166e-05 | None | +| author:five:float64 | 通过 | True | 3.836930773104541e-13 | None | +| author:five:float32 | 通过 | True | 0.0002123713493347168 | None | +| author:feedforward:float64 | 通过 | True | 3.765876499528531e-13 | None | +| author:feedforward:float32 | 通过 | True | 0.00020179152488708496 | None | +| author:no_input:float64 | 通过 | True | 7.105427357601002e-15 | None | +| author:no_input:float32 | 通过 | True | 1.0728836059570312e-06 | None | + +float32与float64交叉比较仅记录精度影响，允许保留分歧，不能用于掩盖各自与独立oracle的失败。 +- precision_cross_record:pair：事件一致=True，最大误差=3.733467101341148e-05 mV，首次事件分歧step=None。 +- precision_cross_record:trio：事件一致=True，最大误差=3.733467101341148e-05 mV，首次事件分歧step=None。 +- precision_cross_record:five：事件一致=True，最大误差=0.00019546693161487383 mV，首次事件分歧step=None。 +- precision_cross_record:feedforward：事件一致=True，最大误差=0.0005722045887850413 mV，首次事件分歧step=None。 +- precision_cross_record:no_input：事件一致=True，最大误差=0.0 mV，首次事件分歧step=None。 + +所有失败轨迹和错误文件原样保留；本简报没有选择获胜变体。 +小回路缺少外部整脑输入与graded APL，不能证明整脑因果必要性、生物真实性或信息保持。初始诊断seed也不是作者的感官Poisson接口。 +环境为Linux宿主，作者记录为Windows；Python补丁版本与环境差异见environment记录，不能称为二进制相同或原论文整脑复现。 +后续整脑嗅觉比较仍须核查固定输入、实际送达事件、持续活动和信息保持；可用学习仍需至少5个训练seed、独立评估、MBON/downstream的A对中性B特异性及acquisition/reversal/retention/delayed-reward对照。 +封存排除 .venv 与 __pycache__，保留环境安装报告；manifest列出payload哈希，checksums另含manifest，不存在自哈希循环。 diff --git a/registry/phase4ad-author-semantics/evidence/audit/all-motif-results.csv b/registry/phase4ad-author-semantics/evidence/audit/all-motif-results.csv new file mode 100644 index 0000000..f5af838 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/audit/all-motif-results.csv @@ -0,0 +1,121 @@ +motif,policy,precision,neuron_idx,spikes,late_spikes,last_ms +pair,frozen,float32,1381,237,119,999.3000000000001 +pair,frozen,float32,1511,236,119,997.5 +pair,reset_g_only,float32,1381,112,56,999.0 +pair,reset_g_only,float32,1511,111,55,994.9000000000001 +pair,refractory_gate_only,float32,1381,318,161,999.1 +pair,refractory_gate_only,float32,1511,317,160,997.5 +pair,reset_and_refractory,float32,1381,112,56,999.0 +pair,reset_and_refractory,float32,1511,111,55,994.9000000000001 +trio,frozen,float32,1197,355,179,999.3000000000001 +trio,frozen,float32,1381,355,178,997.8000000000001 +trio,frozen,float32,1511,354,178,997.4000000000001 +trio,reset_g_only,float32,1197,188,94,995.4000000000001 +trio,reset_g_only,float32,1381,189,95,998.7 +trio,reset_g_only,float32,1511,188,94,996.1 +trio,refractory_gate_only,float32,1197,369,185,998.3000000000001 +trio,refractory_gate_only,float32,1381,367,184,999.1 +trio,refractory_gate_only,float32,1511,364,183,997.2 +trio,reset_and_refractory,float32,1197,156,78,995.3000000000001 +trio,reset_and_refractory,float32,1381,157,79,999.6 +trio,reset_and_refractory,float32,1511,156,78,997.5 +five,frozen,float32,1197,370,185,998.8000000000001 +five,frozen,float32,1381,369,185,997.4000000000001 +five,frozen,float32,1511,367,186,999.5 +five,frozen,float32,82312,80,41,990.3000000000001 +five,frozen,float32,133666,297,150,999.5 +five,reset_g_only,float32,1197,249,125,996.2 +five,reset_g_only,float32,1381,211,104,999.2 +five,reset_g_only,float32,1511,209,104,996.5 +five,reset_g_only,float32,82312,33,17,994.9000000000001 +five,reset_g_only,float32,133666,166,83,996.7 +five,refractory_gate_only,float32,1197,372,188,998.0 +five,refractory_gate_only,float32,1381,375,191,998.6 +five,refractory_gate_only,float32,1511,371,187,997.5 +five,refractory_gate_only,float32,82312,85,43,991.9000000000001 +five,refractory_gate_only,float32,133666,307,154,997.7 +five,reset_and_refractory,float32,1197,165,82,995.7 +five,reset_and_refractory,float32,1381,166,83,999.8000000000001 +five,reset_and_refractory,float32,1511,165,83,997.5 +five,reset_and_refractory,float32,82312,15,8,972.7 +five,reset_and_refractory,float32,133666,123,62,993.0 +feedforward,frozen,float32,1197,1,0,10.0 +feedforward,frozen,float32,1381,1,0,0.0 +feedforward,frozen,float32,1511,1,0,4.9 +feedforward,frozen,float32,82312,0,0, +feedforward,frozen,float32,133666,0,0, +feedforward,reset_g_only,float32,1197,1,0,10.0 +feedforward,reset_g_only,float32,1381,1,0,0.0 +feedforward,reset_g_only,float32,1511,1,0,4.9 +feedforward,reset_g_only,float32,82312,0,0, +feedforward,reset_g_only,float32,133666,0,0, +feedforward,refractory_gate_only,float32,1197,1,0,10.0 +feedforward,refractory_gate_only,float32,1381,1,0,0.0 +feedforward,refractory_gate_only,float32,1511,1,0,4.9 +feedforward,refractory_gate_only,float32,82312,0,0, +feedforward,refractory_gate_only,float32,133666,0,0, +feedforward,reset_and_refractory,float32,1197,1,0,10.0 +feedforward,reset_and_refractory,float32,1381,1,0,0.0 +feedforward,reset_and_refractory,float32,1511,1,0,4.9 +feedforward,reset_and_refractory,float32,82312,0,0, +feedforward,reset_and_refractory,float32,133666,0,0, +no_input,frozen,float32,1197,0,0, +no_input,frozen,float32,1381,0,0, +no_input,frozen,float32,1511,0,0, +no_input,frozen,float32,82312,0,0, +no_input,frozen,float32,133666,0,0, +no_input,reset_g_only,float32,1197,0,0, +no_input,reset_g_only,float32,1381,0,0, +no_input,reset_g_only,float32,1511,0,0, +no_input,reset_g_only,float32,82312,0,0, +no_input,reset_g_only,float32,133666,0,0, +no_input,refractory_gate_only,float32,1197,0,0, +no_input,refractory_gate_only,float32,1381,0,0, +no_input,refractory_gate_only,float32,1511,0,0, +no_input,refractory_gate_only,float32,82312,0,0, +no_input,refractory_gate_only,float32,133666,0,0, +no_input,reset_and_refractory,float32,1197,0,0, +no_input,reset_and_refractory,float32,1381,0,0, +no_input,reset_and_refractory,float32,1511,0,0, +no_input,reset_and_refractory,float32,82312,0,0, +no_input,reset_and_refractory,float32,133666,0,0, +pair,author_complete,float64,1381,107,53,996.4000000000001 +pair,author_complete,float64,1511,106,53,992.1 +pair,author_complete,float32,1381,107,53,996.4000000000001 +pair,author_complete,float32,1511,106,53,992.1 +trio,author_complete,float64,1197,149,74,994.8000000000001 +trio,author_complete,float64,1381,150,75,999.3000000000001 +trio,author_complete,float64,1511,149,75,997.0 +trio,author_complete,float32,1197,149,74,994.8000000000001 +trio,author_complete,float32,1381,150,75,999.3000000000001 +trio,author_complete,float32,1511,149,75,997.0 +five,author_complete,float64,1197,159,79,995.2 +five,author_complete,float64,1381,160,80,999.5 +five,author_complete,float64,1511,159,80,997.4000000000001 +five,author_complete,float64,82312,13,7,992.4000000000001 +five,author_complete,float64,133666,119,60,996.0 +five,author_complete,float32,1197,159,79,995.2 +five,author_complete,float32,1381,160,80,999.5 +five,author_complete,float32,1511,159,80,997.4000000000001 +five,author_complete,float32,82312,13,7,992.4000000000001 +five,author_complete,float32,133666,119,60,996.0 +feedforward,author_complete,float64,1197,1,0,10.4 +feedforward,author_complete,float64,1381,1,0,0.0 +feedforward,author_complete,float64,1511,1,0,5.1000000000000005 +feedforward,author_complete,float64,82312,0,0, +feedforward,author_complete,float64,133666,0,0, +feedforward,author_complete,float32,1197,1,0,10.4 +feedforward,author_complete,float32,1381,1,0,0.0 +feedforward,author_complete,float32,1511,1,0,5.1000000000000005 +feedforward,author_complete,float32,82312,0,0, +feedforward,author_complete,float32,133666,0,0, +no_input,author_complete,float64,1197,0,0, +no_input,author_complete,float64,1381,0,0, +no_input,author_complete,float64,1511,0,0, +no_input,author_complete,float64,82312,0,0, +no_input,author_complete,float64,133666,0,0, 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This interface is not the common initial seed experiment.", + "scope": "Compile-time interface audit only; no stochastic trial, learning, or whole-brain simulation. 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0.0002123713493347168, + "mean_abs_mv": 1.7726411819458007e-05, + "same_event_prefix_max_abs_mv": 0.0002123713493347168, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true + }, + "repeat_exact": { + "step": true, + "neuron_idx": true, + "counts": true, + "v": true, + "g": true, + "ref": true, + "history": true, + "weights": true + } + }, + { + "name": "author:feedforward:float64", + "pass": true, + "raw_comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 3.765876499528531e-13, + "mean_abs_mv": 3.893371799264915e-14, + "same_event_prefix_max_abs_mv": 3.765876499528531e-13, + "first_event_divergence_step": null, + "tolerance_mv": 1e-08, + "pass_oracle": true + }, + "repeat_exact": { + "step": true, + "neuron_idx": true, + "counts": true, + "v": true, + "g": true, + "ref": true, + "history": true, + "weights": true + } + }, + { + "name": "author:feedforward:float32", + "pass": true, + "raw_comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.00020179152488708496, + "mean_abs_mv": 1.9821550031807453e-05, + "same_event_prefix_max_abs_mv": 0.00020179152488708496, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true + }, + "repeat_exact": { + "step": true, + "neuron_idx": true, + "counts": true, + "v": true, + "g": true, + "ref": true, + "history": true, + "weights": true + } + }, + { + "name": "author:no_input:float64", + "pass": true, + "raw_comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 7.105427357601002e-15, + "mean_abs_mv": 3.552713678800501e-15, + "same_event_prefix_max_abs_mv": 7.105427357601002e-15, + "first_event_divergence_step": null, + "tolerance_mv": 1e-08, + "pass_oracle": true + }, + "repeat_exact": { + "step": true, + "neuron_idx": true, + "counts": true, + "v": true, + "g": true, + "ref": true, + "history": true, + "weights": true + } + }, + { + "name": "author:no_input:float32", + "pass": true, + "raw_comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 1.0728836059570312e-06, + "mean_abs_mv": 5.364418029785156e-07, + "same_event_prefix_max_abs_mv": 1.0728836059570312e-06, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true + }, + "repeat_exact": { + "step": true, + "neuron_idx": true, + "counts": true, + "v": true, + "g": true, + "ref": true, + "history": true, + "weights": true + } + } + ], + "precision_cross_checks": [ + { + "name": "precision_cross_record:pair", + "pass": true, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 3.733467101341148e-05, + "mean_abs_mv": 3.280381464815818e-06, + "same_event_prefix_max_abs_mv": 3.733467101341148e-05, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true + }, + "interpretation": "Reporting consistency only; cross-precision divergence is allowed and retained." + }, + { + "name": "precision_cross_record:trio", + "pass": true, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 3.733467101341148e-05, + "mean_abs_mv": 3.6417296913128893e-06, + "same_event_prefix_max_abs_mv": 3.733467101341148e-05, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true + }, + "interpretation": "Reporting consistency only; cross-precision divergence is allowed and retained." + }, + { + "name": "precision_cross_record:five", + "pass": true, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.00019546693161487383, + "mean_abs_mv": 1.7966433624798595e-05, + "same_event_prefix_max_abs_mv": 0.00019546693161487383, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true + }, + "interpretation": "Reporting consistency only; cross-precision divergence is allowed and retained." + }, + { + "name": "precision_cross_record:feedforward", + "pass": true, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.0005722045887850413, + "mean_abs_mv": 4.780100484587312e-05, + "same_event_prefix_max_abs_mv": 0.0005722045887850413, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true + }, + "interpretation": "Reporting consistency only; cross-precision divergence is allowed and retained." + }, + { + "name": "precision_cross_record:no_input", + "pass": true, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.0, + "mean_abs_mv": 0.0, + "same_event_prefix_max_abs_mv": 0.0, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true + }, + "interpretation": "Reporting consistency only; cross-precision divergence is allowed and retained." + } + ], + "motif_outcomes": [ + { + "motif": "pair", + 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graded APL.", + "Author equations on MaleCNS motifs do not reproduce the original paper's full brain or sensory interface.", + "Linux host and Python patch differences prevent a binary-identical author-environment claim." + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/audit/finalize-start.json b/registry/phase4ad-author-semantics/evidence/audit/finalize-start.json new file mode 100644 index 0000000..ab6633b --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/audit/finalize-start.json @@ -0,0 +1,7 @@ +{ + "timestamp_utc": "2026-09-29T23:18:24.492697+00:00", + "python": "3.10.12 (main, Aug 31 2026, 10:18:17) [GCC 11.4.0]", + "executable": "/data/digital-drosophila/models/male-cns-lif/.venv/bin/python", + "learning": false, + "whole_brain_alternative_run": false +} diff --git a/registry/phase4ad-author-semantics/evidence/audit/run-complete.json b/registry/phase4ad-author-semantics/evidence/audit/run-complete.json new file mode 100644 index 0000000..02715ab --- 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b/registry/phase4ad-author-semantics/evidence/components/no_input-refractory_gate_only/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/components/no_input-refractory_gate_only/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/components/no_input-reset_and_refractory/events.csv b/registry/phase4ad-author-semantics/evidence/components/no_input-reset_and_refractory/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/components/no_input-reset_and_refractory/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/components/no_input-reset_g_only/events.csv b/registry/phase4ad-author-semantics/evidence/components/no_input-reset_g_only/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ 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\n\n-----------------\n\n# pandas: powerful Python data analysis toolkit\n[![PyPI Latest Release](https://img.shields.io/pypi/v/pandas.svg)](https://pypi.org/project/pandas/)\n[![Conda Latest Release](https://anaconda.org/conda-forge/pandas/badges/version.svg)](https://anaconda.org/anaconda/pandas/)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3509134.svg)](https://doi.org/10.5281/zenodo.3509134)\n[![Package Status](https://img.shields.io/pypi/status/pandas.svg)](https://pypi.org/project/pandas/)\n[![License](https://img.shields.io/pypi/l/pandas.svg)](https://github.com/pandas-dev/pandas/blob/main/LICENSE)\n[![Coverage](https://codecov.io/github/pandas-dev/pandas/coverage.svg?branch=main)](https://codecov.io/gh/pandas-dev/pandas)\n[![Downloads](https://static.pepy.tech/personalized-badge/pandas?period=month&units=international_system&left_color=black&right_color=orange&left_text=PyPI%20downloads%20per%20month)](https://pepy.tech/project/pandas)\n[![Gitter](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/pydata/pandas)\n[![Powered by NumFOCUS](https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](https://numfocus.org)\n[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)\n[![Imports: isort](https://img.shields.io/badge/%20imports-isort-%231674b1?style=flat&labelColor=ef8336)](https://pycqa.github.io/isort/)\n\n## What is it?\n\n**pandas** is a Python package that provides fast, flexible, and expressive data\nstructures designed to make working with \"relational\" or \"labeled\" data both\neasy and intuitive. It aims to be the fundamental high-level building block for\ndoing practical, **real world** data analysis in Python. Additionally, it has\nthe broader goal of becoming **the most powerful and flexible open source data\nanalysis / manipulation tool available in any language**. It is already well on\nits way towards this goal.\n\n## Main Features\nHere are just a few of the things that pandas does well:\n\n - Easy handling of [**missing data**][missing-data] (represented as\n `NaN`, `NA`, or `NaT`) in floating point as well as non-floating point data\n - Size mutability: columns can be [**inserted and\n deleted**][insertion-deletion] from DataFrame and higher dimensional\n objects\n - Automatic and explicit [**data alignment**][alignment]: objects can\n be explicitly aligned to a set of labels, or the user can simply\n ignore the labels and let `Series`, `DataFrame`, etc. automatically\n align the data for you in computations\n - Powerful, flexible [**group by**][groupby] functionality to perform\n split-apply-combine operations on data sets, for both aggregating\n and transforming data\n - Make it [**easy to convert**][conversion] ragged,\n differently-indexed data in other Python and NumPy data structures\n into DataFrame objects\n - Intelligent label-based [**slicing**][slicing], [**fancy\n indexing**][fancy-indexing], and [**subsetting**][subsetting] of\n large data sets\n - Intuitive [**merging**][merging] and [**joining**][joining] data\n sets\n - Flexible [**reshaping**][reshape] and [**pivoting**][pivot-table] of\n data sets\n - [**Hierarchical**][mi] labeling of axes (possible to have multiple\n labels per tick)\n - Robust IO tools for loading data from [**flat files**][flat-files]\n (CSV and delimited), [**Excel files**][excel], [**databases**][db],\n and saving/loading data from the ultrafast [**HDF5 format**][hdfstore]\n - [**Time series**][timeseries]-specific functionality: date range\n generation and frequency conversion, moving window statistics,\n date shifting and lagging\n\n\n [missing-data]: https://pandas.pydata.org/pandas-docs/stable/user_guide/missing_data.html\n [insertion-deletion]: https://pandas.pydata.org/pandas-docs/stable/user_guide/dsintro.html#column-selection-addition-deletion\n [alignment]: https://pandas.pydata.org/pandas-docs/stable/user_guide/dsintro.html?highlight=alignment#intro-to-data-structures\n [groupby]: https://pandas.pydata.org/pandas-docs/stable/user_guide/groupby.html#group-by-split-apply-combine\n [conversion]: https://pandas.pydata.org/pandas-docs/stable/user_guide/dsintro.html#dataframe\n [slicing]: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#slicing-ranges\n [fancy-indexing]: https://pandas.pydata.org/pandas-docs/stable/user_guide/advanced.html#advanced\n [subsetting]: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#boolean-indexing\n [merging]: https://pandas.pydata.org/pandas-docs/stable/user_guide/merging.html#database-style-dataframe-or-named-series-joining-merging\n [joining]: https://pandas.pydata.org/pandas-docs/stable/user_guide/merging.html#joining-on-index\n [reshape]: https://pandas.pydata.org/pandas-docs/stable/user_guide/reshaping.html\n [pivot-table]: https://pandas.pydata.org/pandas-docs/stable/user_guide/reshaping.html\n [mi]: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#hierarchical-indexing-multiindex\n [flat-files]: https://pandas.pydata.org/pandas-docs/stable/user_guide/io.html#csv-text-files\n [excel]: https://pandas.pydata.org/pandas-docs/stable/user_guide/io.html#excel-files\n [db]: https://pandas.pydata.org/pandas-docs/stable/user_guide/io.html#sql-queries\n [hdfstore]: https://pandas.pydata.org/pandas-docs/stable/user_guide/io.html#hdf5-pytables\n [timeseries]: https://pandas.pydata.org/pandas-docs/stable/user_guide/timeseries.html#time-series-date-functionality\n\n## Where to get it\nThe source code is currently hosted on GitHub at:\nhttps://github.com/pandas-dev/pandas\n\nBinary installers for the latest released version are available at the [Python\nPackage Index (PyPI)](https://pypi.org/project/pandas) and on [Conda](https://docs.conda.io/en/latest/).\n\n```sh\n# conda\nconda install pandas\n```\n\n```sh\n# or PyPI\npip install pandas\n```\n\n## Dependencies\n- [NumPy - Adds support for large, multi-dimensional arrays, matrices and high-level mathematical functions to operate on these arrays](https://www.numpy.org)\n- [python-dateutil - Provides powerful extensions to the standard datetime module](https://dateutil.readthedocs.io/en/stable/index.html)\n- [pytz - Brings the Olson tz database into Python which allows accurate and cross platform timezone calculations](https://github.com/stub42/pytz)\n\nSee the [full installation instructions](https://pandas.pydata.org/pandas-docs/stable/install.html#dependencies) for minimum supported versions of required, recommended and optional dependencies.\n\n## Installation from sources\nTo install pandas from source you need [Cython](https://cython.org/) in addition to the normal\ndependencies above. Cython can be installed from PyPI:\n\n```sh\npip install cython\n```\n\nIn the `pandas` directory (same one where you found this file after\ncloning the git repo), execute:\n\n```sh\npython setup.py install\n```\n\nor for installing in [development mode](https://pip.pypa.io/en/latest/cli/pip_install/#install-editable):\n\n\n```sh\npython -m pip install -e . --no-build-isolation --no-use-pep517\n```\n\nIf you have `make`, you can also use `make develop` to run the same command.\n\nor alternatively\n\n```sh\npython setup.py develop\n```\n\nSee the full instructions for [installing from source](https://pandas.pydata.org/pandas-docs/stable/install.html#installing-from-source).\n\n## License\n[BSD 3](LICENSE)\n\n## Documentation\nThe official documentation is hosted on PyData.org: https://pandas.pydata.org/pandas-docs/stable\n\n## Background\nWork on ``pandas`` started at [AQR](https://www.aqr.com/) (a quantitative hedge fund) in 2008 and\nhas been under active development since then.\n\n## Getting Help\n\nFor usage questions, the best place to go to is [StackOverflow](https://stackoverflow.com/questions/tagged/pandas).\nFurther, general questions and discussions can also take place on the [pydata mailing list](https://groups.google.com/forum/?fromgroups#!forum/pydata).\n\n## Discussion and Development\nMost development discussions take place on GitHub in this repo. Further, the [pandas-dev mailing list](https://mail.python.org/mailman/listinfo/pandas-dev) can also be used for specialized discussions or design issues, and a [Gitter channel](https://gitter.im/pydata/pandas) is available for quick development related questions.\n\n## Contributing to pandas [![Open Source Helpers](https://www.codetriage.com/pandas-dev/pandas/badges/users.svg)](https://www.codetriage.com/pandas-dev/pandas)\n\nAll contributions, bug reports, bug fixes, documentation improvements, enhancements, and ideas are welcome.\n\nA detailed overview on how to contribute can be found in the **[contributing guide](https://pandas.pydata.org/docs/dev/development/contributing.html)**.\n\nIf you are simply looking to start working with the pandas codebase, navigate to the [GitHub \"issues\" tab](https://github.com/pandas-dev/pandas/issues) and start looking through interesting issues. There are a number of issues listed under [Docs](https://github.com/pandas-dev/pandas/issues?labels=Docs&sort=updated&state=open) and [good first issue](https://github.com/pandas-dev/pandas/issues?labels=good+first+issue&sort=updated&state=open) where you could start out.\n\nYou can also triage issues which may include reproducing bug reports, or asking for vital information such as version numbers or reproduction instructions. If you would like to start triaging issues, one easy way to get started is to [subscribe to pandas on CodeTriage](https://www.codetriage.com/pandas-dev/pandas).\n\nOr maybe through using pandas you have an idea of your own or are looking for something in the documentation and thinking ‘this can be improved’...you can do something about it!\n\nFeel free to ask questions on the [mailing list](https://groups.google.com/forum/?fromgroups#!forum/pydata) or on [Gitter](https://gitter.im/pydata/pandas).\n\nAs contributors and maintainers to this project, you are expected to abide by pandas' code of conduct. More information can be found at: [Contributor Code of Conduct](https://github.com/pandas-dev/pandas/blob/main/.github/CODE_OF_CONDUCT.md)\n" + } + }, + { + "download_info": { + "url": "https://files.pythonhosted.org/packages/bc/fe/72b611ba221c3367b06163992af4807515d6e0e09b3b9beee8ec22162d6f/scipy-1.8.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", + "archive_info": { + "hash": "sha256=a0aa8220b89b2e3748a2836fbfa116194378910f1a6e78e4675a095bcd2c762d", + "hashes": { + "sha256": "a0aa8220b89b2e3748a2836fbfa116194378910f1a6e78e4675a095bcd2c762d" + } + } + }, + "is_direct": false, + "requested": true, + "metadata": { + "metadata_version": "2.1", + "name": "scipy", + "version": "1.8.1", + "platform": [ + "Windows", + "Linux", + "Solaris", + "Mac OS-X", + "Unix" + ], + "summary": "SciPy: Scientific Library for Python", + "home_page": "https://www.scipy.org", + "download_url": "https://github.com/scipy/scipy/releases", + "maintainer": "SciPy Developers", + "maintainer_email": "scipy-dev@python.org", + "license": "BSD", + "classifier": [ + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Science/Research", + "Intended Audience :: Developers", + "License :: OSI Approved :: BSD License", + "Programming Language :: C", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Topic :: Software Development :: Libraries", + "Topic :: Scientific/Engineering", + "Operating System :: Microsoft :: Windows", + "Operating System :: POSIX :: Linux", + "Operating System :: POSIX", + "Operating System :: Unix", + "Operating System :: MacOS" + ], + "requires_dist": [ + "numpy (<1.25.0,>=1.17.3)" + ], + "requires_python": ">=3.8,<3.11", + "project_url": [ + "Bug Tracker, https://github.com/scipy/scipy/issues", + "Documentation, https://docs.scipy.org/doc/scipy/reference/", + "Source Code, https://github.com/scipy/scipy" + ], + "description": "SciPy (pronounced \"Sigh Pie\") is open-source software for mathematics,\nscience, and engineering. The SciPy library\ndepends on NumPy, which provides convenient and fast N-dimensional\narray manipulation. The SciPy library is built to work with NumPy\narrays, and provides many user-friendly and efficient numerical\nroutines such as routines for numerical integration and optimization.\nTogether, they run on all popular operating systems, are quick to\ninstall, and are free of charge. NumPy and SciPy are easy to use,\nbut powerful enough to be depended upon by some of the world's\nleading scientists and engineers. If you need to manipulate\nnumbers on a computer and display or publish the results,\ngive SciPy a try!\n\n\n\n" + } + }, + { + "download_info": { + "url": "https://files.pythonhosted.org/packages/bc/5b/cee81fdfbd963e08a50eda1500fc9142fa08a7dec5f7dcd9c7c2a33536b6/pyarrow-11.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", + "archive_info": { + "hash": "sha256=ad7c53def8dbbc810282ad308cc46a523ec81e653e60a91c609c2233ae407689", + "hashes": { + "sha256": "ad7c53def8dbbc810282ad308cc46a523ec81e653e60a91c609c2233ae407689" + } + } + }, + "is_direct": false, + "requested": true, + "metadata": { + "metadata_version": "2.1", + "name": "pyarrow", + "version": "11.0.0", + "summary": "Python library for Apache Arrow", + "description_content_type": "text/markdown", + "home_page": "https://arrow.apache.org/", + "maintainer": "Apache Arrow Developers", + "maintainer_email": "dev@arrow.apache.org", + "license": "Apache License, Version 2.0", + "classifier": [ + "License :: OSI Approved :: Apache Software License", + "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11" + ], + "requires_dist": [ + "numpy (>=1.16.6)" + ], + "requires_python": ">=3.7", + "project_url": [ + "Documentation, https://arrow.apache.org/docs/python", + "Source, https://github.com/apache/arrow" + ], + "description": "\n\n## Python library for Apache Arrow\n\n[![pypi](https://img.shields.io/pypi/v/pyarrow.svg)](https://pypi.org/project/pyarrow/) [![conda-forge](https://img.shields.io/conda/vn/conda-forge/pyarrow.svg)](https://anaconda.org/conda-forge/pyarrow)\n\nThis library provides a Python API for functionality provided by the Arrow C++\nlibraries, along with tools for Arrow integration and interoperability with\npandas, NumPy, and other software in the Python ecosystem.\n\n## Installing\n\nAcross platforms, you can install a recent version of pyarrow with the conda\npackage manager:\n\n```shell\nconda install pyarrow -c conda-forge\n```\n\nOn Linux, macOS, and Windows, you can also install binary wheels from PyPI with\npip:\n\n```shell\npip install pyarrow\n```\n\nIf you encounter any issues importing the pip wheels on Windows, you may need\nto install the [Visual C++ Redistributable for Visual Studio 2015][6].\n\n## Development\n\nSee [Python Development][2] in the documentation subproject.\n\n### Building the documentation\n\nSee [documentation build instructions][1] in the documentation subproject.\n\n[1]: https://github.com/apache/arrow/blob/master/docs/source/developers/documentation.rst\n[2]: https://github.com/apache/arrow/blob/master/docs/source/developers/python.rst\n[3]: https://github.com/pandas-dev/pandas\n[5]: https://arrow.apache.org/docs/latest/python/benchmarks.html\n[6]: https://www.microsoft.com/en-us/download/details.aspx?id=48145\n" + } + }, + { + "download_info": { + "url": "https://files.pythonhosted.org/packages/91/d4/3b4c8e5a30604df4c7518c562d4bf0502f2fa29221459226e140cf846512/joblib-1.2.0-py3-none-any.whl", + "archive_info": { + "hash": "sha256=091138ed78f800342968c523bdde947e7a305b8594b910a0fea2ab83c3c6d385", + "hashes": { + "sha256": "091138ed78f800342968c523bdde947e7a305b8594b910a0fea2ab83c3c6d385" + } + } + }, + "is_direct": false, + "requested": true, + "metadata": { + "metadata_version": "2.1", + "name": "joblib", + "version": "1.2.0", + "platform": [ + "any" + ], + "summary": "Lightweight pipelining with Python functions", + "description_content_type": "text/x-rst", + "home_page": "https://joblib.readthedocs.io", + "author": "Gael Varoquaux", + "author_email": "gael.varoquaux@normalesup.org", + "license": "BSD", + "classifier": [ + "Development Status :: 5 - Production/Stable", + "Environment :: Console", + "Intended Audience :: Developers", + "Intended Audience :: Science/Research", + "Intended Audience :: Education", + "License :: OSI Approved :: BSD License", + "Operating System :: OS Independent", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Topic :: Scientific/Engineering", + "Topic :: Utilities", + "Topic :: Software Development :: Libraries" + ], + "requires_python": ">=3.7", + "project_url": [ + "Source, https://github.com/joblib/joblib" + ], + "description": "|PyPi| |Azure| |ReadTheDocs| |Codecov| \n\n.. |PyPi| image:: https://badge.fury.io/py/joblib.svg\n :target: https://badge.fury.io/py/joblib\n :alt: Joblib version\n\n.. |Azure| image:: https://dev.azure.com/joblib/joblib/_apis/build/status/joblib.joblib?branchName=master\n :target: https://dev.azure.com/joblib/joblib/_build?definitionId=3&_a=summary&branchFilter=40\n :alt: Azure CI status\n\n.. |ReadTheDocs| image:: https://readthedocs.org/projects/joblib/badge/?version=latest\n :target: https://joblib.readthedocs.io/en/latest/?badge=latest\n :alt: Documentation Status\n\n.. |Codecov| image:: https://codecov.io/gh/joblib/joblib/branch/master/graph/badge.svg\n :target: https://codecov.io/gh/joblib/joblib\n :alt: Codecov coverage\n\n\nThe homepage of joblib with user documentation is located on:\n\nhttps://joblib.readthedocs.io\n\nGetting the latest code\n=======================\n\nTo get the latest code using git, simply type::\n\n git clone git://github.com/joblib/joblib.git\n\nIf you don't have git installed, you can download a zip or tarball\nof the latest code: http://github.com/joblib/joblib/archives/master\n\nInstalling\n==========\n\nYou can use `pip` to install joblib::\n\n pip install joblib\n\nfrom any directory or::\n\n python setup.py install\n\nfrom the source directory.\n\nDependencies\n============\n\n- Joblib has no mandatory dependencies besides Python (supported versions are\n 3.7+).\n- Joblib has an optional dependency on Numpy (at least version 1.6.1) for array\n manipulation.\n- Joblib includes its own vendored copy of\n `loky `_ for process management.\n- Joblib can efficiently dump and load numpy arrays but does not require numpy\n to be installed.\n- Joblib has an optional dependency on\n `python-lz4 `_ as a faster alternative to\n zlib and gzip for compressed serialization.\n- Joblib has an optional dependency on psutil to mitigate memory leaks in\n parallel worker processes.\n- Some examples require external dependencies such as pandas. See the\n instructions in the `Building the docs`_ section for details.\n\nWorkflow to contribute\n======================\n\nTo contribute to joblib, first create an account on `github\n`_. Once this is done, fork the `joblib repository\n`_ to have your own repository,\nclone it using 'git clone' on the computers where you want to work. Make\nyour changes in your clone, push them to your github account, test them\non several computers, and when you are happy with them, send a pull\nrequest to the main repository.\n\nRunning the test suite\n======================\n\nTo run the test suite, you need the pytest (version >= 3) and coverage modules.\nRun the test suite using::\n\n pytest joblib\n\nfrom the root of the project.\n\nBuilding the docs\n=================\n\nTo build the docs you need to have sphinx (>=1.4) and some dependencies\ninstalled::\n\n pip install -U -r .readthedocs-requirements.txt\n\nThe docs can then be built with the following command::\n\n make doc\n\nThe html docs are located in the ``doc/_build/html`` directory.\n\n\nMaking a source tarball\n=======================\n\nTo create a source tarball, eg for packaging or distributing, run the\nfollowing command::\n\n python setup.py sdist\n\nThe tarball will be created in the `dist` directory. This command will\ncompile the docs, and the resulting tarball can be installed with\nno extra dependencies than the Python standard library. You will need\nsetuptool and sphinx.\n\nMaking a release and uploading it to PyPI\n=========================================\n\nThis command is only run by project manager, to make a release, and\nupload in to PyPI::\n\n python setup.py sdist bdist_wheel\n twine upload dist/*\n\n\nNote that the documentation should automatically get updated at each git\npush. If that is not the case, try building th doc locally and resolve\nany doc build error (in particular when running the examples).\n\nUpdating the changelog\n======================\n\nChanges are listed in the CHANGES.rst file. They must be manually updated\nbut, the following git command may be used to generate the lines::\n\n git log --abbrev-commit --date=short --no-merges --sparse\n\n\n\n" + } + }, + { + "download_info": { + "url": "https://files.pythonhosted.org/packages/21/76/ef852189cc39a33cedc08d30189de2d1e44d826ddcf101e24c82c8b8ea0c/Cython-0.29.33-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl", + "archive_info": { + "hash": "sha256=0168482495b75fea1c97a9641a95bac991f313e85f378003f9a4909fdeb3d454", + "hashes": { + "sha256": "0168482495b75fea1c97a9641a95bac991f313e85f378003f9a4909fdeb3d454" + } + } + }, + "is_direct": false, + "requested": true, + "metadata": { + "metadata_version": "2.1", + "name": "Cython", + "version": "0.29.33", + "summary": "The Cython compiler for writing C extensions for the Python language.", + "home_page": "http://cython.org/", + "author": "Robert Bradshaw, Stefan Behnel, Dag Seljebotn, Greg Ewing, et al.", + "author_email": "cython-devel@python.org", + "license": "Apache", + "classifier": [ + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Developers", + "License :: OSI Approved :: Apache Software License", + "Operating System :: OS Independent", + "Programming Language :: Python", + "Programming Language :: Python :: 2", + "Programming Language :: Python :: 2.6", + "Programming Language :: Python :: 2.7", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.4", + "Programming Language :: Python :: 3.5", + "Programming Language :: Python :: 3.6", + "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: Implementation :: CPython", + "Programming Language :: Python :: Implementation :: PyPy", + "Programming Language :: C", + "Programming Language :: Cython", + "Topic :: Software Development :: Code Generators", + "Topic :: Software Development :: Compilers", + "Topic :: Software Development :: Libraries :: Python Modules" + ], + "requires_python": ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*", + "project_url": [ + "Documentation, https://cython.readthedocs.io/", + "Donate, https://cython.readthedocs.io/en/latest/src/donating.html", + "Source Code, https://github.com/cython/cython", + "Bug Tracker, https://github.com/cython/cython/issues", + "User Group, https://groups.google.com/g/cython-users" + ], + "description": "The Cython language makes writing C extensions for the Python language as\neasy as Python itself. Cython is a source code translator based on Pyrex_,\nbut supports more cutting edge functionality and optimizations.\n\nThe Cython language is a superset of the Python language (almost all Python\ncode is also valid Cython code), but Cython additionally supports optional\nstatic typing to natively call C functions, operate with C++ classes and\ndeclare fast C types on variables and class attributes. 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Special\nplaceholders in the template allow writing code similar to Python\nsyntax. Then the template is passed data to render the final document.\n\nIt includes:\n\n- Template inheritance and inclusion.\n- Define and import macros within templates.\n- HTML templates can use autoescaping to prevent XSS from untrusted\n user input.\n- A sandboxed environment can safely render untrusted templates.\n- AsyncIO support for generating templates and calling async\n functions.\n- I18N support with Babel.\n- Templates are compiled to optimized Python code just-in-time and\n cached, or can be compiled ahead-of-time.\n- Exceptions point to the correct line in templates to make debugging\n easier.\n- Extensible filters, tests, functions, and even syntax.\n\nJinja's philosophy is that while application logic belongs in Python if\npossible, it shouldn't make the template designer's job difficult by\nrestricting functionality too much.\n\n\nInstalling\n----------\n\nInstall and update using `pip`_:\n\n.. code-block:: text\n\n $ pip install -U Jinja2\n\n.. _pip: https://pip.pypa.io/en/stable/quickstart/\n\n\nIn A Nutshell\n-------------\n\n.. code-block:: jinja\n\n {% extends \"base.html\" %}\n {% block title %}Members{% endblock %}\n {% block content %}\n \n {% endblock %}\n\n\nLinks\n-----\n\n- Website: https://palletsprojects.com/p/jinja/\n- Documentation: https://jinja.palletsprojects.com/\n- Releases: https://pypi.org/project/Jinja2/\n- Code: https://github.com/pallets/jinja\n- Issue tracker: https://github.com/pallets/jinja/issues\n- Test status: https://dev.azure.com/pallets/jinja/_build\n- Official chat: https://discord.gg/t6rrQZH\n\n\n" + } + }, + { + "download_info": { + "url": "https://files.pythonhosted.org/packages/b9/2e/64db92e53b86efccfaea71321f597fa2e1b2bd3853d8ce658568f7a13094/MarkupSafe-1.1.1.tar.gz", + "archive_info": { + "hash": "sha256=29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b", + "hashes": { + "sha256": "29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b" + } + } + }, + "is_direct": false, + "requested": true, + "metadata": { + "metadata_version": "2.1", + "name": "MarkupSafe", + "version": "1.1.1", + "platform": [ + "UNKNOWN" + ], + "summary": "Safely add untrusted strings to HTML/XML markup.", + "home_page": "https://palletsprojects.com/p/markupsafe/", + "author": "Armin Ronacher", + "author_email": "armin.ronacher@active-4.com", + "maintainer": "The Pallets Team", + "maintainer_email": "contact@palletsprojects.com", + "license": "BSD-3-Clause", + "classifier": [ + "Development Status :: 5 - Production/Stable", + "Environment :: Web Environment", + "Intended Audience :: Developers", + "License :: OSI Approved :: BSD License", + "Operating System :: OS Independent", + "Programming Language :: Python", + "Programming Language :: Python :: 2", + "Programming Language :: Python :: 2.7", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.4", + "Programming Language :: Python :: 3.5", + "Programming Language :: Python :: 3.6", + "Programming Language :: Python :: 3.7", + "Topic :: Internet :: WWW/HTTP :: Dynamic Content", + "Topic :: Software Development :: Libraries :: Python Modules", + "Topic :: Text Processing :: Markup :: HTML" + ], + "requires_python": ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*", + "project_url": [ + "Documentation, https://markupsafe.palletsprojects.com/", + "Code, https://github.com/pallets/markupsafe", + "Issue tracker, https://github.com/pallets/markupsafe/issues" + ], + "description": "MarkupSafe\n==========\n\nMarkupSafe implements a text object that escapes characters so it is\nsafe to use in HTML and XML. Characters that have special meanings are\nreplaced so that they display as the actual characters. This mitigates\ninjection attacks, meaning untrusted user input can safely be displayed\non a page.\n\n\nInstalling\n----------\n\nInstall and update using `pip`_:\n\n.. code-block:: text\n\n pip install -U MarkupSafe\n\n.. _pip: https://pip.pypa.io/en/stable/quickstart/\n\n\nExamples\n--------\n\n.. code-block:: pycon\n\n >>> from markupsafe import Markup, escape\n >>> # escape replaces special characters and wraps in Markup\n >>> escape('')\n Markup(u'<script>alert(document.cookie);</script>')\n >>> # wrap in Markup to mark text \"safe\" and prevent escaping\n >>> Markup('Hello')\n Markup('hello')\n >>> escape(Markup('Hello'))\n Markup('hello')\n >>> # Markup is a text subclass (str on Python 3, unicode on Python 2)\n >>> # methods and operators escape their arguments\n >>> template = Markup(\"Hello %s\")\n >>> template % '\"World\"'\n Markup('Hello "World"')\n\n\nDonate\n------\n\nThe Pallets organization develops and supports MarkupSafe and other\nlibraries that use it. In order to grow the community of contributors\nand users, and allow the maintainers to devote more time to the\nprojects, `please donate today`_.\n\n.. _please donate today: https://palletsprojects.com/donate\n\n\nLinks\n-----\n\n* Website: https://palletsprojects.com/p/markupsafe/\n* Documentation: https://markupsafe.palletsprojects.com/\n* License: `BSD-3-Clause `_\n* Releases: https://pypi.org/project/MarkupSafe/\n* Code: https://github.com/pallets/markupsafe\n* Issue tracker: https://github.com/pallets/markupsafe/issues\n* Test status:\n\n * Linux, Mac: https://travis-ci.org/pallets/markupsafe\n * Windows: https://ci.appveyor.com/project/pallets/markupsafe\n\n* Test coverage: https://codecov.io/gh/pallets/markupsafe\n\n\n" + } + }, + { + "download_info": { + "url": "https://files.pythonhosted.org/packages/d2/05/e6600db80270777c4a64238a98d442f0fd07cc8915be2a1c16da7f2b9e74/sympy-1.12-py3-none-any.whl", + "archive_info": { + "hash": "sha256=c3588cd4295d0c0f603d0f2ae780587e64e2efeedb3521e46b9bb1d08d184fa5", + "hashes": { + "sha256": "c3588cd4295d0c0f603d0f2ae780587e64e2efeedb3521e46b9bb1d08d184fa5" + } + } + }, + "is_direct": false, + "requested": true, + "metadata": { + "metadata_version": "2.1", + "name": "sympy", + "version": "1.12", + "summary": "Computer algebra system (CAS) in Python", + "description_content_type": "text/markdown", + "keywords": [ + "Math", + "CAS" + ], + "home_page": "https://sympy.org", + "author": "SymPy development team", + "author_email": "sympy@googlegroups.com", + "license": "BSD", + "classifier": [ + "License :: OSI Approved :: BSD License", + "Operating System :: OS Independent", + "Programming Language :: Python", + "Topic :: Scientific/Engineering", + "Topic :: Scientific/Engineering :: Mathematics", + "Topic :: Scientific/Engineering :: Physics", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3 :: Only", + "Programming Language :: Python :: Implementation :: CPython", + "Programming Language :: Python :: Implementation :: PyPy" + ], + "requires_dist": [ + "mpmath (>=0.19)" + ], + "requires_python": ">=3.8", + "project_url": [ + "Source, https://github.com/sympy/sympy" + ], + "description": "# SymPy\n\n[![pypi version](https://img.shields.io/pypi/v/sympy.svg)](https://pypi.python.org/pypi/sympy)\n[![Join the chat at https://gitter.im/sympy/sympy](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/sympy/sympy?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)\n[![Zenodo Badge](https://zenodo.org/badge/18918/sympy/sympy.svg)](https://zenodo.org/badge/latestdoi/18918/sympy/sympy)\n[![Downloads](https://pepy.tech/badge/sympy/month)](https://pepy.tech/project/sympy)\n[![GitHub Issues](https://img.shields.io/badge/issue_tracking-github-blue.svg)](https://github.com/sympy/sympy/issues)\n[![Git Tutorial](https://img.shields.io/badge/PR-Welcome-%23FF8300.svg?)](https://git-scm.com/book/en/v2/GitHub-Contributing-to-a-Project)\n[![Powered by NumFocus](https://img.shields.io/badge/powered%20by-NumFOCUS-orange.svg?style=flat&colorA=E1523D&colorB=007D8A)](https://numfocus.org)\n[![Commits since last release](https://img.shields.io/github/commits-since/sympy/sympy/latest.svg?longCache=true&style=flat-square&logo=git&logoColor=fff)](https://github.com/sympy/sympy/releases)\n\n[![SymPy Banner](https://github.com/sympy/sympy/raw/master/banner.svg)](https://sympy.org/)\n\n\nSee the [AUTHORS](AUTHORS) file for the list of authors.\n\nAnd many more people helped on the SymPy mailing list, reported bugs,\nhelped organize SymPy's participation in the Google Summer of Code, the\nGoogle Highly Open Participation Contest, Google Code-In, wrote and\nblogged about SymPy...\n\nLicense: New BSD License (see the [LICENSE](LICENSE) file for details) covers all\nfiles in the sympy repository unless stated otherwise.\n\nOur mailing list is at\n.\n\nWe have a community chat at [Gitter](https://gitter.im/sympy/sympy). Feel\nfree to ask us anything there. We have a very welcoming and helpful\ncommunity.\n\n## Download\n\nThe recommended installation method is through Anaconda,\n\n\nYou can also get the latest version of SymPy from\n\n\nTo get the git version do\n\n $ git clone https://github.com/sympy/sympy.git\n\nFor other options (tarballs, debs, etc.), see\n.\n\n## Documentation and Usage\n\nFor in-depth instructions on installation and building the\ndocumentation, see the [SymPy Documentation Style Guide](https://docs.sympy.org/dev/documentation-style-guide.html).\n\nEverything is at:\n\n\n\nYou can generate everything at the above site in your local copy of\nSymPy by:\n\n $ cd doc\n $ make html\n\nThen the docs will be in \\_build/html. If\nyou don't want to read that, here is a short usage:\n\nFrom this directory, start Python and:\n\n``` python\n>>> from sympy import Symbol, cos\n>>> x = Symbol('x')\n>>> e = 1/cos(x)\n>>> print(e.series(x, 0, 10))\n1 + x**2/2 + 5*x**4/24 + 61*x**6/720 + 277*x**8/8064 + O(x**10)\n```\n\nSymPy also comes with a console that is a simple wrapper around the\nclassic python console (or IPython when available) that loads the SymPy\nnamespace and executes some common commands for you.\n\nTo start it, issue:\n\n $ bin/isympy\n\nfrom this directory, if SymPy is not installed or simply:\n\n $ isympy\n\nif SymPy is installed.\n\n## Installation\n\nSymPy has a hard dependency on the [mpmath](http://mpmath.org/) library\n(version \\>= 0.19). You should install it first, please refer to the\nmpmath installation guide:\n\n\n\nTo install SymPy using PyPI, run the following command:\n\n $ pip install sympy\n\nTo install SymPy using Anaconda, run the following command:\n\n $ conda install -c anaconda sympy\n\nTo install SymPy from GitHub source, first clone SymPy using `git`:\n\n $ git clone https://github.com/sympy/sympy.git\n\nThen, in the `sympy` repository that you cloned, simply run:\n\n $ pip install .\n\nSee for more information.\n\n## Contributing\n\nWe welcome contributions from anyone, even if you are new to open\nsource. Please read our [Introduction to Contributing](https://github.com/sympy/sympy/wiki/Introduction-to-contributing)\npage and the [SymPy Documentation Style Guide](https://docs.sympy.org/dev/documentation-style-guide.html). If you\nare new and looking for some way to contribute, a good place to start is\nto look at the issues tagged [Easy to Fix](https://github.com/sympy/sympy/issues?q=is%3Aopen+is%3Aissue+label%3A%22Easy+to+Fix%22).\n\nPlease note that all participants in this project are expected to follow\nour Code of Conduct. By participating in this project you agree to abide\nby its terms. See [CODE\\_OF\\_CONDUCT.md](CODE_OF_CONDUCT.md).\n\n## Tests\n\nTo execute all tests, run:\n\n $./setup.py test\n\nin the current directory.\n\nFor the more fine-grained running of tests or doctests, use `bin/test`\nor respectively `bin/doctest`. The master branch is automatically tested\nby GitHub Actions.\n\nTo test pull requests, use\n[sympy-bot](https://github.com/sympy/sympy-bot).\n\n## Regenerate Experimental LaTeX Parser/Lexer\n\nThe parser and lexer were generated with the [ANTLR4](http://antlr4.org)\ntoolchain in `sympy/parsing/latex/_antlr` and checked into the repo.\nPresently, most users should not need to regenerate these files, but\nif you plan to work on this feature, you will need the `antlr4`\ncommand-line tool (and you must ensure that it is in your `PATH`).\nOne way to get it is:\n\n $ conda install -c conda-forge antlr=4.11.1\n\nAlternatively, follow the instructions on the ANTLR website and download\nthe `antlr-4.11.1-complete.jar`. Then export the `CLASSPATH` as instructed\nand instead of creating `antlr4` as an alias, make it an executable file\nwith the following contents:\n``` bash\n#!/bin/bash\njava -jar /usr/local/lib/antlr-4.11.1-complete.jar \"$@\"\n```\n\nAfter making changes to `sympy/parsing/latex/LaTeX.g4`, run:\n\n $ ./setup.py antlr\n\n## Clean\n\nTo clean everything (thus getting the same tree as in the repository):\n\n $ git clean -Xdf\n\nwhich will clear everything ignored by `.gitignore`, and:\n\n $ git clean -df\n\nto clear all untracked files. You can revert the most recent changes in\ngit with:\n\n $ git reset --hard\n\nWARNING: The above commands will all clear changes you may have made,\nand you will lose them forever. Be sure to check things with `git\nstatus`, `git diff`, `git clean -Xn`, and `git clean -n` before doing any\nof those.\n\n## Bugs\n\nOur issue tracker is at . Please\nreport any bugs that you find. Or, even better, fork the repository on\nGitHub and create a pull request. We welcome all changes, big or small,\nand we will help you make the pull request if you are new to git (just\nask on our mailing list or Gitter Channel). If you further have any queries, you can find answers\non Stack Overflow using the [sympy](https://stackoverflow.com/questions/tagged/sympy) tag.\n\n## Brief History\n\nSymPy was started by Ondřej Čertík in 2005, he wrote some code during\nthe summer, then he wrote some more code during summer 2006. In February\n2007, Fabian Pedregosa joined the project and helped fix many things,\ncontributed documentation, and made it alive again. 5 students (Mateusz\nPaprocki, Brian Jorgensen, Jason Gedge, Robert Schwarz, and Chris Wu)\nimproved SymPy incredibly during summer 2007 as part of the Google\nSummer of Code. Pearu Peterson joined the development during the summer\n2007 and he has made SymPy much more competitive by rewriting the core\nfrom scratch, which has made it from 10x to 100x faster. Jurjen N.E. Bos\nhas contributed pretty-printing and other patches. Fredrik Johansson has\nwritten mpmath and contributed a lot of patches.\n\nSymPy has participated in every Google Summer of Code since 2007. You\ncan see for\nfull details. Each year has improved SymPy by bounds. Most of SymPy's\ndevelopment has come from Google Summer of Code students.\n\nIn 2011, Ondřej Čertík stepped down as lead developer, with Aaron\nMeurer, who also started as a Google Summer of Code student, taking his\nplace. Ondřej Čertík is still active in the community but is too busy\nwith work and family to play a lead development role.\n\nSince then, a lot more people have joined the development and some\npeople have also left. You can see the full list in doc/src/aboutus.rst,\nor online at:\n\n\n\nThe git history goes back to 2007 when development moved from svn to hg.\nTo see the history before that point, look at\n.\n\nYou can use git to see the biggest developers. The command:\n\n $ git shortlog -ns\n\nwill show each developer, sorted by commits to the project. The command:\n\n $ git shortlog -ns --since=\"1 year\"\n\nwill show the top developers from the last year.\n\n## Citation\n\nTo cite SymPy in publications use\n\n> Meurer A, Smith CP, Paprocki M, Čertík O, Kirpichev SB, Rocklin M,\n> Kumar A, Ivanov S, Moore JK, Singh S, Rathnayake T, Vig S, Granger BE,\n> Muller RP, Bonazzi F, Gupta H, Vats S, Johansson F, Pedregosa F, Curry\n> MJ, Terrel AR, Roučka Š, Saboo A, Fernando I, Kulal S, Cimrman R,\n> Scopatz A. (2017) SymPy: symbolic computing in Python. *PeerJ Computer\n> Science* 3:e103 \n\nA BibTeX entry for LaTeX users is\n\n``` bibtex\n@article{10.7717/peerj-cs.103,\n title = {SymPy: symbolic computing in Python},\n author = {Meurer, Aaron and Smith, Christopher P. and Paprocki, Mateusz and \\v{C}ert\\'{i}k, Ond\\v{r}ej and Kirpichev, Sergey B. and Rocklin, Matthew and Kumar, Amit and Ivanov, Sergiu and Moore, Jason K. and Singh, Sartaj and Rathnayake, Thilina and Vig, Sean and Granger, Brian E. and Muller, Richard P. and Bonazzi, Francesco and Gupta, Harsh and Vats, Shivam and Johansson, Fredrik and Pedregosa, Fabian and Curry, Matthew J. and Terrel, Andy R. and Rou\\v{c}ka, \\v{S}t\\v{e}p\\'{a}n and Saboo, Ashutosh and Fernando, Isuru and Kulal, Sumith and Cimrman, Robert and Scopatz, Anthony},\n year = 2017,\n month = Jan,\n keywords = {Python, Computer algebra system, Symbolics},\n abstract = {\n SymPy is an open-source computer algebra system written in pure Python. It is built with a focus on extensibility and ease of use, through both interactive and programmatic applications. These characteristics have led SymPy to become a popular symbolic library for the scientific Python ecosystem. This paper presents the architecture of SymPy, a description of its features, and a discussion of select submodules. The supplementary material provides additional examples and further outlines details of the architecture and features of SymPy.\n },\n volume = 3,\n pages = {e103},\n journal = {PeerJ Computer Science},\n issn = {2376-5992},\n url = {https://doi.org/10.7717/peerj-cs.103},\n doi = {10.7717/peerj-cs.103}\n}\n```\n\nSymPy is BSD licensed, so you are free to use it whatever you like, be\nit academic, commercial, creating forks or derivatives, as long as you\ncopy the BSD statement if you redistribute it (see the LICENSE file for\ndetails). That said, although not required by the SymPy license, if it\nis convenient for you, please cite SymPy when using it in your work and\nalso consider contributing all your changes back, so that we can\nincorporate it and all of us will benefit in the end.\n" + } + }, + { + "download_info": { + "url": "https://files.pythonhosted.org/packages/43/e3/7d92a15f894aa0c9c4b49b8ee9ac9850d6e63b03c9c32c0367a13ae62209/mpmath-1.3.0-py3-none-any.whl", + "archive_info": { + "hash": "sha256=a0b2b9fe80bbcd81a6647ff13108738cfb482d481d826cc0e02f5b35e5c88d2c", + "hashes": { + "sha256": "a0b2b9fe80bbcd81a6647ff13108738cfb482d481d826cc0e02f5b35e5c88d2c" + } + } + }, + "is_direct": false, + "requested": true, + "metadata": { + "metadata_version": "2.1", + "name": "mpmath", + "version": "1.3.0", + "summary": "Python library for arbitrary-precision floating-point arithmetic", + "home_page": "http://mpmath.org/", + "author": "Fredrik Johansson", + "author_email": "fredrik.johansson@gmail.com", + "license": "BSD", + "classifier": [ + "License :: OSI Approved :: BSD License", + "Topic :: Scientific/Engineering :: Mathematics", + "Topic :: Software Development :: Libraries :: Python Modules", + "Programming Language :: Python", + "Programming Language :: Python :: 2", + "Programming Language :: Python :: 2.7", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.5", + "Programming Language :: Python :: 3.6", + "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: Implementation :: CPython", + "Programming Language :: Python :: Implementation :: PyPy" + ], + "requires_dist": [ + "pytest (>=4.6) ; extra == 'develop'", + "pycodestyle ; extra == 'develop'", + "pytest-cov ; extra == 'develop'", + "codecov ; extra == 'develop'", + "wheel ; extra == 'develop'", + "sphinx ; extra == 'docs'", + "gmpy2 (>=2.1.0a4) ; (platform_python_implementation != \"PyPy\") and extra == 'gmpy'", + "pytest (>=4.6) ; extra == 'tests'" + ], + "project_url": [ + "Source, https://github.com/fredrik-johansson/mpmath", + "Tracker, https://github.com/fredrik-johansson/mpmath/issues", + "Documentation, http://mpmath.org/doc/current/" + ], + "provides_extra": [ + "develop", + "docs", + "gmpy", + "tests" + ], + "description": "mpmath\n======\n\n|pypi version| |Build status| |Code coverage status| |Zenodo Badge|\n\n.. |pypi version| image:: https://img.shields.io/pypi/v/mpmath.svg\n :target: https://pypi.python.org/pypi/mpmath\n.. |Build status| image:: https://github.com/fredrik-johansson/mpmath/workflows/test/badge.svg\n :target: https://github.com/fredrik-johansson/mpmath/actions?workflow=test\n.. |Code coverage status| image:: https://codecov.io/gh/fredrik-johansson/mpmath/branch/master/graph/badge.svg\n :target: https://codecov.io/gh/fredrik-johansson/mpmath\n.. |Zenodo Badge| image:: https://zenodo.org/badge/2934512.svg\n :target: https://zenodo.org/badge/latestdoi/2934512\n\nA Python library for arbitrary-precision floating-point arithmetic.\n\nWebsite: http://mpmath.org/\nMain author: Fredrik Johansson \n\nMpmath is free software released under the New BSD License (see the\nLICENSE file for details)\n\n0. History and credits\n----------------------\n\nThe following people (among others) have contributed major patches\nor new features to mpmath:\n\n* Pearu Peterson \n* Mario Pernici \n* Ondrej Certik \n* Vinzent Steinberg \n* Nimish Telang \n* Mike Taschuk \n* Case Van Horsen \n* Jorn Baayen \n* Chris Smith \n* Juan Arias de Reyna \n* Ioannis Tziakos \n* Aaron Meurer \n* Stefan Krastanov \n* Ken Allen \n* Timo Hartmann \n* Sergey B Kirpichev \n* Kris Kuhlman \n* Paul Masson \n* Michael Kagalenko \n* Jonathan Warner \n* Max Gaukler \n* Guillermo Navas-Palencia \n* Nike Dattani \n\nNumerous other people have contributed by reporting bugs,\nrequesting new features, or suggesting improvements to the\ndocumentation.\n\nFor a detailed changelog, including individual contributions,\nsee the CHANGES file.\n\nFredrik's work on mpmath during summer 2008 was sponsored by Google\nas part of the Google Summer of Code program.\n\nFredrik's work on mpmath during summer 2009 was sponsored by the\nAmerican Institute of Mathematics under the support of the National Science\nFoundation Grant No. 0757627 (FRG: L-functions and Modular Forms).\n\nAny opinions, findings, and conclusions or recommendations expressed in this\nmaterial are those of the author(s) and do not necessarily reflect the\nviews of the sponsors.\n\nCredit also goes to:\n\n* The authors of the GMP library and the Python wrapper\n gmpy, enabling mpmath to become much faster at\n high precision\n* The authors of MPFR, pari/gp, MPFUN, and other arbitrary-\n precision libraries, whose documentation has been helpful\n for implementing many of the algorithms in mpmath\n* Wikipedia contributors; Abramowitz & Stegun; Gradshteyn & Ryzhik;\n Wolfram Research for MathWorld and the Wolfram Functions site.\n These are the main references used for special functions\n implementations.\n* George Brandl for developing the Sphinx documentation tool\n used to build mpmath's documentation\n\nRelease history:\n\n* Version 1.3.0 released on March 7, 2023\n* Version 1.2.0 released on February 1, 2021\n* Version 1.1.0 released on December 11, 2018\n* Version 1.0.0 released on September 27, 2017\n* Version 0.19 released on June 10, 2014\n* Version 0.18 released on December 31, 2013\n* Version 0.17 released on February 1, 2011\n* Version 0.16 released on September 24, 2010\n* Version 0.15 released on June 6, 2010\n* Version 0.14 released on February 5, 2010\n* Version 0.13 released on August 13, 2009\n* Version 0.12 released on June 9, 2009\n* Version 0.11 released on January 26, 2009\n* Version 0.10 released on October 15, 2008\n* Version 0.9 released on August 23, 2008\n* Version 0.8 released on April 20, 2008\n* Version 0.7 released on March 12, 2008\n* Version 0.6 released on January 13, 2008\n* Version 0.5 released on November 24, 2007\n* Version 0.4 released on November 3, 2007\n* Version 0.3 released on October 5, 2007\n* Version 0.2 released on October 2, 2007\n* Version 0.1 released on September 27, 2007\n\n1. Download & installation\n--------------------------\n\nMpmath requires Python 2.7 or 3.5 (or later versions). It has been tested\nwith CPython 2.7, 3.5 through 3.7 and for PyPy.\n\nThe latest release of mpmath can be downloaded from the mpmath\nwebsite and from https://github.com/fredrik-johansson/mpmath/releases\n\nIt should also be available in the Python Package Index at\nhttps://pypi.python.org/pypi/mpmath\n\nTo install latest release of Mpmath with pip, simply run\n\n``pip install mpmath``\n\nOr unpack the mpmath archive and run\n\n``python setup.py install``\n\nMpmath can also be installed using\n\n``python -m easy_install mpmath``\n\nThe latest development code is available from\nhttps://github.com/fredrik-johansson/mpmath\n\nSee the main documentation for more detailed instructions.\n\n2. Running tests\n----------------\n\nThe unit tests in mpmath/tests/ can be run via the script\nruntests.py, but it is recommended to run them with py.test\n(https://pytest.org/), especially\nto generate more useful reports in case there are failures.\n\nYou may also want to check out the demo scripts in the demo\ndirectory.\n\nThe master branch is automatically tested by Travis CI.\n\n3. Documentation\n----------------\n\nDocumentation in reStructuredText format is available in the\ndoc directory included with the source package. These files\nare human-readable, but can be compiled to prettier HTML using\nthe build.py script (requires Sphinx, http://sphinx.pocoo.org/).\n\nSee setup.txt in the documentation for more information.\n\nThe most recent documentation is also available in HTML format:\n\nhttp://mpmath.org/doc/current/\n\n4. Known problems\n-----------------\n\nMpmath is a work in progress. Major issues include:\n\n* Some functions may return incorrect values when given extremely\n large arguments or arguments very close to singularities.\n\n* Directed rounding works for arithmetic operations. It is implemented\n heuristically for other operations, and their results may be off by one\n or two units in the last place (even if otherwise accurate).\n\n* Some IEEE 754 features are not available. Inifinities and NaN are\n partially supported; denormal rounding is currently not available\n at all.\n\n* The interface for switching precision and rounding is not finalized.\n The current method is not threadsafe.\n\n5. Help and bug reports\n-----------------------\n\nGeneral questions and comments can be sent to the mpmath mailinglist,\nmpmath@googlegroups.com\n\nYou can also report bugs and send patches to the mpmath issue tracker,\nhttps://github.com/fredrik-johansson/mpmath/issues\n" + } + }, + { + "download_info": { + "url": "https://files.pythonhosted.org/packages/6c/10/a7d0fa5baea8fe7b50f448ab742f26f52b80bfca85ac2be9d35cdd9a3246/pyparsing-3.0.9-py3-none-any.whl", + "archive_info": { + "hash": "sha256=5026bae9a10eeaefb61dab2f09052b9f4307d44aee4eda64b309723d8d206bbc", + "hashes": { + "sha256": "5026bae9a10eeaefb61dab2f09052b9f4307d44aee4eda64b309723d8d206bbc" + } + } + }, + "is_direct": false, + "requested": true, + "metadata": { + "metadata_version": "2.1", + "name": "pyparsing", + "version": "3.0.9", + "summary": "pyparsing module - Classes and methods to define and execute parsing grammars", + "description_content_type": "text/x-rst", + "author_email": "Paul McGuire ", + "classifier": [ + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Developers", + "Intended Audience :: Information Technology", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.6", + "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3 :: Only", + "Programming Language :: Python :: Implementation :: CPython", + "Programming Language :: Python :: Implementation :: PyPy", + "Typing :: Typed" + ], + "requires_dist": [ + "railroad-diagrams ; extra == \"diagrams\"", + "jinja2 ; extra == \"diagrams\"" + ], + "requires_python": ">=3.6.8", + "project_url": [ + "Homepage, https://github.com/pyparsing/pyparsing/" + ], + "provides_extra": [ + "diagrams" + ], + "description": "PyParsing -- A Python Parsing Module\n====================================\n\n|Build Status| |Coverage|\n\nIntroduction\n============\n\nThe pyparsing module is an alternative approach to creating and\nexecuting simple grammars, vs. the traditional lex/yacc approach, or the\nuse of regular expressions. The pyparsing module provides a library of\nclasses that client code uses to construct the grammar directly in\nPython code.\n\n*[Since first writing this description of pyparsing in late 2003, this\ntechnique for developing parsers has become more widespread, under the\nname Parsing Expression Grammars - PEGs. See more information on PEGs*\n`here `__\n*.]*\n\nHere is a program to parse ``\"Hello, World!\"`` (or any greeting of the form\n``\"salutation, addressee!\"``):\n\n.. code:: python\n\n from pyparsing import Word, alphas\n greet = Word(alphas) + \",\" + Word(alphas) + \"!\"\n hello = \"Hello, World!\"\n print(hello, \"->\", greet.parseString(hello))\n\nThe program outputs the following::\n\n Hello, World! -> ['Hello', ',', 'World', '!']\n\nThe Python representation of the grammar is quite readable, owing to the\nself-explanatory class names, and the use of '+', '|' and '^' operator\ndefinitions.\n\nThe parsed results returned from ``parseString()`` is a collection of type\n``ParseResults``, which can be accessed as a\nnested list, a dictionary, or an object with named attributes.\n\nThe pyparsing module handles some of the problems that are typically\nvexing when writing text parsers:\n\n- extra or missing whitespace (the above program will also handle ``\"Hello,World!\"``, ``\"Hello , World !\"``, etc.)\n- quoted strings\n- embedded comments\n\nThe examples directory includes a simple SQL parser, simple CORBA IDL\nparser, a config file parser, a chemical formula parser, and a four-\nfunction algebraic notation parser, among many others.\n\nDocumentation\n=============\n\nThere are many examples in the online docstrings of the classes\nand methods in pyparsing. You can find them compiled into `online docs `__. Additional\ndocumentation resources and project info are listed in the online\n`GitHub wiki `__. An\nentire directory of examples can be found `here `__.\n\nLicense\n=======\n\nMIT License. See header of the `pyparsing.py `__ file.\n\nHistory\n=======\n\nSee `CHANGES `__ file.\n\n.. |Build Status| image:: https://github.com/pyparsing/pyparsing/actions/workflows/ci.yml/badge.svg\n :target: https://github.com/pyparsing/pyparsing/actions/workflows/ci.yml\n.. |Coverage| image:: https://codecov.io/gh/pyparsing/pyparsing/branch/master/graph/badge.svg\n :target: https://codecov.io/gh/pyparsing/pyparsing\n\n" + } + }, + { + "download_info": { + "url": "https://files.pythonhosted.org/packages/ab/c3/57f0601a2d4fe15de7a553c00adbc901425661bf048f2a22dfc500caf121/packaging-23.1-py3-none-any.whl", + "archive_info": { + "hash": "sha256=994793af429502c4ea2ebf6bf664629d07c1a9fe974af92966e4b8d2df7edc61", + "hashes": { + "sha256": "994793af429502c4ea2ebf6bf664629d07c1a9fe974af92966e4b8d2df7edc61" + } + } + }, + "is_direct": false, + "requested": true, + "metadata": { + "metadata_version": "2.1", + "name": "packaging", + "version": "23.1", + "summary": "Core utilities for Python packages", + "description_content_type": "text/x-rst", + "author_email": "Donald Stufft ", + "classifier": [ + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Developers", + "License :: OSI Approved :: Apache Software License", + "License :: OSI Approved :: BSD License", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3 :: Only", + "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: Implementation :: CPython", + "Programming Language :: Python :: Implementation :: PyPy", + "Typing :: Typed" + ], + "requires_python": ">=3.7", + "project_url": [ + "Documentation, https://packaging.pypa.io/", + "Source, https://github.com/pypa/packaging" + ], + "description": "packaging\n=========\n\n.. start-intro\n\nReusable core utilities for various Python Packaging\n`interoperability specifications `_.\n\nThis library provides utilities that implement the interoperability\nspecifications which have clearly one correct behaviour (eg: :pep:`440`)\nor benefit greatly from having a single shared implementation (eg: :pep:`425`).\n\n.. end-intro\n\nThe ``packaging`` project includes the following: version handling, specifiers,\nmarkers, requirements, tags, utilities.\n\nDocumentation\n-------------\n\nThe `documentation`_ provides information and the API for the following:\n\n- Version Handling\n- Specifiers\n- Markers\n- Requirements\n- Tags\n- Utilities\n\nInstallation\n------------\n\nUse ``pip`` to install these utilities::\n\n pip install packaging\n\nDiscussion\n----------\n\nIf you run into bugs, you can file them in our `issue tracker`_.\n\nYou can also join ``#pypa`` on Freenode to ask questions or get involved.\n\n\n.. _`documentation`: https://packaging.pypa.io/\n.. _`issue tracker`: https://github.com/pypa/packaging/issues\n\n\nCode of Conduct\n---------------\n\nEveryone interacting in the packaging project's codebases, issue trackers, chat\nrooms, and mailing lists is expected to follow the `PSF Code of Conduct`_.\n\n.. _PSF Code of Conduct: https://github.com/pypa/.github/blob/main/CODE_OF_CONDUCT.md\n\nContributing\n------------\n\nThe ``CONTRIBUTING.rst`` file outlines how to contribute to this project as\nwell as how to report a potential security issue. The documentation for this\nproject also covers information about `project development`_ and `security`_.\n\n.. _`project development`: https://packaging.pypa.io/en/latest/development/\n.. _`security`: https://packaging.pypa.io/en/latest/security/\n\nProject History\n---------------\n\nPlease review the ``CHANGELOG.rst`` file or the `Changelog documentation`_ for\nrecent changes and project history.\n\n.. _`Changelog documentation`: https://packaging.pypa.io/en/latest/changelog/\n\n" + } + }, + { + "download_info": { + "url": "https://files.pythonhosted.org/packages/36/7a/87837f39d0296e723bb9b62bbb257d0355c7f6128853c78955f57342a56d/python_dateutil-2.8.2-py2.py3-none-any.whl", + "archive_info": { + "hash": "sha256=961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9", + "hashes": { + "sha256": "961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9" + } + } + }, + "is_direct": false, + "requested": true, + "metadata": { + "metadata_version": "2.1", + "name": "python-dateutil", + "version": "2.8.2", + "platform": [ + "UNKNOWN" + ], + "summary": "Extensions to the standard Python datetime module", + "description_content_type": "text/x-rst", + "home_page": "https://github.com/dateutil/dateutil", + "author": "Gustavo Niemeyer", + "author_email": "gustavo@niemeyer.net", + "maintainer": "Paul Ganssle", + "maintainer_email": "dateutil@python.org", + "license": "Dual License", + "classifier": [ + "Development Status :: 5 - Production/Stable", + "Intended Audience :: Developers", + "License :: OSI Approved :: BSD License", + "License :: OSI Approved :: Apache Software License", + "Programming Language :: Python", + "Programming Language :: Python :: 2", + "Programming Language :: Python :: 2.7", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.3", + "Programming Language :: Python :: 3.4", + "Programming Language :: Python :: 3.5", + "Programming Language :: Python :: 3.6", + "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Topic :: Software Development :: Libraries" + ], + "requires_dist": [ + "six (>=1.5)" + ], + "requires_python": "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7", + "project_url": [ + "Documentation, https://dateutil.readthedocs.io/en/stable/", + "Source, https://github.com/dateutil/dateutil" + ], + "description": "dateutil - powerful extensions to datetime\n==========================================\n\n|pypi| |support| |licence|\n\n|gitter| |readthedocs|\n\n|travis| |appveyor| |pipelines| |coverage|\n\n.. |pypi| image:: https://img.shields.io/pypi/v/python-dateutil.svg?style=flat-square\n :target: https://pypi.org/project/python-dateutil/\n :alt: pypi version\n\n.. |support| image:: https://img.shields.io/pypi/pyversions/python-dateutil.svg?style=flat-square\n :target: https://pypi.org/project/python-dateutil/\n :alt: supported Python version\n\n.. |travis| image:: https://img.shields.io/travis/dateutil/dateutil/master.svg?style=flat-square&label=Travis%20Build\n :target: https://travis-ci.org/dateutil/dateutil\n :alt: travis build status\n\n.. |appveyor| image:: https://img.shields.io/appveyor/ci/dateutil/dateutil/master.svg?style=flat-square&logo=appveyor\n :target: https://ci.appveyor.com/project/dateutil/dateutil\n :alt: appveyor build status\n\n.. |pipelines| image:: https://dev.azure.com/pythondateutilazure/dateutil/_apis/build/status/dateutil.dateutil?branchName=master\n :target: https://dev.azure.com/pythondateutilazure/dateutil/_build/latest?definitionId=1&branchName=master\n :alt: azure pipelines build status\n\n.. |coverage| image:: https://codecov.io/gh/dateutil/dateutil/branch/master/graphs/badge.svg?branch=master\n :target: https://codecov.io/gh/dateutil/dateutil?branch=master\n :alt: Code coverage\n\n.. |gitter| image:: https://badges.gitter.im/dateutil/dateutil.svg\n :alt: Join the chat at https://gitter.im/dateutil/dateutil\n :target: https://gitter.im/dateutil/dateutil\n\n.. |licence| image:: https://img.shields.io/pypi/l/python-dateutil.svg?style=flat-square\n :target: https://pypi.org/project/python-dateutil/\n :alt: licence\n\n.. |readthedocs| image:: https://img.shields.io/readthedocs/dateutil/latest.svg?style=flat-square&label=Read%20the%20Docs\n :alt: Read the documentation at https://dateutil.readthedocs.io/en/latest/\n :target: https://dateutil.readthedocs.io/en/latest/\n\nThe `dateutil` module provides powerful extensions to\nthe standard `datetime` module, available in Python.\n\nInstallation\n============\n`dateutil` can be installed from PyPI using `pip` (note that the package name is\ndifferent from the importable name)::\n\n pip install python-dateutil\n\nDownload\n========\ndateutil is available on PyPI\nhttps://pypi.org/project/python-dateutil/\n\nThe documentation is hosted at:\nhttps://dateutil.readthedocs.io/en/stable/\n\nCode\n====\nThe code and issue tracker are hosted on GitHub:\nhttps://github.com/dateutil/dateutil/\n\nFeatures\n========\n\n* Computing of relative deltas (next month, next year,\n next Monday, last week of month, etc);\n* Computing of relative deltas between two given\n date and/or datetime objects;\n* Computing of dates based on very flexible recurrence rules,\n using a superset of the `iCalendar `_\n specification. Parsing of RFC strings is supported as well.\n* Generic parsing of dates in almost any string format;\n* Timezone (tzinfo) implementations for tzfile(5) format\n files (/etc/localtime, /usr/share/zoneinfo, etc), TZ\n environment string (in all known formats), iCalendar\n format files, given ranges (with help from relative deltas),\n local machine timezone, fixed offset timezone, UTC timezone,\n and Windows registry-based time zones.\n* Internal up-to-date world timezone information based on\n Olson's database.\n* Computing of Easter Sunday dates for any given year,\n using Western, Orthodox or Julian algorithms;\n* A comprehensive test suite.\n\nQuick example\n=============\nHere's a snapshot, just to give an idea about the power of the\npackage. For more examples, look at the documentation.\n\nSuppose you want to know how much time is left, in\nyears/months/days/etc, before the next easter happening on a\nyear with a Friday 13th in August, and you want to get today's\ndate out of the \"date\" unix system command. Here is the code:\n\n.. code-block:: python3\n\n >>> from dateutil.relativedelta import *\n >>> from dateutil.easter import *\n >>> from dateutil.rrule import *\n >>> from dateutil.parser import *\n >>> from datetime import *\n >>> now = parse(\"Sat Oct 11 17:13:46 UTC 2003\")\n >>> today = now.date()\n >>> year = rrule(YEARLY,dtstart=now,bymonth=8,bymonthday=13,byweekday=FR)[0].year\n >>> rdelta = relativedelta(easter(year), today)\n >>> print(\"Today is: %s\" % today)\n Today is: 2003-10-11\n >>> print(\"Year with next Aug 13th on a Friday is: %s\" % year)\n Year with next Aug 13th on a Friday is: 2004\n >>> print(\"How far is the Easter of that year: %s\" % rdelta)\n How far is the Easter of that year: relativedelta(months=+6)\n >>> print(\"And the Easter of that year is: %s\" % (today+rdelta))\n And the Easter of that year is: 2004-04-11\n\nBeing exactly 6 months ahead was **really** a coincidence :)\n\nContributing\n============\n\nWe welcome many types of contributions - bug reports, pull requests (code, infrastructure or documentation fixes). For more information about how to contribute to the project, see the ``CONTRIBUTING.md`` file in the repository.\n\n\nAuthor\n======\nThe dateutil module was written by Gustavo Niemeyer \nin 2003.\n\nIt is maintained by:\n\n* Gustavo Niemeyer 2003-2011\n* Tomi Pieviläinen 2012-2014\n* Yaron de Leeuw 2014-2016\n* Paul Ganssle 2015-\n\nStarting with version 2.4.1 and running until 2.8.2, all source and binary\ndistributions will be signed by a PGP key that has, at the very least, been\nsigned by the key which made the previous release. A table of release signing\nkeys can be found below:\n\n=========== ============================\nReleases Signing key fingerprint\n=========== ============================\n2.4.1-2.8.2 `6B49 ACBA DCF6 BD1C A206 67AB CD54 FCE3 D964 BEFB`_ \n=========== ============================\n\nNew releases *may* have signed tags, but binary and source distributions\nuploaded to PyPI will no longer have GPG signatures attached.\n\nContact\n=======\nOur mailing list is available at `dateutil@python.org `_. As it is hosted by the PSF, it is subject to the `PSF code of\nconduct `_.\n\nLicense\n=======\n\nAll contributions after December 1, 2017 released under dual license - either `Apache 2.0 License `_ or the `BSD 3-Clause License `_. Contributions before December 1, 2017 - except those those explicitly relicensed - are released only under the BSD 3-Clause License.\n\n\n.. _6B49 ACBA DCF6 BD1C A206 67AB CD54 FCE3 D964 BEFB:\n https://pgp.mit.edu/pks/lookup?op=vindex&search=0xCD54FCE3D964BEFB\n\n\n" + } + }, + { + "download_info": { + "url": "https://files.pythonhosted.org/packages/7f/99/ad6bd37e748257dd70d6f85d916cafe79c0b0f5e2e95b11f7fbc82bf3110/pytz-2023.3-py2.py3-none-any.whl", + "archive_info": { + "hash": "sha256=a151b3abb88eda1d4e34a9814df37de2a80e301e68ba0fd856fb9b46bfbbbffb", + "hashes": { + "sha256": "a151b3abb88eda1d4e34a9814df37de2a80e301e68ba0fd856fb9b46bfbbbffb" + } + } + }, + "is_direct": false, + "requested": true, + "metadata": { + "metadata_version": "2.1", + "name": "pytz", + "version": "2023.3", + "platform": [ + "Independent" + ], + "summary": "World timezone definitions, modern and historical", + "keywords": [ + "timezone", + "tzinfo", + "datetime", + "olson", + "time" + ], + "home_page": "http://pythonhosted.org/pytz", + "download_url": "https://pypi.org/project/pytz/", + "author": "Stuart Bishop", + "author_email": "stuart@stuartbishop.net", + "maintainer": "Stuart Bishop", + "maintainer_email": "stuart@stuartbishop.net", + "license": "MIT", + "classifier": [ + "Development Status :: 6 - Mature", + "Intended Audience :: Developers", + "License :: OSI Approved :: MIT License", + "Natural Language :: English", + "Operating System :: OS Independent", + "Programming Language :: Python", + "Programming Language :: Python :: 2", + "Programming Language :: Python :: 2.4", + "Programming Language :: Python :: 2.5", + "Programming Language :: Python :: 2.6", + "Programming Language :: Python :: 2.7", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3.1", + "Programming Language :: Python :: 3.2", + "Programming Language :: Python :: 3.3", + "Programming Language :: Python :: 3.4", + "Programming Language :: Python :: 3.5", + "Programming Language :: Python :: 3.6", + "Programming Language :: Python :: 3.7", + "Programming Language :: Python :: 3.8", + "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Topic :: Software Development :: Libraries :: Python Modules" + ], + "description": "pytz - World Timezone Definitions for Python\n============================================\n\n:Author: Stuart Bishop \n\nIntroduction\n~~~~~~~~~~~~\n\npytz brings the Olson tz database into Python. This library allows\naccurate and cross platform timezone calculations using Python 2.4\nor higher. It also solves the issue of ambiguous times at the end\nof daylight saving time, which you can read more about in the Python\nLibrary Reference (``datetime.tzinfo``).\n\nAlmost all of the Olson timezones are supported.\n\n.. note::\n\n Projects using Python 3.9 or later should be using the support\n now included as part of the standard library, and third party\n packages work with it such as `tzdata `_.\n pytz offers no advantages beyond backwards compatibility with\n code written for earlier versions of Python.\n\n.. note::\n\n This library differs from the documented Python API for\n tzinfo implementations; if you want to create local wallclock\n times you need to use the ``localize()`` method documented in this\n document. In addition, if you perform date arithmetic on local\n times that cross DST boundaries, the result may be in an incorrect\n timezone (ie. subtract 1 minute from 2002-10-27 1:00 EST and you get\n 2002-10-27 0:59 EST instead of the correct 2002-10-27 1:59 EDT). A\n ``normalize()`` method is provided to correct this. Unfortunately these\n issues cannot be resolved without modifying the Python datetime\n implementation (see PEP-431).\n\n\nInstallation\n~~~~~~~~~~~~\n\nThis package can either be installed using ``pip`` or from a tarball using the\nstandard Python distutils.\n\nIf you are installing using ``pip``, you don't need to download anything as the\nlatest version will be downloaded for you from PyPI::\n\n pip install pytz\n\nIf you are installing from a tarball, run the following command as an\nadministrative user::\n\n python setup.py install\n\n\npytz for Enterprise\n~~~~~~~~~~~~~~~~~~~\n\nAvailable as part of the Tidelift Subscription.\n\nThe maintainers of pytz and thousands of other packages are working with Tidelift to deliver commercial support and maintenance for the open source dependencies you use to build your applications. Save time, reduce risk, and improve code health, while paying the maintainers of the exact dependencies you use. `Learn more. `_.\n\n\nExample & Usage\n~~~~~~~~~~~~~~~\n\nLocalized times and date arithmetic\n-----------------------------------\n\n>>> from datetime import datetime, timedelta\n>>> from pytz import timezone\n>>> import pytz\n>>> utc = pytz.utc\n>>> utc.zone\n'UTC'\n>>> eastern = timezone('US/Eastern')\n>>> eastern.zone\n'US/Eastern'\n>>> amsterdam = timezone('Europe/Amsterdam')\n>>> fmt = '%Y-%m-%d %H:%M:%S %Z%z'\n\nThis library only supports two ways of building a localized time. The\nfirst is to use the ``localize()`` method provided by the pytz library.\nThis is used to localize a naive datetime (datetime with no timezone\ninformation):\n\n>>> loc_dt = eastern.localize(datetime(2002, 10, 27, 6, 0, 0))\n>>> print(loc_dt.strftime(fmt))\n2002-10-27 06:00:00 EST-0500\n\nThe second way of building a localized time is by converting an existing\nlocalized time using the standard ``astimezone()`` method:\n\n>>> ams_dt = loc_dt.astimezone(amsterdam)\n>>> ams_dt.strftime(fmt)\n'2002-10-27 12:00:00 CET+0100'\n\nUnfortunately using the tzinfo argument of the standard datetime\nconstructors ''does not work'' with pytz for many timezones.\n\n>>> datetime(2002, 10, 27, 12, 0, 0, tzinfo=amsterdam).strftime(fmt) # /!\\ Does not work this way!\n'2002-10-27 12:00:00 LMT+0018'\n\nIt is safe for timezones without daylight saving transitions though, such\nas UTC:\n\n>>> datetime(2002, 10, 27, 12, 0, 0, tzinfo=pytz.utc).strftime(fmt) # /!\\ Not recommended except for UTC\n'2002-10-27 12:00:00 UTC+0000'\n\nThe preferred way of dealing with times is to always work in UTC,\nconverting to localtime only when generating output to be read\nby humans.\n\n>>> utc_dt = datetime(2002, 10, 27, 6, 0, 0, tzinfo=utc)\n>>> loc_dt = utc_dt.astimezone(eastern)\n>>> loc_dt.strftime(fmt)\n'2002-10-27 01:00:00 EST-0500'\n\nThis library also allows you to do date arithmetic using local\ntimes, although it is more complicated than working in UTC as you\nneed to use the ``normalize()`` method to handle daylight saving time\nand other timezone transitions. In this example, ``loc_dt`` is set\nto the instant when daylight saving time ends in the US/Eastern\ntimezone.\n\n>>> before = loc_dt - timedelta(minutes=10)\n>>> before.strftime(fmt)\n'2002-10-27 00:50:00 EST-0500'\n>>> eastern.normalize(before).strftime(fmt)\n'2002-10-27 01:50:00 EDT-0400'\n>>> after = eastern.normalize(before + timedelta(minutes=20))\n>>> after.strftime(fmt)\n'2002-10-27 01:10:00 EST-0500'\n\nCreating local times is also tricky, and the reason why working with\nlocal times is not recommended. Unfortunately, you cannot just pass\na ``tzinfo`` argument when constructing a datetime (see the next\nsection for more details)\n\n>>> dt = datetime(2002, 10, 27, 1, 30, 0)\n>>> dt1 = eastern.localize(dt, is_dst=True)\n>>> dt1.strftime(fmt)\n'2002-10-27 01:30:00 EDT-0400'\n>>> dt2 = eastern.localize(dt, is_dst=False)\n>>> dt2.strftime(fmt)\n'2002-10-27 01:30:00 EST-0500'\n\nConverting between timezones is more easily done, using the\nstandard astimezone method.\n\n>>> utc_dt = utc.localize(datetime.utcfromtimestamp(1143408899))\n>>> utc_dt.strftime(fmt)\n'2006-03-26 21:34:59 UTC+0000'\n>>> au_tz = timezone('Australia/Sydney')\n>>> au_dt = utc_dt.astimezone(au_tz)\n>>> au_dt.strftime(fmt)\n'2006-03-27 08:34:59 AEDT+1100'\n>>> utc_dt2 = au_dt.astimezone(utc)\n>>> utc_dt2.strftime(fmt)\n'2006-03-26 21:34:59 UTC+0000'\n>>> utc_dt == utc_dt2\nTrue\n\nYou can take shortcuts when dealing with the UTC side of timezone\nconversions. ``normalize()`` and ``localize()`` are not really\nnecessary when there are no daylight saving time transitions to\ndeal with.\n\n>>> utc_dt = datetime.utcfromtimestamp(1143408899).replace(tzinfo=utc)\n>>> utc_dt.strftime(fmt)\n'2006-03-26 21:34:59 UTC+0000'\n>>> au_tz = timezone('Australia/Sydney')\n>>> au_dt = au_tz.normalize(utc_dt.astimezone(au_tz))\n>>> au_dt.strftime(fmt)\n'2006-03-27 08:34:59 AEDT+1100'\n>>> utc_dt2 = au_dt.astimezone(utc)\n>>> utc_dt2.strftime(fmt)\n'2006-03-26 21:34:59 UTC+0000'\n\n\n``tzinfo`` API\n--------------\n\nThe ``tzinfo`` instances returned by the ``timezone()`` function have\nbeen extended to cope with ambiguous times by adding an ``is_dst``\nparameter to the ``utcoffset()``, ``dst()`` && ``tzname()`` methods.\n\n>>> tz = timezone('America/St_Johns')\n\n>>> normal = datetime(2009, 9, 1)\n>>> ambiguous = datetime(2009, 10, 31, 23, 30)\n\nThe ``is_dst`` parameter is ignored for most timestamps. It is only used\nduring DST transition ambiguous periods to resolve that ambiguity.\n\n>>> print(tz.utcoffset(normal, is_dst=True))\n-1 day, 21:30:00\n>>> print(tz.dst(normal, is_dst=True))\n1:00:00\n>>> tz.tzname(normal, is_dst=True)\n'NDT'\n\n>>> print(tz.utcoffset(ambiguous, is_dst=True))\n-1 day, 21:30:00\n>>> print(tz.dst(ambiguous, is_dst=True))\n1:00:00\n>>> tz.tzname(ambiguous, is_dst=True)\n'NDT'\n\n>>> print(tz.utcoffset(normal, is_dst=False))\n-1 day, 21:30:00\n>>> tz.dst(normal, is_dst=False).seconds\n3600\n>>> tz.tzname(normal, is_dst=False)\n'NDT'\n\n>>> print(tz.utcoffset(ambiguous, is_dst=False))\n-1 day, 20:30:00\n>>> tz.dst(ambiguous, is_dst=False)\ndatetime.timedelta(0)\n>>> tz.tzname(ambiguous, is_dst=False)\n'NST'\n\nIf ``is_dst`` is not specified, ambiguous timestamps will raise\nan ``pytz.exceptions.AmbiguousTimeError`` exception.\n\n>>> print(tz.utcoffset(normal))\n-1 day, 21:30:00\n>>> print(tz.dst(normal))\n1:00:00\n>>> tz.tzname(normal)\n'NDT'\n\n>>> import pytz.exceptions\n>>> try:\n... tz.utcoffset(ambiguous)\n... except pytz.exceptions.AmbiguousTimeError:\n... print('pytz.exceptions.AmbiguousTimeError: %s' % ambiguous)\npytz.exceptions.AmbiguousTimeError: 2009-10-31 23:30:00\n>>> try:\n... tz.dst(ambiguous)\n... except pytz.exceptions.AmbiguousTimeError:\n... print('pytz.exceptions.AmbiguousTimeError: %s' % ambiguous)\npytz.exceptions.AmbiguousTimeError: 2009-10-31 23:30:00\n>>> try:\n... tz.tzname(ambiguous)\n... except pytz.exceptions.AmbiguousTimeError:\n... print('pytz.exceptions.AmbiguousTimeError: %s' % ambiguous)\npytz.exceptions.AmbiguousTimeError: 2009-10-31 23:30:00\n\n\nProblems with Localtime\n~~~~~~~~~~~~~~~~~~~~~~~\n\nThe major problem we have to deal with is that certain datetimes\nmay occur twice in a year. For example, in the US/Eastern timezone\non the last Sunday morning in October, the following sequence\nhappens:\n\n - 01:00 EDT occurs\n - 1 hour later, instead of 2:00am the clock is turned back 1 hour\n and 01:00 happens again (this time 01:00 EST)\n\nIn fact, every instant between 01:00 and 02:00 occurs twice. This means\nthat if you try and create a time in the 'US/Eastern' timezone\nthe standard datetime syntax, there is no way to specify if you meant\nbefore of after the end-of-daylight-saving-time transition. Using the\npytz custom syntax, the best you can do is make an educated guess:\n\n>>> loc_dt = eastern.localize(datetime(2002, 10, 27, 1, 30, 00))\n>>> loc_dt.strftime(fmt)\n'2002-10-27 01:30:00 EST-0500'\n\nAs you can see, the system has chosen one for you and there is a 50%\nchance of it being out by one hour. For some applications, this does\nnot matter. However, if you are trying to schedule meetings with people\nin different timezones or analyze log files it is not acceptable.\n\nThe best and simplest solution is to stick with using UTC. The pytz\npackage encourages using UTC for internal timezone representation by\nincluding a special UTC implementation based on the standard Python\nreference implementation in the Python documentation.\n\nThe UTC timezone unpickles to be the same instance, and pickles to a\nsmaller size than other pytz tzinfo instances. The UTC implementation\ncan be obtained as pytz.utc, pytz.UTC, or pytz.timezone('UTC').\n\n>>> import pickle, pytz\n>>> dt = datetime(2005, 3, 1, 14, 13, 21, tzinfo=utc)\n>>> naive = dt.replace(tzinfo=None)\n>>> p = pickle.dumps(dt, 1)\n>>> naive_p = pickle.dumps(naive, 1)\n>>> len(p) - len(naive_p)\n17\n>>> new = pickle.loads(p)\n>>> new == dt\nTrue\n>>> new is dt\nFalse\n>>> new.tzinfo is dt.tzinfo\nTrue\n>>> pytz.utc is pytz.UTC is pytz.timezone('UTC')\nTrue\n\nNote that some other timezones are commonly thought of as the same (GMT,\nGreenwich, Universal, etc.). The definition of UTC is distinct from these\nother timezones, and they are not equivalent. For this reason, they will\nnot compare the same in Python.\n\n>>> utc == pytz.timezone('GMT')\nFalse\n\nSee the section `What is UTC`_, below.\n\nIf you insist on working with local times, this library provides a\nfacility for constructing them unambiguously:\n\n>>> loc_dt = datetime(2002, 10, 27, 1, 30, 00)\n>>> est_dt = eastern.localize(loc_dt, is_dst=True)\n>>> edt_dt = eastern.localize(loc_dt, is_dst=False)\n>>> print(est_dt.strftime(fmt) + ' / ' + edt_dt.strftime(fmt))\n2002-10-27 01:30:00 EDT-0400 / 2002-10-27 01:30:00 EST-0500\n\nIf you pass None as the is_dst flag to localize(), pytz will refuse to\nguess and raise exceptions if you try to build ambiguous or non-existent\ntimes.\n\nFor example, 1:30am on 27th Oct 2002 happened twice in the US/Eastern\ntimezone when the clocks where put back at the end of Daylight Saving\nTime:\n\n>>> dt = datetime(2002, 10, 27, 1, 30, 00)\n>>> try:\n... eastern.localize(dt, is_dst=None)\n... except pytz.exceptions.AmbiguousTimeError:\n... print('pytz.exceptions.AmbiguousTimeError: %s' % dt)\npytz.exceptions.AmbiguousTimeError: 2002-10-27 01:30:00\n\nSimilarly, 2:30am on 7th April 2002 never happened at all in the\nUS/Eastern timezone, as the clocks where put forward at 2:00am skipping\nthe entire hour:\n\n>>> dt = datetime(2002, 4, 7, 2, 30, 00)\n>>> try:\n... eastern.localize(dt, is_dst=None)\n... except pytz.exceptions.NonExistentTimeError:\n... print('pytz.exceptions.NonExistentTimeError: %s' % dt)\npytz.exceptions.NonExistentTimeError: 2002-04-07 02:30:00\n\nBoth of these exceptions share a common base class to make error handling\neasier:\n\n>>> isinstance(pytz.AmbiguousTimeError(), pytz.InvalidTimeError)\nTrue\n>>> isinstance(pytz.NonExistentTimeError(), pytz.InvalidTimeError)\nTrue\n\n\nA special case is where countries change their timezone definitions\nwith no daylight savings time switch. For example, in 1915 Warsaw\nswitched from Warsaw time to Central European time with no daylight savings\ntransition. So at the stroke of midnight on August 5th 1915 the clocks\nwere wound back 24 minutes creating an ambiguous time period that cannot\nbe specified without referring to the timezone abbreviation or the\nactual UTC offset. In this case midnight happened twice, neither time\nduring a daylight saving time period. pytz handles this transition by\ntreating the ambiguous period before the switch as daylight savings\ntime, and the ambiguous period after as standard time.\n\n\n>>> warsaw = pytz.timezone('Europe/Warsaw')\n>>> amb_dt1 = warsaw.localize(datetime(1915, 8, 4, 23, 59, 59), is_dst=True)\n>>> amb_dt1.strftime(fmt)\n'1915-08-04 23:59:59 WMT+0124'\n>>> amb_dt2 = warsaw.localize(datetime(1915, 8, 4, 23, 59, 59), is_dst=False)\n>>> amb_dt2.strftime(fmt)\n'1915-08-04 23:59:59 CET+0100'\n>>> switch_dt = warsaw.localize(datetime(1915, 8, 5, 00, 00, 00), is_dst=False)\n>>> switch_dt.strftime(fmt)\n'1915-08-05 00:00:00 CET+0100'\n>>> str(switch_dt - amb_dt1)\n'0:24:01'\n>>> str(switch_dt - amb_dt2)\n'0:00:01'\n\nThe best way of creating a time during an ambiguous time period is\nby converting from another timezone such as UTC:\n\n>>> utc_dt = datetime(1915, 8, 4, 22, 36, tzinfo=pytz.utc)\n>>> utc_dt.astimezone(warsaw).strftime(fmt)\n'1915-08-04 23:36:00 CET+0100'\n\nThe standard Python way of handling all these ambiguities is not to\nhandle them, such as demonstrated in this example using the US/Eastern\ntimezone definition from the Python documentation (Note that this\nimplementation only works for dates between 1987 and 2006 - it is\nincluded for tests only!):\n\n>>> from pytz.reference import Eastern # pytz.reference only for tests\n>>> dt = datetime(2002, 10, 27, 0, 30, tzinfo=Eastern)\n>>> str(dt)\n'2002-10-27 00:30:00-04:00'\n>>> str(dt + timedelta(hours=1))\n'2002-10-27 01:30:00-05:00'\n>>> str(dt + timedelta(hours=2))\n'2002-10-27 02:30:00-05:00'\n>>> str(dt + timedelta(hours=3))\n'2002-10-27 03:30:00-05:00'\n\nNotice the first two results? At first glance you might think they are\ncorrect, but taking the UTC offset into account you find that they are\nactually two hours appart instead of the 1 hour we asked for.\n\n>>> from pytz.reference import UTC # pytz.reference only for tests\n>>> str(dt.astimezone(UTC))\n'2002-10-27 04:30:00+00:00'\n>>> str((dt + timedelta(hours=1)).astimezone(UTC))\n'2002-10-27 06:30:00+00:00'\n\n\nCountry Information\n~~~~~~~~~~~~~~~~~~~\n\nA mechanism is provided to access the timezones commonly in use\nfor a particular country, looked up using the ISO 3166 country code.\nIt returns a list of strings that can be used to retrieve the relevant\ntzinfo instance using ``pytz.timezone()``:\n\n>>> print(' '.join(pytz.country_timezones['nz']))\nPacific/Auckland Pacific/Chatham\n\nThe Olson database comes with a ISO 3166 country code to English country\nname mapping that pytz exposes as a dictionary:\n\n>>> print(pytz.country_names['nz'])\nNew Zealand\n\n\nWhat is UTC\n~~~~~~~~~~~\n\n'UTC' is `Coordinated Universal Time`_. It is a successor to, but distinct\nfrom, Greenwich Mean Time (GMT) and the various definitions of Universal\nTime. UTC is now the worldwide standard for regulating clocks and time\nmeasurement.\n\nAll other timezones are defined relative to UTC, and include offsets like\nUTC+0800 - hours to add or subtract from UTC to derive the local time. No\ndaylight saving time occurs in UTC, making it a useful timezone to perform\ndate arithmetic without worrying about the confusion and ambiguities caused\nby daylight saving time transitions, your country changing its timezone, or\nmobile computers that roam through multiple timezones.\n\n.. _Coordinated Universal Time: https://en.wikipedia.org/wiki/Coordinated_Universal_Time\n\n\nHelpers\n~~~~~~~\n\nThere are two lists of timezones provided.\n\n``all_timezones`` is the exhaustive list of the timezone names that can\nbe used.\n\n>>> from pytz import all_timezones\n>>> len(all_timezones) >= 500\nTrue\n>>> 'Etc/Greenwich' in all_timezones\nTrue\n\n``common_timezones`` is a list of useful, current timezones. It doesn't\ncontain deprecated zones or historical zones, except for a few I've\ndeemed in common usage, such as US/Eastern (open a bug report if you\nthink other timezones are deserving of being included here). It is also\na sequence of strings.\n\n>>> from pytz import common_timezones\n>>> len(common_timezones) < len(all_timezones)\nTrue\n>>> 'Etc/Greenwich' in common_timezones\nFalse\n>>> 'Australia/Melbourne' in common_timezones\nTrue\n>>> 'US/Eastern' in common_timezones\nTrue\n>>> 'Canada/Eastern' in common_timezones\nTrue\n>>> 'Australia/Yancowinna' in all_timezones\nTrue\n>>> 'Australia/Yancowinna' in common_timezones\nFalse\n\nBoth ``common_timezones`` and ``all_timezones`` are alphabetically\nsorted:\n\n>>> common_timezones_dupe = common_timezones[:]\n>>> common_timezones_dupe.sort()\n>>> common_timezones == common_timezones_dupe\nTrue\n>>> all_timezones_dupe = all_timezones[:]\n>>> all_timezones_dupe.sort()\n>>> all_timezones == all_timezones_dupe\nTrue\n\n``all_timezones`` and ``common_timezones`` are also available as sets.\n\n>>> from pytz import all_timezones_set, common_timezones_set\n>>> 'US/Eastern' in all_timezones_set\nTrue\n>>> 'US/Eastern' in common_timezones_set\nTrue\n>>> 'Australia/Victoria' in common_timezones_set\nFalse\n\nYou can also retrieve lists of timezones used by particular countries\nusing the ``country_timezones()`` function. It requires an ISO-3166\ntwo letter country code.\n\n>>> from pytz import country_timezones\n>>> print(' '.join(country_timezones('ch')))\nEurope/Zurich\n>>> print(' '.join(country_timezones('CH')))\nEurope/Zurich\n\n\nInternationalization - i18n/l10n\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nPytz is an interface to the IANA database, which uses ASCII names. The `Unicode Consortium's Unicode Locales (CLDR) `_\nproject provides translations. Python packages such as\n`Babel `_\nand Thomas Khyn's `l18n `_ package can be used\nto access these translations from Python.\n\n\nLicense\n~~~~~~~\n\nMIT license.\n\nThis code is also available as part of Zope 3 under the Zope Public\nLicense, Version 2.1 (ZPL).\n\nI'm happy to relicense this code if necessary for inclusion in other\nopen source projects.\n\n\nLatest Versions\n~~~~~~~~~~~~~~~\n\nThis package will be updated after releases of the Olson timezone\ndatabase. The latest version can be downloaded from the `Python Package\nIndex `_. The code that is used\nto generate this distribution is hosted on Github and available\nusing git::\n\n git clone https://github.com/stub42/pytz.git\n\nAnnouncements of new releases are made on\n`Launchpad `_, and the\n`Atom feed `_\nhosted there.\n\n\nBugs, Feature Requests & Patches\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nBugs should be reported on `Github `_.\nFeature requests are unlikely to be considered, and efforts instead directed\nto timezone support now built into Python or packages that work with it.\n\n\nSecurity Issues\n~~~~~~~~~~~~~~~\n\nReports about security issues can be made via `Tidelift `_.\n\n\nIssues & Limitations\n~~~~~~~~~~~~~~~~~~~~\n\n- This project is in maintenance mode. Projects using Python 3.9 or later\n are best served by using the timezone functionaly now included in core\n Python and packages that work with it such as `tzdata `_.\n\n- Offsets from UTC are rounded to the nearest whole minute, so timezones\n such as Europe/Amsterdam pre 1937 will be up to 30 seconds out. 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"version": "23.0.1" + }, + { + "name": "pyarrow", + "version": "11.0.0" + }, + { + "name": "pyparsing", + "version": "3.0.9" + }, + { + "name": "python-dateutil", + "version": "2.8.2" + }, + { + "name": "pytz", + "version": "2023.3" + }, + { + "name": "scipy", + "version": "1.8.1" + }, + { + "name": "setuptools", + "version": "67.8.0" + }, + { + "name": "six", + "version": "1.16.0" + }, + { + "name": "sympy", + "version": "1.12" + }, + { + "name": "wheel", + "version": "0.38.4" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/external-resources/LICENSE b/registry/phase4ad-author-semantics/evidence/external-resources/LICENSE new file mode 100644 index 0000000..deca2d0 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/external-resources/LICENSE @@ -0,0 +1,21 @@ +MIT License + +Copyright (c) 2023 Philip Shiu and Nico Spiller + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. diff --git a/registry/phase4ad-author-semantics/evidence/external-resources/environment_full.yml b/registry/phase4ad-author-semantics/evidence/external-resources/environment_full.yml new file mode 100644 index 0000000..1428b31 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/external-resources/environment_full.yml @@ -0,0 +1,109 @@ +name: brian2 +channels: + - defaults + - conda-forge +dependencies: + - abseil-cpp=20211102.0=h0e60522_0 + - arrow-cpp=11.0.0=py310h7cee713_0 + - asttokens=2.2.1=pyhd8ed1ab_0 + - aws-c-common=0.4.57=ha925a31_1 + - aws-c-event-stream=0.1.6=hd77b12b_5 + - aws-checksums=0.1.9=ha925a31_0 + - aws-sdk-cpp=1.8.185=hd77b12b_0 + - backcall=0.2.0=pyh9f0ad1d_0 + - backports=1.0=pyhd8ed1ab_3 + - 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zstd=1.5.5=hd43e919_0 diff --git a/registry/phase4ad-author-semantics/evidence/external-resources/model.py b/registry/phase4ad-author-semantics/evidence/external-resources/model.py new file mode 100644 index 0000000..5ba7083 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/external-resources/model.py @@ -0,0 +1,373 @@ +import pandas as pd +from textwrap import dedent + +# brian 2 +from brian2 import NeuronGroup, Synapses, PoissonInput, SpikeMonitor, Network +from brian2 import mV, ms, Hz + +# file handling +from pathlib import Path + +# parallelization +from joblib import Parallel, delayed, parallel_backend +from time import time + +default_params = { + # trials + 't_run' : 1000 * ms, # duration of trial + 'n_run' : 30, # number of runs + + # network constants + # Kakaria and de Bivort 2017 https://doi.org/10.3389/fnbeh.2017.00008 + 'v_0' : -52 * mV, # resting potential + 'v_rst' : -52 * mV, # reset potential after spike + 'v_th' : -45 * mV, # threshold for spiking + 't_mbr' : 20 * ms, # membrane time scale (capacitance * resistance = .002 * uF * 10. * Mohm) + + # Jürgensen et al https://doi.org/10.1088/2634-4386/ac3ba6 + 'tau' : 5 * ms, # time constant + + # Lazar et al https://doi.org/10.7554/eLife.62362 + 't_rfc' : 2.2 * ms, # refractory period + + # Paul et al 2015 doi: 10.3389/fncel.2015.00029 + 't_dly' : 1.8*ms, # delay for changes in post-synaptic neuron + + # Free parameter + 'w_syn' : .275 * mV, # weight per synapse (note: modulated by exponential decay) + # Default activation rates + 'r_poi' : 150*Hz, # default rate of the Poisson inputs + 'r_poi2' : 0*Hz, # default rate of a 2nd class of Poisson inputs + 'f_poi' : 250, # scaling factor for Poisson synapse; 250 is sufficient to cause spiking + + # equations for neurons # alpha synapse https://doi.org/10.1017/CBO9780511815706; See https://brian2.readthedocs.io/en/stable/user/converting_from_integrated_form.html + 'eqs' : dedent(''' + dv/dt = (v_0 - v + g) / t_mbr : volt (unless refractory) + dg/dt = -g / tau : volt (unless refractory) + rfc : second + '''), + # condition for spike + 'eq_th' : 'v > v_th', + # rules for spike + 'eq_rst' : 'v = v_rst; w = 0; g = 0 * mV', +} + + +####################### +# brian2 model setup +def poi(neu, exc, exc2, params): + '''Create PoissonInput for neurons. + + For each neuron in 'names' a PoissonInput is generated and + the refractory period of that neuron is set to 0 in NeuronGroup. + + Parameters + ---------- + neu : NeuronGroup + Defined brian2.NeuronGroup object + exc : list + Indices of neurons for which to create Poisson input + exc2 : list + Indices of neurons for which to create Poisson input with `r_poi` + params : dict + Constants and equations that are used to construct the brian2 network model + + Returns + ------- + pois : list + PoissonInput objects for each neuron in 'exc' + neu : NeuronGroup + NeuronGroup with adjusted refractory periods + ''' + + pois = [] + for i in exc: + p = PoissonInput( + target=neu[i], + target_var='v', + N=1, + rate=params['r_poi'], + weight=params['w_syn']*params['f_poi'] + ) + neu[i].rfc = 0 * ms # no refractory period for Poisson targets + pois.append(p) + + for i in exc2: + p = PoissonInput( + target=neu[i], + target_var='v', + N=1, + rate=params['r_poi2'], + weight=params['w_syn']*params['f_poi'] + ) + neu[i].rfc = 0 * ms # no refractory period for Poisson targets + pois.append(p) + + return pois, neu + +def silence(slnc, syn): + '''Silence neuron by setting weights of all synapses from it to 0 + + Parameters + ---------- + slnc : list + List of neuron indices to silence + syn : brian2.Synapses + Defined synapses object + + Returns + ------- + syn : brian2.Synapses + Synapses with modified weights + ''' + + for i in slnc: + syn.w[' {} == i'.format(i)] = 0*mV + + return syn + +def create_model(path_comp, path_con, params): + '''Create default network model. + + Convert the "completeness materialization" and "connectivity" dataframes + into a brian2 neural network model. Network constants and equations + are defined at the beginning of this file. + + Parameters + ---------- + path_comp : str + path to "completeness materialization" dataframe + path_con : str + path to "connectivity" dataframe + params : dict + Constants and equations that are used to construct the brian2 network model + + + Returns + ------- + neu : NeuronGroup + brian2.NeuronGroup object with neurons as in 'path_comp' + syn : Synapses + brian2.Synapses object with connections as in 'path_con' + spk_mon : SpikeMonitor + brian2.SpikeMonitor object, which records time of spike events + ''' + + # load neuron connectivity dataframes + df_comp = pd.read_csv(path_comp, index_col=0) + df_con = pd.read_parquet(path_con) + + neu = NeuronGroup( # create neurons + N=len(df_comp), + model=params['eqs'], + method='linear', + threshold=params['eq_th'], + reset=params['eq_rst'], + refractory='rfc', + name='default_neurons', + namespace=params, + ) + neu.v = params['v_0'] # initialize values + neu.g = 0 + neu.rfc = params['t_rfc'] + + # create synapses + syn = Synapses(neu, neu, 'w : volt', on_pre='g += w', delay=params['t_dly'], name='default_synapses') + + # connect synapses + i_pre = df_con.loc[:, 'Presynaptic_Index'].values + i_post = df_con.loc[:, 'Postsynaptic_Index'].values + syn.connect(i=i_pre, j=i_post) + + # define connection weight + syn.w = df_con.loc[:,'Excitatory x Connectivity'].values * params['w_syn'] + + # object to record spikes + spk_mon = SpikeMonitor(neu) + + return neu, syn, spk_mon + +##################### +# running simulations +def get_spk_trn(spk_mon): + '''Extracts spike times from 'spk_mon' + + The spike times recorded in the SpikeMonitor object during + simulation are converted to a list of times for each neurons. + Returns dict with "brian ID": "list of spike times". + + Parameters + ---------- + spk_mon : SpikeMonitor + Contains recorded spike times + + Returns + ------- + spk_trn : dict + Mapping between brian neuron IDs and spike times + ''' + + spk_trn = {k: v for k, v in spk_mon.spike_trains().items() if len(v)} + + return spk_trn + +def construct_dataframe(res, exp_name, i2flyid): + '''Take spike time dict and collects spikes in pandas dataframe + + Parameters + ---------- + res : list + List with spike time dicts for each trial + exp_name : str + Name of the experiment + i2flyid : dict + Mapping between Brian IDs and flywire IDs + + Returns + ------- + df : pandas.DataFrame + Dataframe where each row is one spike + ''' + + ids, ts, nrun = [], [], [] + + for n, i in enumerate(res): + for j, k in i.items(): + ids.extend([j for _ in k]) + nrun.extend([n for _ in k]) + ts.extend([float(l) for l in k]) + + d = { + 't': ts, + 'trial': nrun, + 'flywire_id': [i2flyid[i] for i in ids], + 'exp_name': exp_name + } + df = pd.DataFrame(d) + + return df + +def run_trial(exc, exc2, slnc, path_comp, path_con, params): + '''Run single trial of coactivation/silencng experiment + + During the coactivation experiment, the neurons in 'exc' are + Poisson inputs. The simulation runs for 't_run'. + + + Parameters + ---------- + exc: list + contains indices of neurons for PoissonInput + exc2: list + contains indices of neurons for PoissonInput of different frequency `r_poi2` + slnc: list + contains indices of neurons to silence + path_comp: Path + path to "completeness materialization" dataframe + path_con: Path + path to "connectivity" dataframe + params : dict + Constants and equations that are used to construct the brian2 network model + + Returns + ------- + spk_trn : dict + Mapping between brian neuron IDs and spike times + ''' + + # get default network + neu, syn, spk_mon = create_model(path_comp, path_con, params) + # define Poisson input for excitation + poi_inp, neu = poi(neu, exc, exc2, params) + # silence neurons + syn = silence(slnc, syn) + # collect in Network object + net = Network(neu, syn, spk_mon, *poi_inp) + + # run simulation + net.run(duration=params['t_run']) + + # spike times + spk_trn = get_spk_trn(spk_mon) + + return spk_trn + + +def run_exp(exp_name, neu_exc, path_res, path_comp, path_con, + params=default_params, neu_slnc=[], neu_exc2=[], + n_proc=-1, force_overwrite=False): + ''' + Run default network experiment + Neurons in `neu_exc` are Poisson external inputs + Neurons in `neu_slnc` are silenced + + + Parameters + ---------- + exp_name: str + name of the experiment + neu_exc: list + contains custom names or flywire IDs of neurons to be excited + path_res: str + path to the output folder where spike data is stored + path_comp: str + path to "completeness materialization" dataframe + path_con: str + path to "connectivity" dataframe + params : dict + Constants and equations that are used to construct the brian2 network model + neu_slnc : list (optional) + contains custom names or flywire IDs of neurons to be silenced + neu_exc2 : list (optional) + contains custom names or flywire IDs of neurons to be excited with different frequency + requires `r_poi2` to be defined in `params` + n_proc: int (optional) + number of cores to be used for parallel runs + default: -1 (use all available cores) + n_proc=1 is equivalent serial code + force_overwrite : bool (optional) + If True, overwrite output files, else skip simulation, by default False + ''' + + # convert to Path objects + path_res, path_comp, path_con = [ Path(i) for i in [path_res, path_comp, path_con] ] + + # define output files + path_save = path_res / '{}.parquet'.format(exp_name) + if path_save.is_file() and not force_overwrite: + print('>>> Skipping experiment {} because {} exists and force_overwrite = {}'.format(exp_name, path_save, force_overwrite)) + return + + # load name/id mappings + df_comp = pd.read_csv(path_comp, index_col=0) # load completeness dataframe + flyid2i = {j: i for i, j in enumerate(df_comp.index)} # flywire id: biran ID + i2flyid = {j: i for i, j in flyid2i.items()} # brian ID: flywire ID + + # print info + print('>>> Experiment: {}'.format(exp_name)) + print(' Output file: {}'.format(path_save)) + print(' Excited neurons: {}'.format(len(neu_exc + neu_exc2))) + if neu_slnc: + print(' Silenced neurons: {}'.format(len(neu_slnc))) + + # start parallel calculation + n_run = params['n_run'] + start = time() + with parallel_backend('loky', n_jobs=n_proc): + exc = [ flyid2i[n] for n in neu_exc ] + exc2 = [ flyid2i[n] for n in neu_exc2 ] + slnc = [ flyid2i[n] for n in neu_slnc ] + res = Parallel()( + delayed( + run_trial)(exc, exc2, slnc, path_comp, path_con, params) for _ in range(n_run)) + + + # print simulation time + walltime = time() - start + print(' Elapsed time: {} s'.format(int(walltime))) + + # dataframe with spike times + df = construct_dataframe(res, exp_name, i2flyid) + + # store spike data + df.to_parquet(path_save, compression='brotli') diff --git a/registry/phase4ad-author-semantics/evidence/gpu-reference/extension.json b/registry/phase4ad-author-semantics/evidence/gpu-reference/extension.json new file mode 100644 index 0000000..9b9de4b --- /dev/null +++ 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"actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32-repeat/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32-repeat/generated-code.json new file mode 100644 index 0000000..5b80ca3 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32-repeat/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_7", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_8", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_4", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_4", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32-repeat/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32-repeat/run-spec.json new file mode 100644 index 0000000..399187c --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32-repeat/run-spec.json @@ -0,0 +1,123 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 1000.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + 1337065, + 1467355, + 1559765, + 20992891 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + 1197, + 1381, + 1511, + 82312, + 133666 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float32", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float32", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": 1381 + }, + "steps": 10000, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32-repeat/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32-repeat/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32-repeat/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32-repeat/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32-repeat/seed.json new file mode 100644 index 0000000..2896d59 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32-repeat/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -43.99999976158142, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": 1381, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/actual-weights.json new file mode 100644 index 0000000..3da2958 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/actual-weights.json @@ -0,0 +1,20 @@ +{ + "edge_id": [ + 1337065, + 1467355, + 1559765, + 20992891 + ], + "weights_mv": [ + 28.599998474121094, + 64.625, + 62.14999771118164, + 11.824999809265137 + ], + "weights_volt": [ + 0.028599999845027924, + 0.06462500244379044, + 0.062150001525878906, + 0.011824999935925007 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/brian-output/events.csv new file mode 100644 index 0000000..05e673a --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/brian-output/events.csv @@ -0,0 +1,4 @@ +step,neuron_idx +0,1381 +51,1511 +104,1197 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/comparison.json new file mode 100644 index 0000000..1b1d646 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.00020179152488708496, + "mean_abs_mv": 1.9821550031807453e-05, + "same_event_prefix_max_abs_mv": 0.00020179152488708496, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/completeness.csv new file mode 100644 index 0000000..9592749 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/completeness.csv @@ -0,0 +1,6 @@ +global_neuron_idx,local_index +1197,0 +1381,1 +1511,2 +82312,3 +133666,4 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/generated-code.json new file mode 100644 index 0000000..e0bc716 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_6", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_7", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_7", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_7", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/independent-output/events.csv new file mode 100644 index 0000000..05e673a --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/independent-output/events.csv @@ -0,0 +1,4 @@ +step,neuron_idx +0,1381 +51,1511 +104,1197 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/run-spec.json new file mode 100644 index 0000000..399187c --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/run-spec.json @@ -0,0 +1,123 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 1000.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + 1337065, + 1467355, + 1559765, + 20992891 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + 1197, + 1381, + 1511, + 82312, + 133666 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float32", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float32", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": 1381 + }, + "steps": 10000, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/seed.json new file mode 100644 index 0000000..2896d59 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -43.99999976158142, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": 1381, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/actual-weights.json new file mode 100644 index 0000000..ef4c108 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/actual-weights.json @@ -0,0 +1,20 @@ +{ + "edge_id": [ + 1337065, + 1467355, + 1559765, + 20992891 + ], + "weights_mv": [ + 28.6, + 64.625, + 62.150000000000006, + 11.825000000000001 + ], + "weights_volt": [ + 0.0286, + 0.064625, + 0.062150000000000004, + 0.011825 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/brian-output/events.csv new file mode 100644 index 0000000..05e673a --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/brian-output/events.csv @@ -0,0 +1,4 @@ +step,neuron_idx +0,1381 +51,1511 +104,1197 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/completeness.csv new file mode 100644 index 0000000..9592749 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/completeness.csv @@ -0,0 +1,6 @@ +global_neuron_idx,local_index +1197,0 +1381,1 +1511,2 +82312,3 +133666,4 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/generated-code.json new file mode 100644 index 0000000..c76747a --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_6", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_6", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_6", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/run-spec.json new file mode 100644 index 0000000..0af564c --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/run-spec.json @@ -0,0 +1,123 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 1000.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + 1337065, + 1467355, + 1559765, + 20992891 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + 1197, + 1381, + 1511, + 82312, + 133666 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float64", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float64", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": 1381 + }, + "steps": 10000, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/seed.json new file mode 100644 index 0000000..37b8750 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -44.0, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": 1381, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/actual-weights.json new file mode 100644 index 0000000..ef4c108 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/actual-weights.json @@ -0,0 +1,20 @@ +{ + "edge_id": [ + 1337065, + 1467355, + 1559765, + 20992891 + ], + "weights_mv": [ + 28.6, + 64.625, + 62.150000000000006, + 11.825000000000001 + ], + "weights_volt": [ + 0.0286, + 0.064625, + 0.062150000000000004, + 0.011825 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/brian-output/events.csv new file mode 100644 index 0000000..05e673a --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/brian-output/events.csv @@ -0,0 +1,4 @@ +step,neuron_idx +0,1381 +51,1511 +104,1197 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/comparison.json new file mode 100644 index 0000000..906245d --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 3.765876499528531e-13, + "mean_abs_mv": 3.893371799264915e-14, + "same_event_prefix_max_abs_mv": 3.765876499528531e-13, + "first_event_divergence_step": null, + "tolerance_mv": 1e-08, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/completeness.csv new file mode 100644 index 0000000..9592749 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/completeness.csv @@ -0,0 +1,6 @@ +global_neuron_idx,local_index +1197,0 +1381,1 +1511,2 +82312,3 +133666,4 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/generated-code.json new file mode 100644 index 0000000..a9b8245 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_4", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/independent-output/events.csv new file mode 100644 index 0000000..05e673a --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/independent-output/events.csv @@ -0,0 +1,4 @@ +step,neuron_idx +0,1381 +51,1511 +104,1197 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/run-spec.json new file mode 100644 index 0000000..0af564c --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/run-spec.json @@ -0,0 +1,123 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 1000.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + 1337065, + 1467355, + 1559765, + 20992891 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + 1197, + 1381, + 1511, + 82312, + 133666 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float64", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float64", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": 1381 + }, + "steps": 10000, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/seed.json new file mode 100644 index 0000000..37b8750 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -44.0, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": 1381, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/actual-weights.json new file mode 100644 index 0000000..8ac25e1 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/actual-weights.json @@ -0,0 +1,47 @@ +{ + "edge_id": [ + 1336648, + 1336655, + 1337065, + 1467340, + 1467355, + 1467852, + 1559765, + 1559772, + 1560267, + 20992285, + 20992291, + 20992294, + 20992891 + ], + "weights_mv": [ + 57.75, + 47.29999923706055, + 28.599998474121094, + 71.2249984741211, + 64.625, + 17.599998474121094, + 62.14999771118164, + 77.82499694824219, + 19.249998092651367, + 26.125, + 15.675000190734863, + 20.899999618530273, + 11.824999809265137 + ], + "weights_volt": [ + 0.057750001549720764, + 0.04729999974370003, + 0.028599999845027924, + 0.07122500240802765, + 0.06462500244379044, + 0.01759999990463257, + 0.062150001525878906, + 0.07782500237226486, + 0.01924999989569187, + 0.026125000789761543, + 0.015675000846385956, + 0.020899999886751175, + 0.011824999935925007 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/brian-output/events.csv new file mode 100644 index 0000000..18a7e41 --- /dev/null +++ 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+9924,82312 +9929,1381 +9952,1197 +9960,133666 +9974,1511 +9995,1381 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/completeness.csv new file mode 100644 index 0000000..9592749 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/completeness.csv @@ -0,0 +1,6 @@ +global_neuron_idx,local_index +1197,0 +1381,1 +1511,2 +82312,3 +133666,4 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/generated-code.json new file mode 100644 index 0000000..173c129 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_3", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_4", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_4", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_4", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/run-spec.json new file mode 100644 index 0000000..4539c9b --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/run-spec.json @@ -0,0 +1,132 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 1000.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + 1336648, + 1336655, + 1337065, + 1467340, + 1467355, + 1467852, + 1559765, + 1559772, + 1560267, + 20992285, + 20992291, + 20992294, + 20992891 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + 1197, + 1381, + 1511, + 82312, + 133666 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float32", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float32", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": 1381 + }, + "steps": 10000, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/seed.json new file mode 100644 index 0000000..2896d59 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -43.99999976158142, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": 1381, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float32/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float32/actual-weights.json new file mode 100644 index 0000000..8ac25e1 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float32/actual-weights.json @@ -0,0 +1,47 @@ +{ + "edge_id": [ + 1336648, + 1336655, + 1337065, + 1467340, + 1467355, + 1467852, + 1559765, + 1559772, + 1560267, + 20992285, + 20992291, + 20992294, + 20992891 + ], + "weights_mv": [ + 57.75, + 47.29999923706055, + 28.599998474121094, + 71.2249984741211, + 64.625, + 17.599998474121094, + 62.14999771118164, + 77.82499694824219, + 19.249998092651367, + 26.125, + 15.675000190734863, + 20.899999618530273, + 11.824999809265137 + ], + "weights_volt": [ + 0.057750001549720764, + 0.04729999974370003, + 0.028599999845027924, + 0.07122500240802765, + 0.06462500244379044, + 0.01759999990463257, + 0.062150001525878906, + 0.07782500237226486, + 0.01924999989569187, + 0.026125000789761543, + 0.015675000846385956, + 0.020899999886751175, + 0.011824999935925007 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float32/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/five-float32/brian-output/events.csv new file mode 100644 index 0000000..18a7e41 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float32/brian-output/events.csv @@ -0,0 +1,611 @@ +step,neuron_idx +0,1381 +46,1197 +51,1511 +79,1381 +91,133666 +99,1197 +120,1511 +140,1381 +163,1197 +170,133666 +185,1511 +205,1381 +220,1197 +246,1511 +259,133666 +268,1381 +288,1197 +306,1511 +330,1381 +341,133666 +351,1197 +371,1511 +391,1381 +414,1197 +422,133666 +436,1511 +457,1381 +471,1197 +497,1511 +510,133666 +519,1381 +539,1197 +557,1511 +581,1381 +592,133666 +602,1197 +622,1511 +642,1381 +665,1197 +673,133666 +687,1511 +708,1381 +722,1197 +748,1511 +761,133666 +770,1381 +790,1197 +808,1511 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+9377,133666 +9387,1197 +9407,1511 +9427,1381 +9450,1197 +9458,133666 +9472,1511 +9493,1381 +9507,1197 +9533,1511 +9546,133666 +9555,1381 +9575,1197 +9593,1511 +9617,1381 +9628,133666 +9638,1197 +9658,1511 +9678,1381 +9701,1197 +9709,133666 +9723,1511 +9744,1381 +9758,1197 +9784,1511 +9797,133666 +9806,1381 +9826,1197 +9844,1511 +9868,1381 +9879,133666 +9889,1197 +9909,1511 +9924,82312 +9929,1381 +9952,1197 +9960,133666 +9974,1511 +9995,1381 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float32/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float32/comparison.json new file mode 100644 index 0000000..1c36ba4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float32/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.0002123713493347168, + "mean_abs_mv": 1.7726411819458007e-05, + "same_event_prefix_max_abs_mv": 0.0002123713493347168, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float32/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/five-float32/completeness.csv new file mode 100644 index 0000000..9592749 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float32/completeness.csv @@ -0,0 +1,6 @@ +global_neuron_idx,local_index +1197,0 +1381,1 +1511,2 +82312,3 +133666,4 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float32/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float32/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float32/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float32/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float32/generated-code.json new file mode 100644 index 0000000..c284726 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float32/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_1", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_3", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_3", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_3", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float32/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/five-float32/independent-output/events.csv new file mode 100644 index 0000000..18a7e41 --- /dev/null +++ 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+9924,82312 +9929,1381 +9952,1197 +9960,133666 +9974,1511 +9995,1381 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float32/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float32/run-spec.json new file mode 100644 index 0000000..4539c9b --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float32/run-spec.json @@ -0,0 +1,132 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 1000.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + 1336648, + 1336655, + 1337065, + 1467340, + 1467355, + 1467852, + 1559765, + 1559772, + 1560267, + 20992285, + 20992291, + 20992294, + 20992891 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + 1197, + 1381, + 1511, + 82312, + 133666 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float32", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float32", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": 1381 + }, + "steps": 10000, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float32/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float32/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float32/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float32/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float32/seed.json new file mode 100644 index 0000000..2896d59 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float32/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -43.99999976158142, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": 1381, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/actual-weights.json new file mode 100644 index 0000000..dd3aa41 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/actual-weights.json @@ -0,0 +1,47 @@ +{ + "edge_id": [ + 1336648, + 1336655, + 1337065, + 1467340, + 1467355, + 1467852, + 1559765, + 1559772, + 1560267, + 20992285, + 20992291, + 20992294, + 20992891 + ], + "weights_mv": [ + 57.75, + 47.300000000000004, + 28.6, + 71.22500000000001, + 64.625, + 17.6, + 62.150000000000006, + 77.825, + 19.25, + 26.125000000000004, + 15.675, + 20.900000000000002, + 11.825000000000001 + ], + "weights_volt": [ + 0.05775, + 0.0473, + 0.0286, + 0.07122500000000001, + 0.064625, + 0.0176, + 0.062150000000000004, + 0.077825, + 0.01925, + 0.026125000000000002, + 0.015675, + 0.020900000000000002, + 0.011825 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/brian-output/events.csv new file mode 100644 index 0000000..18a7e41 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/brian-output/events.csv @@ -0,0 +1,611 @@ +step,neuron_idx +0,1381 +46,1197 +51,1511 +79,1381 +91,133666 +99,1197 +120,1511 +140,1381 +163,1197 +170,133666 +185,1511 +205,1381 +220,1197 +246,1511 +259,133666 +268,1381 +288,1197 +306,1511 +330,1381 +341,133666 +351,1197 +371,1511 +391,1381 +414,1197 +422,133666 +436,1511 +457,1381 +471,1197 +497,1511 +510,133666 +519,1381 +539,1197 +557,1511 +581,1381 +592,133666 +602,1197 +622,1511 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--git a/registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/generated-code.json new file mode 100644 index 0000000..128ac1e --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/run-spec.json new file mode 100644 index 0000000..2d00e44 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/run-spec.json @@ -0,0 +1,132 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 1000.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + 1336648, + 1336655, + 1337065, + 1467340, + 1467355, + 1467852, + 1559765, + 1559772, + 1560267, + 20992285, + 20992291, + 20992294, + 20992891 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + 1197, + 1381, + 1511, + 82312, + 133666 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float64", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float64", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": 1381 + }, + "steps": 10000, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/seed.json new file mode 100644 index 0000000..37b8750 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -44.0, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": 1381, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float64/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float64/actual-weights.json new file mode 100644 index 0000000..dd3aa41 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float64/actual-weights.json @@ -0,0 +1,47 @@ +{ + "edge_id": [ + 1336648, + 1336655, + 1337065, + 1467340, + 1467355, + 1467852, + 1559765, + 1559772, + 1560267, + 20992285, + 20992291, + 20992294, + 20992891 + ], + "weights_mv": [ + 57.75, + 47.300000000000004, + 28.6, + 71.22500000000001, + 64.625, + 17.6, + 62.150000000000006, + 77.825, + 19.25, + 26.125000000000004, + 15.675, + 20.900000000000002, + 11.825000000000001 + ], + "weights_volt": [ + 0.05775, + 0.0473, + 0.0286, + 0.07122500000000001, + 0.064625, + 0.0176, + 0.062150000000000004, + 0.077825, + 0.01925, + 0.026125000000000002, + 0.015675, + 0.020900000000000002, + 0.011825 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float64/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/five-float64/brian-output/events.csv new file mode 100644 index 0000000..18a7e41 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float64/brian-output/events.csv @@ -0,0 +1,611 @@ +step,neuron_idx +0,1381 +46,1197 +51,1511 +79,1381 +91,133666 +99,1197 +120,1511 +140,1381 +163,1197 +170,133666 +185,1511 +205,1381 +220,1197 +246,1511 +259,133666 +268,1381 +288,1197 +306,1511 +330,1381 +341,133666 +351,1197 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b/registry/phase4ad-author-semantics/evidence/oracle/five-float64/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 3.836930773104541e-13, + "mean_abs_mv": 3.28896643253529e-14, + "same_event_prefix_max_abs_mv": 3.836930773104541e-13, + "first_event_divergence_step": null, + "tolerance_mv": 1e-08, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float64/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/five-float64/completeness.csv new file mode 100644 index 0000000..9592749 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float64/completeness.csv @@ -0,0 +1,6 @@ +global_neuron_idx,local_index +1197,0 +1381,1 +1511,2 +82312,3 +133666,4 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float64/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float64/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float64/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float64/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float64/generated-code.json new file mode 100644 index 0000000..9dbc8f9 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float64/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_1", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float64/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/five-float64/independent-output/events.csv new file mode 100644 index 0000000..18a7e41 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float64/independent-output/events.csv @@ -0,0 +1,611 @@ +step,neuron_idx +0,1381 +46,1197 +51,1511 +79,1381 +91,133666 +99,1197 +120,1511 +140,1381 +163,1197 +170,133666 +185,1511 +205,1381 +220,1197 +246,1511 +259,133666 +268,1381 +288,1197 +306,1511 +330,1381 +341,133666 +351,1197 +371,1511 +391,1381 +414,1197 +422,133666 +436,1511 +457,1381 +471,1197 +497,1511 +510,133666 +519,1381 +539,1197 +557,1511 +581,1381 +592,133666 +602,1197 +622,1511 +642,1381 +665,1197 +673,133666 +687,1511 +708,1381 +722,1197 +748,1511 +761,133666 +770,1381 +790,1197 +808,1511 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"comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 1000.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + 1336648, + 1336655, + 1337065, + 1467340, + 1467355, + 1467852, + 1559765, + 1559772, + 1560267, + 20992285, + 20992291, + 20992294, + 20992891 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + 1197, + 1381, + 1511, + 82312, + 133666 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float64", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float64", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": 1381 + }, + "steps": 10000, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float64/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float64/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float64/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/five-float64/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/five-float64/seed.json new file mode 100644 index 0000000..37b8750 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/five-float64/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -44.0, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": 1381, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/actual-weights.json new file mode 100644 index 0000000..8ac25e1 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/actual-weights.json @@ -0,0 +1,47 @@ +{ + "edge_id": [ + 1336648, + 1336655, + 1337065, + 1467340, + 1467355, + 1467852, + 1559765, + 1559772, + 1560267, + 20992285, + 20992291, + 20992294, + 20992891 + ], + "weights_mv": [ + 57.75, + 47.29999923706055, + 28.599998474121094, + 71.2249984741211, + 64.625, + 17.599998474121094, + 62.14999771118164, + 77.82499694824219, + 19.249998092651367, + 26.125, + 15.675000190734863, + 20.899999618530273, + 11.824999809265137 + ], + "weights_volt": [ + 0.057750001549720764, + 0.04729999974370003, + 0.028599999845027924, + 0.07122500240802765, + 0.06462500244379044, + 0.01759999990463257, + 0.062150001525878906, + 0.07782500237226486, + 0.01924999989569187, + 0.026125000789761543, + 0.015675000846385956, + 0.020899999886751175, + 0.011824999935925007 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/brian-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/brian-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/completeness.csv new file mode 100644 index 0000000..9592749 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/completeness.csv @@ -0,0 +1,6 @@ +global_neuron_idx,local_index +1197,0 +1381,1 +1511,2 +82312,3 +133666,4 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/generated-code.json new file mode 100644 index 0000000..0748450 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/generated-code.json @@ -0,0 +1,119 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_6", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_7", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_8", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_8", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/run-spec.json new file mode 100644 index 0000000..e659585 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/run-spec.json @@ -0,0 +1,132 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 1000.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + 1336648, + 1336655, + 1337065, + 1467340, + 1467355, + 1467852, + 1559765, + 1559772, + 1560267, + 20992285, + 20992291, + 20992294, + 20992891 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + 1197, + 1381, + 1511, + 82312, + 133666 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float32", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float32", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null + }, + "steps": 10000, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/schedule.json new file mode 100644 index 0000000..cd48c36 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/seed.json new file mode 100644 index 0000000..f164c97 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32-repeat/seed.json @@ -0,0 +1,5 @@ +{ + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/actual-weights.json new file mode 100644 index 0000000..8ac25e1 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/actual-weights.json @@ -0,0 +1,47 @@ +{ + "edge_id": [ + 1336648, + 1336655, + 1337065, + 1467340, + 1467355, + 1467852, + 1559765, + 1559772, + 1560267, + 20992285, + 20992291, + 20992294, + 20992891 + ], + "weights_mv": [ + 57.75, + 47.29999923706055, + 28.599998474121094, + 71.2249984741211, + 64.625, + 17.599998474121094, + 62.14999771118164, + 77.82499694824219, + 19.249998092651367, + 26.125, + 15.675000190734863, + 20.899999618530273, + 11.824999809265137 + ], + "weights_volt": [ + 0.057750001549720764, + 0.04729999974370003, + 0.028599999845027924, + 0.07122500240802765, + 0.06462500244379044, + 0.01759999990463257, + 0.062150001525878906, + 0.07782500237226486, + 0.01924999989569187, + 0.026125000789761543, + 0.015675000846385956, + 0.020899999886751175, + 0.011824999935925007 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/brian-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/brian-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/comparison.json new file mode 100644 index 0000000..a9e3395 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 1.0728836059570312e-06, + "mean_abs_mv": 5.364418029785156e-07, + "same_event_prefix_max_abs_mv": 1.0728836059570312e-06, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/completeness.csv new file mode 100644 index 0000000..9592749 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/completeness.csv @@ -0,0 +1,6 @@ +global_neuron_idx,local_index +1197,0 +1381,1 +1511,2 +82312,3 +133666,4 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/generated-code.json new file mode 100644 index 0000000..ae98e74 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/generated-code.json @@ -0,0 +1,119 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_6", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_7", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_7", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/independent-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/independent-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/run-spec.json new file mode 100644 index 0000000..e659585 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/run-spec.json @@ -0,0 +1,132 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 1000.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + 1336648, + 1336655, + 1337065, + 1467340, + 1467355, + 1467852, + 1559765, + 1559772, + 1560267, + 20992285, + 20992291, + 20992294, + 20992891 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + 1197, + 1381, + 1511, + 82312, + 133666 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float32", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float32", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null + }, + "steps": 10000, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/schedule.json new file mode 100644 index 0000000..cd48c36 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/seed.json new file mode 100644 index 0000000..f164c97 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float32/seed.json @@ -0,0 +1,5 @@ +{ + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/actual-weights.json new file mode 100644 index 0000000..dd3aa41 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/actual-weights.json @@ -0,0 +1,47 @@ +{ + "edge_id": [ + 1336648, + 1336655, + 1337065, + 1467340, + 1467355, + 1467852, + 1559765, + 1559772, + 1560267, + 20992285, + 20992291, + 20992294, + 20992891 + ], + "weights_mv": [ + 57.75, + 47.300000000000004, + 28.6, + 71.22500000000001, + 64.625, + 17.6, + 62.150000000000006, + 77.825, + 19.25, + 26.125000000000004, + 15.675, + 20.900000000000002, + 11.825000000000001 + ], + "weights_volt": [ + 0.05775, + 0.0473, + 0.0286, + 0.07122500000000001, + 0.064625, + 0.0176, + 0.062150000000000004, + 0.077825, + 0.01925, + 0.026125000000000002, + 0.015675, + 0.020900000000000002, + 0.011825 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/brian-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/brian-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/completeness.csv new file mode 100644 index 0000000..9592749 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/completeness.csv @@ -0,0 +1,6 @@ +global_neuron_idx,local_index +1197,0 +1381,1 +1511,2 +82312,3 +133666,4 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/generated-code.json new file mode 100644 index 0000000..3117e6f --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/generated-code.json @@ -0,0 +1,119 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_4", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_6", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_6", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/run-spec.json new file mode 100644 index 0000000..69bef84 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/run-spec.json @@ -0,0 +1,132 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 1000.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + 1336648, + 1336655, + 1337065, + 1467340, + 1467355, + 1467852, + 1559765, + 1559772, + 1560267, + 20992285, + 20992291, + 20992294, + 20992891 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + 1197, + 1381, + 1511, + 82312, + 133666 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float64", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float64", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null + }, + "steps": 10000, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/schedule.json new file mode 100644 index 0000000..cd48c36 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/seed.json new file mode 100644 index 0000000..f164c97 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64-repeat/seed.json @@ -0,0 +1,5 @@ +{ + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/actual-weights.json new file mode 100644 index 0000000..dd3aa41 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/actual-weights.json @@ -0,0 +1,47 @@ +{ + "edge_id": [ + 1336648, + 1336655, + 1337065, + 1467340, + 1467355, + 1467852, + 1559765, + 1559772, + 1560267, + 20992285, + 20992291, + 20992294, + 20992891 + ], + "weights_mv": [ + 57.75, + 47.300000000000004, + 28.6, + 71.22500000000001, + 64.625, + 17.6, + 62.150000000000006, + 77.825, + 19.25, + 26.125000000000004, + 15.675, + 20.900000000000002, + 11.825000000000001 + ], + "weights_volt": [ + 0.05775, + 0.0473, + 0.0286, + 0.07122500000000001, + 0.064625, + 0.0176, + 0.062150000000000004, + 0.077825, + 0.01925, + 0.026125000000000002, + 0.015675, + 0.020900000000000002, + 0.011825 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/brian-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/brian-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/comparison.json new file mode 100644 index 0000000..9ae07c7 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 7.105427357601002e-15, + "mean_abs_mv": 3.552713678800501e-15, + "same_event_prefix_max_abs_mv": 7.105427357601002e-15, + "first_event_divergence_step": null, + "tolerance_mv": 1e-08, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/completeness.csv new file mode 100644 index 0000000..9592749 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/completeness.csv @@ -0,0 +1,6 @@ +global_neuron_idx,local_index +1197,0 +1381,1 +1511,2 +82312,3 +133666,4 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/generated-code.json new file mode 100644 index 0000000..264bb2c --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/generated-code.json @@ -0,0 +1,119 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_3", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_4", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/independent-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/independent-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/run-spec.json new file mode 100644 index 0000000..69bef84 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/run-spec.json @@ -0,0 +1,132 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 1000.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + 1336648, + 1336655, + 1337065, + 1467340, + 1467355, + 1467852, + 1559765, + 1559772, + 1560267, + 20992285, + 20992291, + 20992294, + 20992891 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + 1197, + 1381, + 1511, + 82312, + 133666 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float64", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float64", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null + }, + "steps": 10000, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/schedule.json new file mode 100644 index 0000000..cd48c36 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/seed.json new file mode 100644 index 0000000..f164c97 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/no_input-float64/seed.json @@ -0,0 +1,5 @@ +{ + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/actual-weights.json new file mode 100644 index 0000000..a4b7db2 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/actual-weights.json @@ -0,0 +1,14 @@ +{ + "edge_id": [ + 1467355, + 1559772 + ], + "weights_mv": [ + 64.625, + 77.82499694824219 + ], + "weights_volt": [ + 0.06462500244379044, + 0.07782500237226486 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/brian-output/events.csv new file mode 100644 index 0000000..19c96f7 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/brian-output/events.csv @@ -0,0 +1,214 @@ +step,neuron_idx +0,1381 +51,1511 +94,1381 +145,1511 +188,1381 +239,1511 +282,1381 +333,1511 +376,1381 +427,1511 +470,1381 +521,1511 +564,1381 +615,1511 +658,1381 +709,1511 +752,1381 +803,1511 +846,1381 +897,1511 +940,1381 +991,1511 +1034,1381 +1085,1511 +1128,1381 +1179,1511 +1222,1381 +1273,1511 +1316,1381 +1367,1511 +1410,1381 +1461,1511 +1504,1381 +1555,1511 +1598,1381 +1649,1511 +1692,1381 +1743,1511 +1786,1381 +1837,1511 +1880,1381 +1931,1511 +1974,1381 +2025,1511 +2068,1381 +2119,1511 +2162,1381 +2213,1511 +2256,1381 +2307,1511 +2350,1381 +2401,1511 +2444,1381 +2495,1511 +2538,1381 +2589,1511 +2632,1381 +2683,1511 +2726,1381 +2777,1511 +2820,1381 +2871,1511 +2914,1381 +2965,1511 +3008,1381 +3059,1511 +3102,1381 +3153,1511 +3196,1381 +3247,1511 +3290,1381 +3341,1511 +3384,1381 +3435,1511 +3478,1381 +3529,1511 +3572,1381 +3623,1511 +3666,1381 +3717,1511 +3760,1381 +3811,1511 +3854,1381 +3905,1511 +3948,1381 +3999,1511 +4042,1381 +4093,1511 +4136,1381 +4187,1511 +4230,1381 +4281,1511 +4324,1381 +4375,1511 +4418,1381 +4469,1511 +4512,1381 +4563,1511 +4606,1381 +4657,1511 +4700,1381 +4751,1511 +4794,1381 +4845,1511 +4888,1381 +4939,1511 +4982,1381 +5033,1511 +5076,1381 +5127,1511 +5170,1381 +5221,1511 +5264,1381 +5315,1511 +5358,1381 +5409,1511 +5452,1381 +5503,1511 +5546,1381 +5597,1511 +5640,1381 +5691,1511 +5734,1381 +5785,1511 +5828,1381 +5879,1511 +5922,1381 +5973,1511 +6016,1381 +6067,1511 +6110,1381 +6161,1511 +6204,1381 +6255,1511 +6298,1381 +6349,1511 +6392,1381 +6443,1511 +6486,1381 +6537,1511 +6580,1381 +6631,1511 +6674,1381 +6725,1511 +6768,1381 +6819,1511 +6862,1381 +6913,1511 +6956,1381 +7007,1511 +7050,1381 +7101,1511 +7144,1381 +7195,1511 +7238,1381 +7289,1511 +7332,1381 +7383,1511 +7426,1381 +7477,1511 +7520,1381 +7571,1511 +7614,1381 +7665,1511 +7708,1381 +7759,1511 +7802,1381 +7853,1511 +7896,1381 +7947,1511 +7990,1381 +8041,1511 +8084,1381 +8135,1511 +8178,1381 +8229,1511 +8272,1381 +8323,1511 +8366,1381 +8417,1511 +8460,1381 +8511,1511 +8554,1381 +8605,1511 +8648,1381 +8699,1511 +8742,1381 +8793,1511 +8836,1381 +8887,1511 +8930,1381 +8981,1511 +9024,1381 +9075,1511 +9118,1381 +9169,1511 +9212,1381 +9263,1511 +9306,1381 +9357,1511 +9400,1381 +9451,1511 +9494,1381 +9545,1511 +9588,1381 +9639,1511 +9682,1381 +9733,1511 +9776,1381 +9827,1511 +9870,1381 +9921,1511 +9964,1381 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/completeness.csv new file mode 100644 index 0000000..8ad30be --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/completeness.csv @@ -0,0 +1,3 @@ +global_neuron_idx,local_index +1381,0 +1511,1 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/generated-code.json new file mode 100644 index 0000000..245d070 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_9", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_9", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_9", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_9", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/run-spec.json new file mode 100644 index 0000000..5891b28 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/run-spec.json @@ -0,0 +1,118 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 1000.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + 1467355, + 1559772 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + 1381, + 1511 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float32", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float32", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": 1381 + }, + "steps": 10000, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/seed.json new file mode 100644 index 0000000..2896d59 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32-repeat/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -43.99999976158142, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": 1381, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/actual-weights.json new file mode 100644 index 0000000..a4b7db2 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/actual-weights.json @@ -0,0 +1,14 @@ +{ + "edge_id": [ + 1467355, + 1559772 + ], + "weights_mv": [ + 64.625, + 77.82499694824219 + ], + "weights_volt": [ + 0.06462500244379044, + 0.07782500237226486 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/brian-output/events.csv new file mode 100644 index 0000000..19c96f7 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/brian-output/events.csv @@ -0,0 +1,214 @@ +step,neuron_idx +0,1381 +51,1511 +94,1381 +145,1511 +188,1381 +239,1511 +282,1381 +333,1511 +376,1381 +427,1511 +470,1381 +521,1511 +564,1381 +615,1511 +658,1381 +709,1511 +752,1381 +803,1511 +846,1381 +897,1511 +940,1381 +991,1511 +1034,1381 +1085,1511 +1128,1381 +1179,1511 +1222,1381 +1273,1511 +1316,1381 +1367,1511 +1410,1381 +1461,1511 +1504,1381 +1555,1511 +1598,1381 +1649,1511 +1692,1381 +1743,1511 +1786,1381 +1837,1511 +1880,1381 +1931,1511 +1974,1381 +2025,1511 +2068,1381 +2119,1511 +2162,1381 +2213,1511 +2256,1381 +2307,1511 +2350,1381 +2401,1511 +2444,1381 +2495,1511 +2538,1381 +2589,1511 +2632,1381 +2683,1511 +2726,1381 +2777,1511 +2820,1381 +2871,1511 +2914,1381 +2965,1511 +3008,1381 +3059,1511 +3102,1381 +3153,1511 +3196,1381 +3247,1511 +3290,1381 +3341,1511 +3384,1381 +3435,1511 +3478,1381 +3529,1511 +3572,1381 +3623,1511 +3666,1381 +3717,1511 +3760,1381 +3811,1511 +3854,1381 +3905,1511 +3948,1381 +3999,1511 +4042,1381 +4093,1511 +4136,1381 +4187,1511 +4230,1381 +4281,1511 +4324,1381 +4375,1511 +4418,1381 +4469,1511 +4512,1381 +4563,1511 +4606,1381 +4657,1511 +4700,1381 +4751,1511 +4794,1381 +4845,1511 +4888,1381 +4939,1511 +4982,1381 +5033,1511 +5076,1381 +5127,1511 +5170,1381 +5221,1511 +5264,1381 +5315,1511 +5358,1381 +5409,1511 +5452,1381 +5503,1511 +5546,1381 +5597,1511 +5640,1381 +5691,1511 +5734,1381 +5785,1511 +5828,1381 +5879,1511 +5922,1381 +5973,1511 +6016,1381 +6067,1511 +6110,1381 +6161,1511 +6204,1381 +6255,1511 +6298,1381 +6349,1511 +6392,1381 +6443,1511 +6486,1381 +6537,1511 +6580,1381 +6631,1511 +6674,1381 +6725,1511 +6768,1381 +6819,1511 +6862,1381 +6913,1511 +6956,1381 +7007,1511 +7050,1381 +7101,1511 +7144,1381 +7195,1511 +7238,1381 +7289,1511 +7332,1381 +7383,1511 +7426,1381 +7477,1511 +7520,1381 +7571,1511 +7614,1381 +7665,1511 +7708,1381 +7759,1511 +7802,1381 +7853,1511 +7896,1381 +7947,1511 +7990,1381 +8041,1511 +8084,1381 +8135,1511 +8178,1381 +8229,1511 +8272,1381 +8323,1511 +8366,1381 +8417,1511 +8460,1381 +8511,1511 +8554,1381 +8605,1511 +8648,1381 +8699,1511 +8742,1381 +8793,1511 +8836,1381 +8887,1511 +8930,1381 +8981,1511 +9024,1381 +9075,1511 +9118,1381 +9169,1511 +9212,1381 +9263,1511 +9306,1381 +9357,1511 +9400,1381 +9451,1511 +9494,1381 +9545,1511 +9588,1381 +9639,1511 +9682,1381 +9733,1511 +9776,1381 +9827,1511 +9870,1381 +9921,1511 +9964,1381 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/comparison.json new file mode 100644 index 0000000..094f4af --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 2.41696834564209e-05, + "mean_abs_mv": 2.619914710521698e-06, + "same_event_prefix_max_abs_mv": 2.41696834564209e-05, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/completeness.csv new file mode 100644 index 0000000..8ad30be --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/completeness.csv @@ -0,0 +1,3 @@ +global_neuron_idx,local_index +1381,0 +1511,1 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/generated-code.json new file mode 100644 index 0000000..8a7e49d --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_8", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_8", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_8", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_8", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/independent-output/events.csv new file mode 100644 index 0000000..19c96f7 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/independent-output/events.csv @@ -0,0 +1,214 @@ +step,neuron_idx +0,1381 +51,1511 +94,1381 +145,1511 +188,1381 +239,1511 +282,1381 +333,1511 +376,1381 +427,1511 +470,1381 +521,1511 +564,1381 +615,1511 +658,1381 +709,1511 +752,1381 +803,1511 +846,1381 +897,1511 +940,1381 +991,1511 +1034,1381 +1085,1511 +1128,1381 +1179,1511 +1222,1381 +1273,1511 +1316,1381 +1367,1511 +1410,1381 +1461,1511 +1504,1381 +1555,1511 +1598,1381 +1649,1511 +1692,1381 +1743,1511 +1786,1381 +1837,1511 +1880,1381 +1931,1511 +1974,1381 +2025,1511 +2068,1381 +2119,1511 +2162,1381 +2213,1511 +2256,1381 +2307,1511 +2350,1381 +2401,1511 +2444,1381 +2495,1511 +2538,1381 +2589,1511 +2632,1381 +2683,1511 +2726,1381 +2777,1511 +2820,1381 +2871,1511 +2914,1381 +2965,1511 +3008,1381 +3059,1511 +3102,1381 +3153,1511 +3196,1381 +3247,1511 +3290,1381 +3341,1511 +3384,1381 +3435,1511 +3478,1381 +3529,1511 +3572,1381 +3623,1511 +3666,1381 +3717,1511 +3760,1381 +3811,1511 +3854,1381 +3905,1511 +3948,1381 +3999,1511 +4042,1381 +4093,1511 +4136,1381 +4187,1511 +4230,1381 +4281,1511 +4324,1381 +4375,1511 +4418,1381 +4469,1511 +4512,1381 +4563,1511 +4606,1381 +4657,1511 +4700,1381 +4751,1511 +4794,1381 +4845,1511 +4888,1381 +4939,1511 +4982,1381 +5033,1511 +5076,1381 +5127,1511 +5170,1381 +5221,1511 +5264,1381 +5315,1511 +5358,1381 +5409,1511 +5452,1381 +5503,1511 +5546,1381 +5597,1511 +5640,1381 +5691,1511 +5734,1381 +5785,1511 +5828,1381 +5879,1511 +5922,1381 +5973,1511 +6016,1381 +6067,1511 +6110,1381 +6161,1511 +6204,1381 +6255,1511 +6298,1381 +6349,1511 +6392,1381 +6443,1511 +6486,1381 +6537,1511 +6580,1381 +6631,1511 +6674,1381 +6725,1511 +6768,1381 +6819,1511 +6862,1381 +6913,1511 +6956,1381 +7007,1511 +7050,1381 +7101,1511 +7144,1381 +7195,1511 +7238,1381 +7289,1511 +7332,1381 +7383,1511 +7426,1381 +7477,1511 +7520,1381 +7571,1511 +7614,1381 +7665,1511 +7708,1381 +7759,1511 +7802,1381 +7853,1511 +7896,1381 +7947,1511 +7990,1381 +8041,1511 +8084,1381 +8135,1511 +8178,1381 +8229,1511 +8272,1381 +8323,1511 +8366,1381 +8417,1511 +8460,1381 +8511,1511 +8554,1381 +8605,1511 +8648,1381 +8699,1511 +8742,1381 +8793,1511 +8836,1381 +8887,1511 +8930,1381 +8981,1511 +9024,1381 +9075,1511 +9118,1381 +9169,1511 +9212,1381 +9263,1511 +9306,1381 +9357,1511 +9400,1381 +9451,1511 +9494,1381 +9545,1511 +9588,1381 +9639,1511 +9682,1381 +9733,1511 +9776,1381 +9827,1511 +9870,1381 +9921,1511 +9964,1381 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/run-spec.json new file mode 100644 index 0000000..5891b28 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/run-spec.json @@ -0,0 +1,118 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 1000.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + 1467355, + 1559772 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + 1381, + 1511 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float32", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float32", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": 1381 + }, + "steps": 10000, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/seed.json new file mode 100644 index 0000000..2896d59 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float32/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -43.99999976158142, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": 1381, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/actual-weights.json new file mode 100644 index 0000000..bbdf21e --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/actual-weights.json @@ -0,0 +1,14 @@ +{ + "edge_id": [ + 1467355, + 1559772 + ], + "weights_mv": [ + 64.625, + 77.825 + ], + "weights_volt": [ + 0.064625, + 0.077825 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/brian-output/events.csv new file mode 100644 index 0000000..19c96f7 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/brian-output/events.csv @@ -0,0 +1,214 @@ +step,neuron_idx +0,1381 +51,1511 +94,1381 +145,1511 +188,1381 +239,1511 +282,1381 +333,1511 +376,1381 +427,1511 +470,1381 +521,1511 +564,1381 +615,1511 +658,1381 +709,1511 +752,1381 +803,1511 +846,1381 +897,1511 +940,1381 +991,1511 +1034,1381 +1085,1511 +1128,1381 +1179,1511 +1222,1381 +1273,1511 +1316,1381 +1367,1511 +1410,1381 +1461,1511 +1504,1381 +1555,1511 +1598,1381 +1649,1511 +1692,1381 +1743,1511 +1786,1381 +1837,1511 +1880,1381 +1931,1511 +1974,1381 +2025,1511 +2068,1381 +2119,1511 +2162,1381 +2213,1511 +2256,1381 +2307,1511 +2350,1381 +2401,1511 +2444,1381 +2495,1511 +2538,1381 +2589,1511 +2632,1381 +2683,1511 +2726,1381 +2777,1511 +2820,1381 +2871,1511 +2914,1381 +2965,1511 +3008,1381 +3059,1511 +3102,1381 +3153,1511 +3196,1381 +3247,1511 +3290,1381 +3341,1511 +3384,1381 +3435,1511 +3478,1381 +3529,1511 +3572,1381 +3623,1511 +3666,1381 +3717,1511 +3760,1381 +3811,1511 +3854,1381 +3905,1511 +3948,1381 +3999,1511 +4042,1381 +4093,1511 +4136,1381 +4187,1511 +4230,1381 +4281,1511 +4324,1381 +4375,1511 +4418,1381 +4469,1511 +4512,1381 +4563,1511 +4606,1381 +4657,1511 +4700,1381 +4751,1511 +4794,1381 +4845,1511 +4888,1381 +4939,1511 +4982,1381 +5033,1511 +5076,1381 +5127,1511 +5170,1381 +5221,1511 +5264,1381 +5315,1511 +5358,1381 +5409,1511 +5452,1381 +5503,1511 +5546,1381 +5597,1511 +5640,1381 +5691,1511 +5734,1381 +5785,1511 +5828,1381 +5879,1511 +5922,1381 +5973,1511 +6016,1381 +6067,1511 +6110,1381 +6161,1511 +6204,1381 +6255,1511 +6298,1381 +6349,1511 +6392,1381 +6443,1511 +6486,1381 +6537,1511 +6580,1381 +6631,1511 +6674,1381 +6725,1511 +6768,1381 +6819,1511 +6862,1381 +6913,1511 +6956,1381 +7007,1511 +7050,1381 +7101,1511 +7144,1381 +7195,1511 +7238,1381 +7289,1511 +7332,1381 +7383,1511 +7426,1381 +7477,1511 +7520,1381 +7571,1511 +7614,1381 +7665,1511 +7708,1381 +7759,1511 +7802,1381 +7853,1511 +7896,1381 +7947,1511 +7990,1381 +8041,1511 +8084,1381 +8135,1511 +8178,1381 +8229,1511 +8272,1381 +8323,1511 +8366,1381 +8417,1511 +8460,1381 +8511,1511 +8554,1381 +8605,1511 +8648,1381 +8699,1511 +8742,1381 +8793,1511 +8836,1381 +8887,1511 +8930,1381 +8981,1511 +9024,1381 +9075,1511 +9118,1381 +9169,1511 +9212,1381 +9263,1511 +9306,1381 +9357,1511 +9400,1381 +9451,1511 +9494,1381 +9545,1511 +9588,1381 +9639,1511 +9682,1381 +9733,1511 +9776,1381 +9827,1511 +9870,1381 +9921,1511 +9964,1381 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/completeness.csv new file mode 100644 index 0000000..8ad30be --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/completeness.csv @@ -0,0 +1,3 @@ +global_neuron_idx,local_index +1381,0 +1511,1 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/generated-code.json new file mode 100644 index 0000000..a3090f6 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_7", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_7", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_7", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_7", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/run-spec.json new file mode 100644 index 0000000..196815b --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/run-spec.json @@ -0,0 +1,118 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 1000.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + 1467355, + 1559772 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + 1381, + 1511 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float64", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float64", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": 1381 + }, + "steps": 10000, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/seed.json new file mode 100644 index 0000000..37b8750 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64-repeat/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -44.0, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": 1381, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/actual-weights.json new file mode 100644 index 0000000..bbdf21e --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/actual-weights.json @@ -0,0 +1,14 @@ +{ + "edge_id": [ + 1467355, + 1559772 + ], + "weights_mv": [ + 64.625, + 77.825 + ], + "weights_volt": [ + 0.064625, + 0.077825 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/brian-output/events.csv new file mode 100644 index 0000000..19c96f7 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/brian-output/events.csv @@ -0,0 +1,214 @@ +step,neuron_idx +0,1381 +51,1511 +94,1381 +145,1511 +188,1381 +239,1511 +282,1381 +333,1511 +376,1381 +427,1511 +470,1381 +521,1511 +564,1381 +615,1511 +658,1381 +709,1511 +752,1381 +803,1511 +846,1381 +897,1511 +940,1381 +991,1511 +1034,1381 +1085,1511 +1128,1381 +1179,1511 +1222,1381 +1273,1511 +1316,1381 +1367,1511 +1410,1381 +1461,1511 +1504,1381 +1555,1511 +1598,1381 +1649,1511 +1692,1381 +1743,1511 +1786,1381 +1837,1511 +1880,1381 +1931,1511 +1974,1381 +2025,1511 +2068,1381 +2119,1511 +2162,1381 +2213,1511 +2256,1381 +2307,1511 +2350,1381 +2401,1511 +2444,1381 +2495,1511 +2538,1381 +2589,1511 +2632,1381 +2683,1511 +2726,1381 +2777,1511 +2820,1381 +2871,1511 +2914,1381 +2965,1511 +3008,1381 +3059,1511 +3102,1381 +3153,1511 +3196,1381 +3247,1511 +3290,1381 +3341,1511 +3384,1381 +3435,1511 +3478,1381 +3529,1511 +3572,1381 +3623,1511 +3666,1381 +3717,1511 +3760,1381 +3811,1511 +3854,1381 +3905,1511 +3948,1381 +3999,1511 +4042,1381 +4093,1511 +4136,1381 +4187,1511 +4230,1381 +4281,1511 +4324,1381 +4375,1511 +4418,1381 +4469,1511 +4512,1381 +4563,1511 +4606,1381 +4657,1511 +4700,1381 +4751,1511 +4794,1381 +4845,1511 +4888,1381 +4939,1511 +4982,1381 +5033,1511 +5076,1381 +5127,1511 +5170,1381 +5221,1511 +5264,1381 +5315,1511 +5358,1381 +5409,1511 +5452,1381 +5503,1511 +5546,1381 +5597,1511 +5640,1381 +5691,1511 +5734,1381 +5785,1511 +5828,1381 +5879,1511 +5922,1381 +5973,1511 +6016,1381 +6067,1511 +6110,1381 +6161,1511 +6204,1381 +6255,1511 +6298,1381 +6349,1511 +6392,1381 +6443,1511 +6486,1381 +6537,1511 +6580,1381 +6631,1511 +6674,1381 +6725,1511 +6768,1381 +6819,1511 +6862,1381 +6913,1511 +6956,1381 +7007,1511 +7050,1381 +7101,1511 +7144,1381 +7195,1511 +7238,1381 +7289,1511 +7332,1381 +7383,1511 +7426,1381 +7477,1511 +7520,1381 +7571,1511 +7614,1381 +7665,1511 +7708,1381 +7759,1511 +7802,1381 +7853,1511 +7896,1381 +7947,1511 +7990,1381 +8041,1511 +8084,1381 +8135,1511 +8178,1381 +8229,1511 +8272,1381 +8323,1511 +8366,1381 +8417,1511 +8460,1381 +8511,1511 +8554,1381 +8605,1511 +8648,1381 +8699,1511 +8742,1381 +8793,1511 +8836,1381 +8887,1511 +8930,1381 +8981,1511 +9024,1381 +9075,1511 +9118,1381 +9169,1511 +9212,1381 +9263,1511 +9306,1381 +9357,1511 +9400,1381 +9451,1511 +9494,1381 +9545,1511 +9588,1381 +9639,1511 +9682,1381 +9733,1511 +9776,1381 +9827,1511 +9870,1381 +9921,1511 +9964,1381 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/comparison.json new file mode 100644 index 0000000..18a335b --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 7.105427357601002e-14, + "mean_abs_mv": 8.832579112549865e-15, + "same_event_prefix_max_abs_mv": 7.105427357601002e-14, + "first_event_divergence_step": null, + "tolerance_mv": 1e-08, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/completeness.csv new file mode 100644 index 0000000..8ad30be --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/completeness.csv @@ -0,0 +1,3 @@ +global_neuron_idx,local_index +1381,0 +1511,1 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/generated-code.json new file mode 100644 index 0000000..8a7e49d --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_8", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_8", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_8", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_8", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/independent-output/events.csv new file mode 100644 index 0000000..19c96f7 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/independent-output/events.csv @@ -0,0 +1,214 @@ +step,neuron_idx +0,1381 +51,1511 +94,1381 +145,1511 +188,1381 +239,1511 +282,1381 +333,1511 +376,1381 +427,1511 +470,1381 +521,1511 +564,1381 +615,1511 +658,1381 +709,1511 +752,1381 +803,1511 +846,1381 +897,1511 +940,1381 +991,1511 +1034,1381 +1085,1511 +1128,1381 +1179,1511 +1222,1381 +1273,1511 +1316,1381 +1367,1511 +1410,1381 +1461,1511 +1504,1381 +1555,1511 +1598,1381 +1649,1511 +1692,1381 +1743,1511 +1786,1381 +1837,1511 +1880,1381 +1931,1511 +1974,1381 +2025,1511 +2068,1381 +2119,1511 +2162,1381 +2213,1511 +2256,1381 +2307,1511 +2350,1381 +2401,1511 +2444,1381 +2495,1511 +2538,1381 +2589,1511 +2632,1381 +2683,1511 +2726,1381 +2777,1511 +2820,1381 +2871,1511 +2914,1381 +2965,1511 +3008,1381 +3059,1511 +3102,1381 +3153,1511 +3196,1381 +3247,1511 +3290,1381 +3341,1511 +3384,1381 +3435,1511 +3478,1381 +3529,1511 +3572,1381 +3623,1511 +3666,1381 +3717,1511 +3760,1381 +3811,1511 +3854,1381 +3905,1511 +3948,1381 +3999,1511 +4042,1381 +4093,1511 +4136,1381 +4187,1511 +4230,1381 +4281,1511 +4324,1381 +4375,1511 +4418,1381 +4469,1511 +4512,1381 +4563,1511 +4606,1381 +4657,1511 +4700,1381 +4751,1511 +4794,1381 +4845,1511 +4888,1381 +4939,1511 +4982,1381 +5033,1511 +5076,1381 +5127,1511 +5170,1381 +5221,1511 +5264,1381 +5315,1511 +5358,1381 +5409,1511 +5452,1381 +5503,1511 +5546,1381 +5597,1511 +5640,1381 +5691,1511 +5734,1381 +5785,1511 +5828,1381 +5879,1511 +5922,1381 +5973,1511 +6016,1381 +6067,1511 +6110,1381 +6161,1511 +6204,1381 +6255,1511 +6298,1381 +6349,1511 +6392,1381 +6443,1511 +6486,1381 +6537,1511 +6580,1381 +6631,1511 +6674,1381 +6725,1511 +6768,1381 +6819,1511 +6862,1381 +6913,1511 +6956,1381 +7007,1511 +7050,1381 +7101,1511 +7144,1381 +7195,1511 +7238,1381 +7289,1511 +7332,1381 +7383,1511 +7426,1381 +7477,1511 +7520,1381 +7571,1511 +7614,1381 +7665,1511 +7708,1381 +7759,1511 +7802,1381 +7853,1511 +7896,1381 +7947,1511 +7990,1381 +8041,1511 +8084,1381 +8135,1511 +8178,1381 +8229,1511 +8272,1381 +8323,1511 +8366,1381 +8417,1511 +8460,1381 +8511,1511 +8554,1381 +8605,1511 +8648,1381 +8699,1511 +8742,1381 +8793,1511 +8836,1381 +8887,1511 +8930,1381 +8981,1511 +9024,1381 +9075,1511 +9118,1381 +9169,1511 +9212,1381 +9263,1511 +9306,1381 +9357,1511 +9400,1381 +9451,1511 +9494,1381 +9545,1511 +9588,1381 +9639,1511 +9682,1381 +9733,1511 +9776,1381 +9827,1511 +9870,1381 +9921,1511 +9964,1381 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/run-spec.json new file mode 100644 index 0000000..196815b --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/run-spec.json @@ -0,0 +1,118 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 1000.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + 1467355, + 1559772 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + 1381, + 1511 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float64", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float64", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": 1381 + }, + "steps": 10000, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/seed.json new file mode 100644 index 0000000..37b8750 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/pair-float64/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -44.0, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": 1381, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/poi-interface/audit.json b/registry/phase4ad-author-semantics/evidence/oracle/poi-interface/audit.json new file mode 100644 index 0000000..7b820ea --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/poi-interface/audit.json @@ -0,0 +1,76 @@ +{ + "gate": true, + "checks": { + "exact_author_source": true, + "one_poisson_input": true, + "initial_refractory_is_original": true, + "only_excited_target_loses_refractory": true, + "actual_voltage_interface": true, + "actual_N_one": true, + "actual_rate_150_hz": true, + "actual_weight_68_75_mv": true, + "actual_synapses_slot_order_zero": true, + "zero_elapsed_time": true, + "no_recorded_spikes": true, + "compile_preserves_voltage": true, + "compile_preserves_g": true, + "compile_preserves_weights": true, + "compile_preserves_refractory_configuration": true + }, + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "fixture": "two synthetic nodes, one raw_count=1 connection", + "nodes": [ + -2, + -1 + ], + "exc_local_indices": [ + 0 + ], + "exc2_local_indices": [], + "rfc_before_ms": [ + 2.2, + 2.2 + ], + "rfc_after_ms": [ + 0.0, + 2.2 + ], + "poisson_inputs": [ + { + "name": "poissoninput", + "type": "PoissonInput", + "target_group": "default_neurons_subgroup", + "target_local_start": 0, + "target_local_stop": 1, + "target_global_nodes": [ + -2 + ], + "target_var": "v", + "N": 1, + "rate_hz": 150.0, + "weight_mv": 68.75, + "weight_volt": 0.06875, + "when": "synapses", + "order": 0, + "dt_ms": 0.1, + "abstract_code": "v += poissoninput_binomial()*68.75 * mvolt", + "generated_code": [ + "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n _lio_1 = 68.75 * mvolt\n # vector code\n _vectorisation_idx = LazyArange(N)\n _sub_idx = _array_default_neurons_subgroup__sub_idx\n v = _array_default_neurons_v[_sub_idx]\n not_refractory = _array_default_neurons_not_refractory[_sub_idx]\n v[not_refractory] += _lio_1 * poissoninput_binomial(_vectorisation_idx[not_refractory])\n _array_default_neurons_v[_sub_idx] = v\n" + ] + } + ], + "synaptic_weight_mv": [ + 0.275 + ], + "input_hashes": { + "completeness.csv": "06e601b217fdbc48eee57eac01cc9a9fa649ec2a1810a2e212efcd3e4b632303", + "connectivity.parquet": "34f12d50889ccf2e637d913a0f3c4104d49032a6a67f9c3fbcd52e68ce95d701" + }, + "simulation_duration_ms": 0.0, + "stochastic_time_steps": 0, + "random_realization_tested": false, + "common_seed_experiment": false, + "interpretation": "Original poi adds 68.75 mV to voltage at 150 Hz with N=1 in the synapses slot and sets its target rfc to zero. This interface is not the common initial seed experiment.", + "scope": "Compile-time interface audit only; no stochastic trial, learning, or whole-brain simulation. The optional exc2 helper branch is not exercised." +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/poi-interface/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/poi-interface/completeness.csv new file mode 100644 index 0000000..3c4f3cb --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/poi-interface/completeness.csv @@ -0,0 +1,3 @@ +synthetic_global_neuron_idx,local_index +-2,0 +-1,1 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/poi-interface/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/poi-interface/environment.json new file mode 100644 index 0000000..76beec3 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/poi-interface/environment.json @@ -0,0 +1,102 @@ +{ + "python": "3.10.12", + "author_python": "3.10.11", + "python_patch_matches": false, + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "author_platform": "Windows", + "packages": { + "brian2": { + "expected": "2.5.1", + "actual": "2.5.1", + "matches": true + }, + "numpy": { + "expected": "1.22.3", + "actual": "1.22.3", + "matches": true + }, + "pandas": { + "expected": "1.4.3", + "actual": "1.4.3", + "matches": true + }, + "scipy": { + "expected": "1.8.1", + "actual": "1.8.1", + "matches": true + }, + "pyarrow": { + "expected": "11.0.0", + "actual": "11.0.0", + "matches": true + }, + "joblib": { + "expected": "1.2.0", + "actual": "1.2.0", + "matches": true + }, + "cython": { + "expected": "0.29.33", + "actual": "0.29.33", + "matches": true + }, + "jinja2": { + "expected": "2.11.3", + "actual": "2.11.3", + "matches": true + }, + "markupsafe": { + "expected": "1.1.1", + "actual": "1.1.1", + "matches": true + }, + "sympy": { + "expected": "1.12", + "actual": "1.12", + "matches": true + }, + "mpmath": { + "expected": "1.3.0", + "actual": "1.3.0", + "matches": true + }, + "pyparsing": { + "expected": "3.0.9", + "actual": "3.0.9", + "matches": true + }, + "packaging": { + "expected": "23.1", + "actual": "23.1", + "matches": true + }, + "setuptools": { + "expected": "67.8.0", + "actual": "67.8.0", + "matches": true + }, + "python-dateutil": { + "expected": "2.8.2", + "actual": "2.8.2", + "matches": true + }, + "pytz": { + "expected": "2023.3", + "actual": "2023.3", + "matches": true + }, + "six": { + "expected": "1.16.0", + "actual": "1.16.0", + "matches": true + }, + "wheel": { + "expected": "0.38.4", + "actual": "0.38.4", + "matches": true + } + }, + "all_package_pins_match": true, + "binary_identical_author_environment_claimed": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/poi-interface/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/poi-interface/generated-code.json new file mode 100644 index 0000000..748d439 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/poi-interface/generated-code.json @@ -0,0 +1,119 @@ +[ + { + "name": "default_neurons", + "type": "NeuronGroup", + "when": "start", + "order": 0, + "active": true, + "code_objects": [] + }, + { + "name": "default_synapses", + "type": "Synapses", + "when": "start", + "order": 0, + "active": true, + "code_objects": [] + }, + { + "name": "default_neurons_stateupdater", + "type": "StateUpdater", + "when": "groups", + "order": 0, + "active": true, + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "code_objects": [ + { + "name": "default_neurons_stateupdater_codeobject_7", + "type": "CallableProxyType", + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n" + } + ] + }, + { + "name": "default_neurons_spike_thresholder", + "type": "Thresholder", + "when": "thresholds", + "order": 0, + "active": true, + "abstract_code": "_cond = (v > v_th) and not_refractory", + "user_code": "_cond = v > v_th", + "code_objects": [ + { + "name": "default_neurons_spike_thresholder_codeobject_7", + "type": "CallableProxyType", + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n" + } + ] + }, + { + "name": "spikemonitor", + "type": "SpikeMonitor", + "when": "thresholds", + "order": 1, + "active": true, + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "user_code": "None", + "code_objects": [ + { + "name": "spikemonitor_codeobject", + "type": "CallableProxyType", + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n" + } + ] + }, + { + "name": "default_synapses_pre", + "type": "SynapticPathway", + "when": "synapses", + "order": -1, + "active": true, + "abstract_code": "g += w\n", + "user_code": "None", + "code_objects": [ + { + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType", + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n" + }, + { + "name": "default_synapses_pre_codeobject_7", + "type": "CallableProxyType", + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n" + } + ] + }, + { + "name": "poissoninput", + "type": "PoissonInput", + "when": "synapses", + "order": 0, + "active": true, + "abstract_code": "v += poissoninput_binomial()*68.75 * mvolt", + "user_code": "", + "code_objects": [ + { + "name": "poissoninput_codeobject", + "type": "CallableProxyType", + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n _lio_1 = 68.75 * mvolt\n # vector code\n _vectorisation_idx = LazyArange(N)\n _sub_idx = _array_default_neurons_subgroup__sub_idx\n v = _array_default_neurons_v[_sub_idx]\n not_refractory = _array_default_neurons_not_refractory[_sub_idx]\n v[not_refractory] += _lio_1 * poissoninput_binomial(_vectorisation_idx[not_refractory])\n _array_default_neurons_v[_sub_idx] = v\n" + } + ] + }, + { + "name": "default_neurons_spike_resetter", + "type": "Resetter", + "when": "resets", + "order": 0, + "active": true, + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "user_code": "None", + "code_objects": [ + { + "name": "default_neurons_spike_resetter_codeobject_7", + "type": "CallableProxyType", + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n" + } + ] + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/poi-interface/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/poi-interface/schedule.json new file mode 100644 index 0000000..f3c3699 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/poi-interface/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+-------------------------------------+----------------------+------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \npoissoninput (PoissonInput) | default_neurons_subgroup (Subgroup) | 100. us (every step) | synapses | 0 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/actual-weights.json new file mode 100644 index 0000000..e7e6a10 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/actual-weights.json @@ -0,0 +1,26 @@ +{ + "edge_id": [ + 1336648, + 1336655, + 1467340, + 1467355, + 1559765, + 1559772 + ], + "weights_mv": [ + 57.75, + 47.29999923706055, + 71.2249984741211, + 64.625, + 62.14999771118164, + 77.82499694824219 + ], + "weights_volt": [ + 0.057750001549720764, + 0.04729999974370003, + 0.07122500240802765, + 0.06462500244379044, + 0.062150001525878906, + 0.07782500237226486 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/brian-output/events.csv new file mode 100644 index 0000000..0b32adf --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/brian-output/events.csv @@ -0,0 +1,449 @@ +step,neuron_idx +0,1381 +46,1197 +51,1511 +79,1381 +99,1197 +122,1511 +144,1381 +166,1197 +188,1511 +211,1381 +233,1197 +255,1511 +278,1381 +300,1197 +322,1511 +345,1381 +367,1197 +389,1511 +412,1381 +434,1197 +456,1511 +479,1381 +501,1197 +523,1511 +546,1381 +568,1197 +590,1511 +613,1381 +635,1197 +657,1511 +680,1381 +702,1197 +724,1511 +747,1381 +769,1197 +791,1511 +814,1381 +836,1197 +858,1511 +881,1381 +903,1197 +925,1511 +948,1381 +970,1197 +992,1511 +1015,1381 +1037,1197 +1059,1511 +1082,1381 +1104,1197 +1126,1511 +1149,1381 +1171,1197 +1193,1511 +1216,1381 +1238,1197 +1260,1511 +1283,1381 +1305,1197 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+9457,1381 +9479,1197 +9501,1511 +9524,1381 +9546,1197 +9568,1511 +9591,1381 +9613,1197 +9635,1511 +9658,1381 +9680,1197 +9702,1511 +9725,1381 +9747,1197 +9769,1511 +9792,1381 +9814,1197 +9836,1511 +9859,1381 +9881,1197 +9903,1511 +9926,1381 +9948,1197 +9970,1511 +9993,1381 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/completeness.csv new file mode 100644 index 0000000..38343a0 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/completeness.csv @@ -0,0 +1,4 @@ +global_neuron_idx,local_index +1197,0 +1381,1 +1511,2 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/generated-code.json new file mode 100644 index 0000000..9dbc8f9 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_1", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/run-spec.json new file mode 100644 index 0000000..01c0515 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/run-spec.json @@ -0,0 +1,123 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 1000.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + 1336648, + 1336655, + 1467340, + 1467355, + 1559765, + 1559772 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + 1197, + 1381, + 1511 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float32", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float32", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": 1381 + }, + "steps": 10000, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/seed.json new file mode 100644 index 0000000..2896d59 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32-repeat/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -43.99999976158142, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": 1381, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/actual-weights.json new file mode 100644 index 0000000..e7e6a10 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/actual-weights.json @@ -0,0 +1,26 @@ +{ + "edge_id": [ + 1336648, + 1336655, + 1467340, + 1467355, + 1559765, + 1559772 + ], + "weights_mv": [ + 57.75, + 47.29999923706055, + 71.2249984741211, + 64.625, + 62.14999771118164, + 77.82499694824219 + ], + "weights_volt": [ + 0.057750001549720764, + 0.04729999974370003, + 0.07122500240802765, + 0.06462500244379044, + 0.062150001525878906, + 0.07782500237226486 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/brian-output/events.csv new file mode 100644 index 0000000..0b32adf --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/brian-output/events.csv @@ -0,0 +1,449 @@ +step,neuron_idx +0,1381 +46,1197 +51,1511 +79,1381 +99,1197 +122,1511 +144,1381 +166,1197 +188,1511 +211,1381 +233,1197 +255,1511 +278,1381 +300,1197 +322,1511 +345,1381 +367,1197 +389,1511 +412,1381 +434,1197 +456,1511 +479,1381 +501,1197 +523,1511 +546,1381 +568,1197 +590,1511 +613,1381 +635,1197 +657,1511 +680,1381 +702,1197 +724,1511 +747,1381 +769,1197 +791,1511 +814,1381 +836,1197 +858,1511 +881,1381 +903,1197 +925,1511 +948,1381 +970,1197 +992,1511 +1015,1381 +1037,1197 +1059,1511 +1082,1381 +1104,1197 +1126,1511 +1149,1381 +1171,1197 +1193,1511 +1216,1381 +1238,1197 +1260,1511 +1283,1381 +1305,1197 +1327,1511 +1350,1381 +1372,1197 +1394,1511 +1417,1381 +1439,1197 +1461,1511 +1484,1381 +1506,1197 +1528,1511 +1551,1381 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+9702,1511 +9725,1381 +9747,1197 +9769,1511 +9792,1381 +9814,1197 +9836,1511 +9859,1381 +9881,1197 +9903,1511 +9926,1381 +9948,1197 +9970,1511 +9993,1381 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/comparison.json new file mode 100644 index 0000000..fb4ff98 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 4.25875186920166e-05, + "mean_abs_mv": 3.7165323893229165e-06, + "same_event_prefix_max_abs_mv": 4.25875186920166e-05, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/completeness.csv new file mode 100644 index 0000000..38343a0 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/completeness.csv @@ -0,0 +1,4 @@ +global_neuron_idx,local_index +1197,0 +1381,1 +1511,2 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/generated-code.json new file mode 100644 index 0000000..dd576cc --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_1", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_1", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_1", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/independent-output/events.csv new file mode 100644 index 0000000..0b32adf --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/independent-output/events.csv @@ -0,0 +1,449 @@ +step,neuron_idx +0,1381 +46,1197 +51,1511 +79,1381 +99,1197 +122,1511 +144,1381 +166,1197 +188,1511 +211,1381 +233,1197 +255,1511 +278,1381 +300,1197 +322,1511 +345,1381 +367,1197 +389,1511 +412,1381 +434,1197 +456,1511 +479,1381 +501,1197 +523,1511 +546,1381 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"91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 1000.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + 1336648, + 1336655, + 1467340, + 1467355, + 1559765, + 1559772 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + 1197, + 1381, + 1511 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float32", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float32", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": 1381 + }, + "steps": 10000, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/seed.json new file mode 100644 index 0000000..2896d59 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float32/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -43.99999976158142, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": 1381, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/actual-weights.json new file mode 100644 index 0000000..bbab456 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/actual-weights.json @@ -0,0 +1,26 @@ +{ + "edge_id": [ + 1336648, + 1336655, + 1467340, + 1467355, + 1559765, + 1559772 + ], + "weights_mv": [ + 57.75, + 47.300000000000004, + 71.22500000000001, + 64.625, + 62.150000000000006, + 77.825 + ], + "weights_volt": [ + 0.05775, + 0.0473, + 0.07122500000000001, + 0.064625, + 0.062150000000000004, + 0.077825 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/brian-output/events.csv new file mode 100644 index 0000000..0b32adf --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/brian-output/events.csv @@ -0,0 +1,449 @@ +step,neuron_idx +0,1381 +46,1197 +51,1511 +79,1381 +99,1197 +122,1511 +144,1381 +166,1197 +188,1511 +211,1381 +233,1197 +255,1511 +278,1381 +300,1197 +322,1511 +345,1381 +367,1197 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b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/completeness.csv @@ -0,0 +1,4 @@ +global_neuron_idx,local_index +1197,0 +1381,1 +1511,2 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/generated-code.json new file mode 100644 index 0000000..dd576cc --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_1", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_1", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_1", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/run-spec.json new file mode 100644 index 0000000..e95601e --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/run-spec.json @@ -0,0 +1,123 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 1000.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + 1336648, + 1336655, + 1467340, + 1467355, + 1559765, + 1559772 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + 1197, + 1381, + 1511 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float64", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float64", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": 1381 + }, + "steps": 10000, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/seed.json new file mode 100644 index 0000000..37b8750 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64-repeat/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -44.0, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": 1381, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/actual-weights.json new file mode 100644 index 0000000..bbab456 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/actual-weights.json @@ -0,0 +1,26 @@ +{ + "edge_id": [ + 1336648, + 1336655, + 1467340, + 1467355, + 1559765, + 1559772 + ], + "weights_mv": [ + 57.75, + 47.300000000000004, + 71.22500000000001, + 64.625, + 62.150000000000006, + 77.825 + ], + "weights_volt": [ + 0.05775, + 0.0473, + 0.07122500000000001, + 0.064625, + 0.062150000000000004, + 0.077825 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/brian-output/events.csv new file mode 100644 index 0000000..0b32adf --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/brian-output/events.csv @@ -0,0 +1,449 @@ +step,neuron_idx +0,1381 +46,1197 +51,1511 +79,1381 +99,1197 +122,1511 +144,1381 +166,1197 +188,1511 +211,1381 +233,1197 +255,1511 +278,1381 +300,1197 +322,1511 +345,1381 +367,1197 +389,1511 +412,1381 +434,1197 +456,1511 +479,1381 +501,1197 +523,1511 +546,1381 +568,1197 +590,1511 +613,1381 +635,1197 +657,1511 +680,1381 +702,1197 +724,1511 +747,1381 +769,1197 +791,1511 +814,1381 +836,1197 +858,1511 +881,1381 +903,1197 +925,1511 +948,1381 +970,1197 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+9122,1381 +9144,1197 +9166,1511 +9189,1381 +9211,1197 +9233,1511 +9256,1381 +9278,1197 +9300,1511 +9323,1381 +9345,1197 +9367,1511 +9390,1381 +9412,1197 +9434,1511 +9457,1381 +9479,1197 +9501,1511 +9524,1381 +9546,1197 +9568,1511 +9591,1381 +9613,1197 +9635,1511 +9658,1381 +9680,1197 +9702,1511 +9725,1381 +9747,1197 +9769,1511 +9792,1381 +9814,1197 +9836,1511 +9859,1381 +9881,1197 +9903,1511 +9926,1381 +9948,1197 +9970,1511 +9993,1381 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/comparison.json new file mode 100644 index 0000000..d25c05c --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 8.526512829121202e-14, + "mean_abs_mv": 8.113095380698118e-15, + "same_event_prefix_max_abs_mv": 8.526512829121202e-14, + "first_event_divergence_step": null, + "tolerance_mv": 1e-08, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/completeness.csv new file mode 100644 index 0000000..38343a0 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/completeness.csv @@ -0,0 +1,4 @@ +global_neuron_idx,local_index +1197,0 +1381,1 +1511,2 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/generated-code.json new file mode 100644 index 0000000..70b0317 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_8", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/independent-output/events.csv new file mode 100644 index 0000000..0b32adf --- /dev/null +++ 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+9993,1381 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/run-spec.json new file mode 100644 index 0000000..e95601e --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/run-spec.json @@ -0,0 +1,123 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 1000.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + 1336648, + 1336655, + 1467340, + 1467355, + 1559765, + 1559772 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + 1197, + 1381, + 1511 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float64", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float64", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": 1381 + }, + "steps": 10000, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/seed.json new file mode 100644 index 0000000..37b8750 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/trio-float64/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -44.0, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": 1381, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/actual-weights.json new file mode 100644 index 0000000..14b16bb --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/actual-weights.json @@ -0,0 +1,11 @@ +{ + "edge_id": [ + -1 + ], + "weights_mv": [ + 0.0 + ], + "weights_volt": [ + 0.0 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/brian-output/events.csv new file mode 100644 index 0000000..9ecbb05 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/brian-output/events.csv @@ -0,0 +1,2 @@ +step,neuron_idx +0,-1 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/comparison.json new file mode 100644 index 0000000..a9e3395 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 1.0728836059570312e-06, + "mean_abs_mv": 5.364418029785156e-07, + "same_event_prefix_max_abs_mv": 1.0728836059570312e-06, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/completeness.csv new file mode 100644 index 0000000..f05fab6 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/completeness.csv @@ -0,0 +1,2 @@ +global_neuron_idx,local_index +-1,0 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/external-arrivals.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/external-arrivals.csv new file mode 100644 index 0000000..1d42707 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/external-arrivals.csv @@ -0,0 +1 @@ +tick,neuron_idx,requested_mv diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/generated-code.json new file mode 100644 index 0000000..8a7e49d --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_8", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_8", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_8", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_8", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/independent-output/events.csv new file mode 100644 index 0000000..9ecbb05 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/independent-output/events.csv @@ -0,0 +1,2 @@ +step,neuron_idx +0,-1 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/run-spec.json new file mode 100644 index 0000000..c607022 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/run-spec.json @@ -0,0 +1,116 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 20.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + -1 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + -1 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float32", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float32", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": -1 + }, + "steps": 200, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/seed.json new file mode 100644 index 0000000..d7e5e06 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float32/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -43.99999976158142, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": -1, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/actual-weights.json new file mode 100644 index 0000000..14b16bb --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/actual-weights.json @@ -0,0 +1,11 @@ +{ + "edge_id": [ + -1 + ], + "weights_mv": [ + 0.0 + ], + "weights_volt": [ + 0.0 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/brian-output/events.csv new file mode 100644 index 0000000..9ecbb05 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/brian-output/events.csv @@ -0,0 +1,2 @@ +step,neuron_idx +0,-1 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/comparison.json new file mode 100644 index 0000000..9ae07c7 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 7.105427357601002e-15, + "mean_abs_mv": 3.552713678800501e-15, + "same_event_prefix_max_abs_mv": 7.105427357601002e-15, + "first_event_divergence_step": null, + "tolerance_mv": 1e-08, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/completeness.csv new file mode 100644 index 0000000..f05fab6 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/completeness.csv @@ -0,0 +1,2 @@ +global_neuron_idx,local_index +-1,0 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/external-arrivals.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/external-arrivals.csv new file mode 100644 index 0000000..1d42707 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/external-arrivals.csv @@ -0,0 +1 @@ +tick,neuron_idx,requested_mv diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/generated-code.json new file mode 100644 index 0000000..80cfaca --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_4", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_4", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_4", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_4", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/independent-output/events.csv new file mode 100644 index 0000000..9ecbb05 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/independent-output/events.csv @@ -0,0 +1,2 @@ +step,neuron_idx +0,-1 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/run-spec.json new file mode 100644 index 0000000..9e9954f --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/run-spec.json @@ -0,0 +1,116 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 20.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + -1 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + -1 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float64", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float64", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": -1 + }, + "steps": 200, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/seed.json new file mode 100644 index 0000000..d555d7c --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-above_threshold-float64/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -44.0, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": -1, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/actual-weights.json new file mode 100644 index 0000000..6b13b96 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/actual-weights.json @@ -0,0 +1,11 @@ +{ + "edge_id": [ + -1 + ], + "weights_mv": [ + 0.2749999761581421 + ], + "weights_volt": [ + 0.0002749999985098839 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/brian-output/events.csv new file mode 100644 index 0000000..ef5e951 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/brian-output/events.csv @@ -0,0 +1,2 @@ +step,neuron_idx +0,-2 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/comparison.json new file mode 100644 index 0000000..dd6790e --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.0001220405101776123, + "mean_abs_mv": 1.6799908344182768e-05, + "same_event_prefix_max_abs_mv": 0.0001220405101776123, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/completeness.csv new file mode 100644 index 0000000..4cf89ed --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/completeness.csv @@ -0,0 +1,3 @@ +global_neuron_idx,local_index +-2,0 +-1,1 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/generated-code.json new file mode 100644 index 0000000..92dd789 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_6", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_6", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/independent-output/events.csv new file mode 100644 index 0000000..ef5e951 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/independent-output/events.csv @@ -0,0 +1,2 @@ +step,neuron_idx +0,-2 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/run-spec.json new file mode 100644 index 0000000..ee9edfa --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/run-spec.json @@ -0,0 +1,117 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 20.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + -1 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + -2, + -1 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float32", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float32", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": -2 + }, + "steps": 200, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/seed.json new file mode 100644 index 0000000..c8c80fa --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float32/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -43.99999976158142, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": -2, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/actual-weights.json new file mode 100644 index 0000000..bc37d47 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/actual-weights.json @@ -0,0 +1,11 @@ +{ + "edge_id": [ + -1 + ], + "weights_mv": [ + 0.275 + ], + "weights_volt": [ + 0.000275 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/brian-output/events.csv new file mode 100644 index 0000000..ef5e951 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/brian-output/events.csv @@ -0,0 +1,2 @@ +step,neuron_idx +0,-2 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/comparison.json new file mode 100644 index 0000000..cc8585b --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 2.3447910280083306e-13, + "mean_abs_mv": 3.262299068038099e-14, + "same_event_prefix_max_abs_mv": 2.3447910280083306e-13, + "first_event_divergence_step": null, + "tolerance_mv": 1e-08, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/completeness.csv new file mode 100644 index 0000000..4cf89ed --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/completeness.csv @@ -0,0 +1,3 @@ +global_neuron_idx,local_index +-2,0 +-1,1 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/generated-code.json new file mode 100644 index 0000000..163e724 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_3", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_3", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/independent-output/events.csv new file mode 100644 index 0000000..ef5e951 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/independent-output/events.csv @@ -0,0 +1,2 @@ +step,neuron_idx +0,-2 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/run-spec.json new file mode 100644 index 0000000..8c5203e --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/run-spec.json @@ -0,0 +1,117 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 20.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + -1 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + -2, + -1 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float64", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float64", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": -2 + }, + "steps": 200, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/seed.json new file mode 100644 index 0000000..67dbaa0 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-delay_18-float64/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -44.0, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": -2, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/actual-weights.json new file mode 100644 index 0000000..14b16bb --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/actual-weights.json @@ -0,0 +1,11 @@ +{ + "edge_id": [ + -1 + ], + "weights_mv": [ + 0.0 + ], + "weights_volt": [ + 0.0 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/brian-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/brian-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/comparison.json new file mode 100644 index 0000000..9f8c75d --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.00012242794036865234, + "mean_abs_mv": 3.6822035908699036e-05, + "same_event_prefix_max_abs_mv": 0.00012242794036865234, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/completeness.csv new file mode 100644 index 0000000..f05fab6 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/completeness.csv @@ -0,0 +1,2 @@ +global_neuron_idx,local_index +-1,0 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/external-arrivals.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/external-arrivals.csv new file mode 100644 index 0000000..1d42707 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/external-arrivals.csv @@ -0,0 +1 @@ +tick,neuron_idx,requested_mv diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/generated-code.json new file mode 100644 index 0000000..a3090f6 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_7", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_7", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_7", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_7", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/independent-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/independent-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/run-spec.json new file mode 100644 index 0000000..25e8979 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/run-spec.json @@ -0,0 +1,116 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 20.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 0.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + -1 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + -1 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float32", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float32", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 0.0, + "requested_global_node": -1 + }, + "steps": 200, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/seed.json new file mode 100644 index 0000000..0672c09 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float32/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -45.00000178813934, + "injections": 1, + "margin_mv": 0.0, + "requested_global_node": -1, + "spiked_at_zero": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/actual-weights.json new file mode 100644 index 0000000..14b16bb --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/actual-weights.json @@ -0,0 +1,11 @@ +{ + "edge_id": [ + -1 + ], + "weights_mv": [ + 0.0 + ], + "weights_volt": [ + 0.0 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/brian-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/brian-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/comparison.json new file mode 100644 index 0000000..233ba94 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 2.2026824808563106e-13, + "mean_abs_mv": 5.400124791776761e-14, + "same_event_prefix_max_abs_mv": 2.2026824808563106e-13, + "first_event_divergence_step": null, + "tolerance_mv": 1e-08, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/completeness.csv new file mode 100644 index 0000000..f05fab6 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/completeness.csv @@ -0,0 +1,2 @@ +global_neuron_idx,local_index +-1,0 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/external-arrivals.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/external-arrivals.csv new file mode 100644 index 0000000..1d42707 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/external-arrivals.csv @@ -0,0 +1 @@ +tick,neuron_idx,requested_mv diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/generated-code.json new file mode 100644 index 0000000..163e724 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/generated-code.json @@ -0,0 +1,127 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_3", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_3", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/independent-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/independent-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/run-spec.json new file mode 100644 index 0000000..525e6ff --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/run-spec.json @@ -0,0 +1,116 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 20.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 0.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + -1 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + -1 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float64", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float64", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 0.0, + "requested_global_node": -1 + }, + "steps": 200, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/schedule.json new file mode 100644 index 0000000..82854df --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/seed.json new file mode 100644 index 0000000..8bbb596 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-equal_threshold-float64/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -45.0, + "injections": 1, + "margin_mv": 0.0, + "requested_global_node": -1, + "spiked_at_zero": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/actual-weights.json new file mode 100644 index 0000000..14b16bb --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/actual-weights.json @@ -0,0 +1,11 @@ +{ + "edge_id": [ + -1 + ], + "weights_mv": [ + 0.0 + ], + "weights_volt": [ + 0.0 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/brian-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/brian-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/comparison.json new file mode 100644 index 0000000..51baee3 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.00011596083641052246, + "mean_abs_mv": 3.622157426434569e-05, + "same_event_prefix_max_abs_mv": 0.00011596083641052246, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/completeness.csv new file mode 100644 index 0000000..f05fab6 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/completeness.csv @@ -0,0 +1,2 @@ +global_neuron_idx,local_index +-1,0 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/external-arrivals.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/external-arrivals.csv new file mode 100644 index 0000000..ce577a4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/external-arrivals.csv @@ -0,0 +1,2 @@ +tick,neuron_idx,requested_mv +0,-1,-1.0 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/generated-code.json new file mode 100644 index 0000000..8924072 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/generated-code.json @@ -0,0 +1,164 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "zz_external_arrivals", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_6", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_6", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _the_period = _array_zz_external_sources__period_bins[0]\n _timebin = _array_defaultclock_timestep[0]\n _n_spikes = 0\n _lastindex_before = _array_zz_external_sources__lastindex[0]\n if _the_period > 0:\n _timebin %= _the_period\n # If there is a periodicity in the SpikeGenerator, we need to reset the\n # lastindex when the period has passed\n if _lastindex_before > 0 and _array_zz_external_sources__timebins[_lastindex_before - 1] >= _timebin:\n _lastindex_before = 0\n _n_spikes = _numpy.searchsorted(_array_zz_external_sources__timebins[_lastindex_before:],\n _timebin, side='right')\n _array_zz_external_sources__lastindex[0] = _lastindex_before + _n_spikes\n _indices = _array_zz_external_sources_neuron_index[_lastindex_before:_lastindex_before+_n_spikes]\n _array_zz_external_sources__spikespace[:_n_spikes] = _indices\n _array_zz_external_sources__spikespace[-1] = _n_spikes\n", + "name": "zz_external_sources_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "zz_external_sources", + "order": 0, + "type": "SpikeGeneratorGroup", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "g_post += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "zz_external_arrivals_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g_post += w\n _postsynaptic_idx = _array_zz_external_arrivals__synaptic_post[_idx]\n w = _array_zz_external_arrivals_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "zz_external_arrivals_pre_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "zz_external_arrivals_pre", + "order": 0, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/independent-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/independent-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/run-spec.json new file mode 100644 index 0000000..eb59eb5 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/run-spec.json @@ -0,0 +1,120 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 20.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + -1 + ], + "external_arrivals": { + "actual_weights_mv": [ + -1.0 + ], + "events": 1, + "ordering": "after default_synapses.pre", + "pathway_order": 0 + }, + "internal_voltage_unit": "volt", + "nodes": [ + -1 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float32", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float32", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null + }, + "steps": 200, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/schedule.json new file mode 100644 index 0000000..2ca6fb3 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+-------------------------------------------+----------------------+------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nzz_external_sources (SpikeGeneratorGroup) | zz_external_sources (SpikeGeneratorGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \nzz_external_arrivals_pre (SynapticPathway) | zz_external_arrivals (Synapses) | 100. us (every step) | synapses | 0 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/seed.json new file mode 100644 index 0000000..f164c97 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float32/seed.json @@ -0,0 +1,5 @@ +{ + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/actual-weights.json new file mode 100644 index 0000000..14b16bb --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/actual-weights.json @@ -0,0 +1,11 @@ +{ + "edge_id": [ + -1 + ], + "weights_mv": [ + 0.0 + ], + "weights_volt": [ + 0.0 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/brian-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/brian-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/comparison.json new file mode 100644 index 0000000..aa74528 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 2.4158453015843406e-13, + "mean_abs_mv": 7.103867841196099e-14, + "same_event_prefix_max_abs_mv": 2.4158453015843406e-13, + "first_event_divergence_step": null, + "tolerance_mv": 1e-08, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/completeness.csv new file mode 100644 index 0000000..f05fab6 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/completeness.csv @@ -0,0 +1,2 @@ +global_neuron_idx,local_index +-1,0 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/external-arrivals.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/external-arrivals.csv new file mode 100644 index 0000000..ce577a4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/external-arrivals.csv @@ -0,0 +1,2 @@ +tick,neuron_idx,requested_mv +0,-1,-1.0 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/generated-code.json new file mode 100644 index 0000000..f7e50b7 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/generated-code.json @@ -0,0 +1,164 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "zz_external_arrivals", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _the_period = _array_zz_external_sources__period_bins[0]\n _timebin = _array_defaultclock_timestep[0]\n _n_spikes = 0\n _lastindex_before = _array_zz_external_sources__lastindex[0]\n if _the_period > 0:\n _timebin %= _the_period\n # If there is a periodicity in the SpikeGenerator, we need to reset the\n # lastindex when the period has passed\n if _lastindex_before > 0 and _array_zz_external_sources__timebins[_lastindex_before - 1] >= _timebin:\n _lastindex_before = 0\n _n_spikes = _numpy.searchsorted(_array_zz_external_sources__timebins[_lastindex_before:],\n _timebin, side='right')\n _array_zz_external_sources__lastindex[0] = _lastindex_before + _n_spikes\n _indices = _array_zz_external_sources_neuron_index[_lastindex_before:_lastindex_before+_n_spikes]\n _array_zz_external_sources__spikespace[:_n_spikes] = _indices\n _array_zz_external_sources__spikespace[-1] = _n_spikes\n", + "name": "zz_external_sources_codeobject_1", + "type": "CallableProxyType" + } + ], + "name": "zz_external_sources", + "order": 0, + "type": "SpikeGeneratorGroup", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "g_post += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "zz_external_arrivals_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g_post += w\n _postsynaptic_idx = _array_zz_external_arrivals__synaptic_post[_idx]\n w = _array_zz_external_arrivals_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "zz_external_arrivals_pre_codeobject_1", + "type": "CallableProxyType" + } + ], + "name": "zz_external_arrivals_pre", + "order": 0, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/independent-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/independent-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/run-spec.json new file mode 100644 index 0000000..a21409e --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/run-spec.json @@ -0,0 +1,120 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 20.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + -1 + ], + "external_arrivals": { + "actual_weights_mv": [ + -1.0 + ], + "events": 1, + "ordering": "after default_synapses.pre", + "pathway_order": 0 + }, + "internal_voltage_unit": "volt", + "nodes": [ + -1 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float64", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float64", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null + }, + "steps": 200, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/schedule.json new file mode 100644 index 0000000..2ca6fb3 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+-------------------------------------------+----------------------+------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nzz_external_sources (SpikeGeneratorGroup) | zz_external_sources (SpikeGeneratorGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \nzz_external_arrivals_pre (SynapticPathway) | zz_external_arrivals (Synapses) | 100. us (every step) | synapses | 0 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/seed.json new file mode 100644 index 0000000..f164c97 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-inhibition-float64/seed.json @@ -0,0 +1,5 @@ +{ + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/actual-weights.json new file mode 100644 index 0000000..14b16bb --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/actual-weights.json @@ -0,0 +1,11 @@ +{ + "edge_id": [ + -1 + ], + "weights_mv": [ + 0.0 + ], + "weights_volt": [ + 0.0 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/brian-output/events.csv new file mode 100644 index 0000000..5cb39e0 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/brian-output/events.csv @@ -0,0 +1,2 @@ +step,neuron_idx +1,-1 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/comparison.json new file mode 100644 index 0000000..1bdb12a --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.0001220703125, + "mean_abs_mv": 8.416175842285156e-07, + "same_event_prefix_max_abs_mv": 0.0001220703125, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/completeness.csv new file mode 100644 index 0000000..f05fab6 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/completeness.csv @@ -0,0 +1,2 @@ +global_neuron_idx,local_index +-1,0 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/external-arrivals.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/external-arrivals.csv new file mode 100644 index 0000000..399fc7a --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/external-arrivals.csv @@ -0,0 +1,2 @@ +tick,neuron_idx,requested_mv +0,-1,2000.0 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/generated-code.json new file mode 100644 index 0000000..c16007d --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/generated-code.json @@ -0,0 +1,164 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "zz_external_arrivals", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_9", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_9", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _the_period = _array_zz_external_sources__period_bins[0]\n _timebin = _array_defaultclock_timestep[0]\n _n_spikes = 0\n _lastindex_before = _array_zz_external_sources__lastindex[0]\n if _the_period > 0:\n _timebin %= _the_period\n # If there is a periodicity in the SpikeGenerator, we need to reset the\n # lastindex when the period has passed\n if _lastindex_before > 0 and _array_zz_external_sources__timebins[_lastindex_before - 1] >= _timebin:\n _lastindex_before = 0\n _n_spikes = _numpy.searchsorted(_array_zz_external_sources__timebins[_lastindex_before:],\n _timebin, side='right')\n _array_zz_external_sources__lastindex[0] = _lastindex_before + _n_spikes\n _indices = _array_zz_external_sources_neuron_index[_lastindex_before:_lastindex_before+_n_spikes]\n _array_zz_external_sources__spikespace[:_n_spikes] = _indices\n _array_zz_external_sources__spikespace[-1] = _n_spikes\n", + "name": "zz_external_sources_codeobject_4", + "type": "CallableProxyType" + } + ], + "name": "zz_external_sources", + "order": 0, + "type": "SpikeGeneratorGroup", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_9", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "g_post += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "zz_external_arrivals_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g_post += w\n _postsynaptic_idx = _array_zz_external_arrivals__synaptic_post[_idx]\n w = _array_zz_external_arrivals_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "zz_external_arrivals_pre_codeobject_4", + "type": "CallableProxyType" + } + ], + "name": "zz_external_arrivals_pre", + "order": 0, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_9", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/independent-output/events.csv new file mode 100644 index 0000000..5cb39e0 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/independent-output/events.csv @@ -0,0 +1,2 @@ +step,neuron_idx +1,-1 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/run-spec.json new file mode 100644 index 0000000..a04fff1 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/run-spec.json @@ -0,0 +1,120 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 20.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + -1 + ], + "external_arrivals": { + "actual_weights_mv": [ + 1999.9998779296875 + ], + "events": 1, + "ordering": "after default_synapses.pre", + "pathway_order": 0 + }, + "internal_voltage_unit": "volt", + "nodes": [ + -1 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float32", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float32", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null + }, + "steps": 200, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/schedule.json new file mode 100644 index 0000000..2ca6fb3 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+-------------------------------------------+----------------------+------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nzz_external_sources (SpikeGeneratorGroup) | zz_external_sources (SpikeGeneratorGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \nzz_external_arrivals_pre (SynapticPathway) | zz_external_arrivals (Synapses) | 100. us (every step) | synapses | 0 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/seed.json new file mode 100644 index 0000000..f164c97 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float32/seed.json @@ -0,0 +1,5 @@ +{ + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/actual-weights.json new file mode 100644 index 0000000..14b16bb --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/actual-weights.json @@ -0,0 +1,11 @@ +{ + "edge_id": [ + -1 + ], + "weights_mv": [ + 0.0 + ], + "weights_volt": [ + 0.0 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/brian-output/events.csv new file mode 100644 index 0000000..5cb39e0 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/brian-output/events.csv @@ -0,0 +1,2 @@ +step,neuron_idx +1,-1 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/comparison.json new file mode 100644 index 0000000..9ae07c7 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 7.105427357601002e-15, + "mean_abs_mv": 3.552713678800501e-15, + "same_event_prefix_max_abs_mv": 7.105427357601002e-15, + "first_event_divergence_step": null, + "tolerance_mv": 1e-08, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/completeness.csv new file mode 100644 index 0000000..f05fab6 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/completeness.csv @@ -0,0 +1,2 @@ +global_neuron_idx,local_index +-1,0 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/external-arrivals.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/external-arrivals.csv new file mode 100644 index 0000000..399fc7a --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/external-arrivals.csv @@ -0,0 +1,2 @@ +tick,neuron_idx,requested_mv +0,-1,2000.0 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/generated-code.json new file mode 100644 index 0000000..b6b2149 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/generated-code.json @@ -0,0 +1,164 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "zz_external_arrivals", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _the_period = _array_zz_external_sources__period_bins[0]\n _timebin = _array_defaultclock_timestep[0]\n _n_spikes = 0\n _lastindex_before = _array_zz_external_sources__lastindex[0]\n if _the_period > 0:\n _timebin %= _the_period\n # If there is a periodicity in the SpikeGenerator, we need to reset the\n # lastindex when the period has passed\n if _lastindex_before > 0 and _array_zz_external_sources__timebins[_lastindex_before - 1] >= _timebin:\n _lastindex_before = 0\n _n_spikes = _numpy.searchsorted(_array_zz_external_sources__timebins[_lastindex_before:],\n _timebin, side='right')\n _array_zz_external_sources__lastindex[0] = _lastindex_before + _n_spikes\n _indices = _array_zz_external_sources_neuron_index[_lastindex_before:_lastindex_before+_n_spikes]\n _array_zz_external_sources__spikespace[:_n_spikes] = _indices\n _array_zz_external_sources__spikespace[-1] = _n_spikes\n", + "name": "zz_external_sources_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "zz_external_sources", + "order": 0, + "type": "SpikeGeneratorGroup", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "g_post += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "zz_external_arrivals_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g_post += w\n _postsynaptic_idx = _array_zz_external_arrivals__synaptic_post[_idx]\n w = _array_zz_external_arrivals_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "zz_external_arrivals_pre_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "zz_external_arrivals_pre", + "order": 0, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/independent-output/events.csv new file mode 100644 index 0000000..5cb39e0 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/independent-output/events.csv @@ -0,0 +1,2 @@ +step,neuron_idx +1,-1 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/run-spec.json new file mode 100644 index 0000000..ed4c8a9 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/run-spec.json @@ -0,0 +1,120 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 20.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + -1 + ], + "external_arrivals": { + "actual_weights_mv": [ + 2000.0 + ], + "events": 1, + "ordering": "after default_synapses.pre", + "pathway_order": 0 + }, + "internal_voltage_unit": "volt", + "nodes": [ + -1 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float64", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float64", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null + }, + "steps": 200, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/schedule.json new file mode 100644 index 0000000..2ca6fb3 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+-------------------------------------------+----------------------+------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nzz_external_sources (SpikeGeneratorGroup) | zz_external_sources (SpikeGeneratorGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \nzz_external_arrivals_pre (SynapticPathway) | zz_external_arrivals (Synapses) | 100. us (every step) | synapses | 0 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/seed.json new file mode 100644 index 0000000..f164c97 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-nonzero_g_reset-float64/seed.json @@ -0,0 +1,5 @@ +{ + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/actual-weights.json new file mode 100644 index 0000000..14b16bb --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/actual-weights.json @@ -0,0 +1,11 @@ +{ + "edge_id": [ + -1 + ], + "weights_mv": [ + 0.0 + ], + "weights_volt": [ + 0.0 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/brian-output/events.csv new file mode 100644 index 0000000..9ecbb05 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/brian-output/events.csv @@ -0,0 +1,2 @@ +step,neuron_idx +0,-1 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/comparison.json new file mode 100644 index 0000000..f4c447d --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.00010353326797485352, + "mean_abs_mv": 2.6278293235009186e-05, + "same_event_prefix_max_abs_mv": 0.00010353326797485352, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/completeness.csv new file mode 100644 index 0000000..f05fab6 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/completeness.csv @@ -0,0 +1,2 @@ +global_neuron_idx,local_index +-1,0 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/external-arrivals.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/external-arrivals.csv new file mode 100644 index 0000000..405bebe --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/external-arrivals.csv @@ -0,0 +1,5 @@ +tick,neuron_idx,requested_mv +0,-1,0.1 +21,-1,0.1 +22,-1,0.1 +23,-1,0.1 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/generated-code.json new file mode 100644 index 0000000..9679389 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/generated-code.json @@ -0,0 +1,172 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "zz_external_arrivals", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _the_period = _array_zz_external_sources__period_bins[0]\n _timebin = _array_defaultclock_timestep[0]\n _n_spikes = 0\n _lastindex_before = _array_zz_external_sources__lastindex[0]\n if _the_period > 0:\n _timebin %= _the_period\n # If there is a periodicity in the SpikeGenerator, we need to reset the\n # lastindex when the period has passed\n if _lastindex_before > 0 and _array_zz_external_sources__timebins[_lastindex_before - 1] >= _timebin:\n _lastindex_before = 0\n _n_spikes = _numpy.searchsorted(_array_zz_external_sources__timebins[_lastindex_before:],\n _timebin, side='right')\n _array_zz_external_sources__lastindex[0] = _lastindex_before + _n_spikes\n _indices = _array_zz_external_sources_neuron_index[_lastindex_before:_lastindex_before+_n_spikes]\n _array_zz_external_sources__spikespace[:_n_spikes] = _indices\n _array_zz_external_sources__spikespace[-1] = _n_spikes\n", + "name": "zz_external_sources_codeobject_3", + "type": "CallableProxyType" + } + ], + "name": "zz_external_sources", + "order": 0, + "type": "SpikeGeneratorGroup", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_6", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "g_post += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "zz_external_arrivals_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g_post += w\n _postsynaptic_idx = _array_zz_external_arrivals__synaptic_post[_idx]\n w = _array_zz_external_arrivals_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "zz_external_arrivals_pre_codeobject_3", + "type": "CallableProxyType" + } + ], + "name": "zz_external_arrivals_pre", + "order": 0, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_6", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/independent-output/events.csv new file mode 100644 index 0000000..9ecbb05 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/independent-output/events.csv @@ -0,0 +1,2 @@ +step,neuron_idx +0,-1 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/run-spec.json new file mode 100644 index 0000000..5967b70 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/run-spec.json @@ -0,0 +1,123 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 20.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + -1 + ], + "external_arrivals": { + "actual_weights_mv": [ + 0.09999999403953552, + 0.09999999403953552, + 0.09999999403953552, + 0.09999999403953552 + ], + "events": 4, + "ordering": "after default_synapses.pre", + "pathway_order": 0 + }, + "internal_voltage_unit": "volt", + "nodes": [ + -1 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float32", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float32", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": -1 + }, + "steps": 200, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/schedule.json new file mode 100644 index 0000000..7f413fa --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+-------------------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nzz_external_sources (SpikeGeneratorGroup) | zz_external_sources (SpikeGeneratorGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \nzz_external_arrivals_pre (SynapticPathway) | zz_external_arrivals (Synapses) | 100. us (every step) | synapses | 0 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/seed.json new file mode 100644 index 0000000..d7e5e06 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float32/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -43.99999976158142, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": -1, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/actual-weights.json new file mode 100644 index 0000000..14b16bb --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/actual-weights.json @@ -0,0 +1,11 @@ +{ + "edge_id": [ + -1 + ], + "weights_mv": [ + 0.0 + ], + "weights_volt": [ + 0.0 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/brian-output/events.csv new file mode 100644 index 0000000..9ecbb05 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/brian-output/events.csv @@ -0,0 +1,2 @@ +step,neuron_idx +0,-1 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/comparison.json new file mode 100644 index 0000000..f81fb07 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 1.9184653865522705e-13, + "mean_abs_mv": 4.753580341854136e-14, + "same_event_prefix_max_abs_mv": 1.9184653865522705e-13, + "first_event_divergence_step": null, + "tolerance_mv": 1e-08, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/completeness.csv new file mode 100644 index 0000000..f05fab6 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/completeness.csv @@ -0,0 +1,2 @@ +global_neuron_idx,local_index +-1,0 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/external-arrivals.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/external-arrivals.csv new file mode 100644 index 0000000..405bebe --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/external-arrivals.csv @@ -0,0 +1,5 @@ +tick,neuron_idx,requested_mv +0,-1,0.1 +21,-1,0.1 +22,-1,0.1 +23,-1,0.1 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/generated-code.json new file mode 100644 index 0000000..8d0fc31 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/generated-code.json @@ -0,0 +1,172 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "zz_external_arrivals", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_3", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "active": true, + "code_objects": [], + "name": "oracle_seed_injection", + "order": 0, + "type": "NetworkOperation", + "when": "before_thresholds" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_3", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _the_period = _array_zz_external_sources__period_bins[0]\n _timebin = _array_defaultclock_timestep[0]\n _n_spikes = 0\n _lastindex_before = _array_zz_external_sources__lastindex[0]\n if _the_period > 0:\n _timebin %= _the_period\n # If there is a periodicity in the SpikeGenerator, we need to reset the\n # lastindex when the period has passed\n if _lastindex_before > 0 and _array_zz_external_sources__timebins[_lastindex_before - 1] >= _timebin:\n _lastindex_before = 0\n _n_spikes = _numpy.searchsorted(_array_zz_external_sources__timebins[_lastindex_before:],\n _timebin, side='right')\n _array_zz_external_sources__lastindex[0] = _lastindex_before + _n_spikes\n _indices = _array_zz_external_sources_neuron_index[_lastindex_before:_lastindex_before+_n_spikes]\n _array_zz_external_sources__spikespace[:_n_spikes] = _indices\n _array_zz_external_sources__spikespace[-1] = _n_spikes\n", + "name": "zz_external_sources_codeobject_1", + "type": "CallableProxyType" + } + ], + "name": "zz_external_sources", + "order": 0, + "type": "SpikeGeneratorGroup", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "g_post += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "zz_external_arrivals_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g_post += w\n _postsynaptic_idx = _array_zz_external_arrivals__synaptic_post[_idx]\n w = _array_zz_external_arrivals_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "zz_external_arrivals_pre_codeobject_1", + "type": "CallableProxyType" + } + ], + "name": "zz_external_arrivals_pre", + "order": 0, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/independent-output/events.csv new file mode 100644 index 0000000..9ecbb05 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/independent-output/events.csv @@ -0,0 +1,2 @@ +step,neuron_idx +0,-1 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/run-spec.json new file mode 100644 index 0000000..424aafd --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/run-spec.json @@ -0,0 +1,123 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 20.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + -1 + ], + "external_arrivals": { + "actual_weights_mv": [ + 0.1, + 0.1, + 0.1, + 0.1 + ], + "events": 4, + "ordering": "after default_synapses.pre", + "pathway_order": 0 + }, + "internal_voltage_unit": "volt", + "nodes": [ + -1 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float64", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float64", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": -1 + }, + "steps": 200, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/schedule.json new file mode 100644 index 0000000..7f413fa --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+-------------------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \noracle_seed_injection (NetworkOperation) | -- | 100. us (every step) | before_thresholds | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nzz_external_sources (SpikeGeneratorGroup) | zz_external_sources (SpikeGeneratorGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \nzz_external_arrivals_pre (SynapticPathway) | zz_external_arrivals (Synapses) | 100. us (every step) | synapses | 0 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/seed.json new file mode 100644 index 0000000..d555d7c --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-refractory_boundary-float64/seed.json @@ -0,0 +1,7 @@ +{ + "applied_mv": -44.0, + "injections": 1, + "margin_mv": 1.0, + "requested_global_node": -1, + "spiked_at_zero": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/actual-weights.json new file mode 100644 index 0000000..14b16bb --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/actual-weights.json @@ -0,0 +1,11 @@ +{ + "edge_id": [ + -1 + ], + "weights_mv": [ + 0.0 + ], + "weights_volt": [ + 0.0 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/brian-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/brian-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/comparison.json new file mode 100644 index 0000000..559a911 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.00012701749801635742, + "mean_abs_mv": 3.341285439091735e-05, + "same_event_prefix_max_abs_mv": 0.00012701749801635742, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/completeness.csv new file mode 100644 index 0000000..f05fab6 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/completeness.csv @@ -0,0 +1,2 @@ +global_neuron_idx,local_index +-1,0 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/external-arrivals.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/external-arrivals.csv new file mode 100644 index 0000000..40c5a00 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/external-arrivals.csv @@ -0,0 +1,2 @@ +tick,neuron_idx,requested_mv +0,-1,1.0 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/generated-code.json new file mode 100644 index 0000000..b6b2149 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/generated-code.json @@ -0,0 +1,164 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "zz_external_arrivals", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _the_period = _array_zz_external_sources__period_bins[0]\n _timebin = _array_defaultclock_timestep[0]\n _n_spikes = 0\n _lastindex_before = _array_zz_external_sources__lastindex[0]\n if _the_period > 0:\n _timebin %= _the_period\n # If there is a periodicity in the SpikeGenerator, we need to reset the\n # lastindex when the period has passed\n if _lastindex_before > 0 and _array_zz_external_sources__timebins[_lastindex_before - 1] >= _timebin:\n _lastindex_before = 0\n _n_spikes = _numpy.searchsorted(_array_zz_external_sources__timebins[_lastindex_before:],\n _timebin, side='right')\n _array_zz_external_sources__lastindex[0] = _lastindex_before + _n_spikes\n _indices = _array_zz_external_sources_neuron_index[_lastindex_before:_lastindex_before+_n_spikes]\n _array_zz_external_sources__spikespace[:_n_spikes] = _indices\n _array_zz_external_sources__spikespace[-1] = _n_spikes\n", + "name": "zz_external_sources_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "zz_external_sources", + "order": 0, + "type": "SpikeGeneratorGroup", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "g_post += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "zz_external_arrivals_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g_post += w\n _postsynaptic_idx = _array_zz_external_arrivals__synaptic_post[_idx]\n w = _array_zz_external_arrivals_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "zz_external_arrivals_pre_codeobject_2", + "type": "CallableProxyType" + } + ], + "name": "zz_external_arrivals_pre", + "order": 0, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_5", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/independent-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/independent-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/run-spec.json new file mode 100644 index 0000000..176709e --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/run-spec.json @@ -0,0 +1,120 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 20.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + -1 + ], + "external_arrivals": { + "actual_weights_mv": [ + 1.0 + ], + "events": 1, + "ordering": "after default_synapses.pre", + "pathway_order": 0 + }, + "internal_voltage_unit": "volt", + "nodes": [ + -1 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float32", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float32", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null + }, + "steps": 200, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/schedule.json new file mode 100644 index 0000000..2ca6fb3 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+-------------------------------------------+----------------------+------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nzz_external_sources (SpikeGeneratorGroup) | zz_external_sources (SpikeGeneratorGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \nzz_external_arrivals_pre (SynapticPathway) | zz_external_arrivals (Synapses) | 100. us (every step) | synapses | 0 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/seed.json new file mode 100644 index 0000000..f164c97 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float32/seed.json @@ -0,0 +1,5 @@ +{ + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/actual-weights.json new file mode 100644 index 0000000..14b16bb --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/actual-weights.json @@ -0,0 +1,11 @@ +{ + "edge_id": [ + -1 + ], + "weights_mv": [ + 0.0 + ], + "weights_volt": [ + 0.0 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/brian-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/brian-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/comparison.json new file mode 100644 index 0000000..a91b042 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 2.3447910280083306e-13, + "mean_abs_mv": 7.853490427423005e-14, + "same_event_prefix_max_abs_mv": 2.3447910280083306e-13, + "first_event_divergence_step": null, + "tolerance_mv": 1e-08, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/completeness.csv new file mode 100644 index 0000000..f05fab6 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/completeness.csv @@ -0,0 +1,2 @@ +global_neuron_idx,local_index +-1,0 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/external-arrivals.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/external-arrivals.csv new file mode 100644 index 0000000..40c5a00 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/external-arrivals.csv @@ -0,0 +1,2 @@ +tick,neuron_idx,requested_mv +0,-1,1.0 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/generated-code.json new file mode 100644 index 0000000..1a7f276 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/generated-code.json @@ -0,0 +1,164 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "zz_external_arrivals", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_1", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_1", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _the_period = _array_zz_external_sources__period_bins[0]\n _timebin = _array_defaultclock_timestep[0]\n _n_spikes = 0\n _lastindex_before = _array_zz_external_sources__lastindex[0]\n if _the_period > 0:\n _timebin %= _the_period\n # If there is a periodicity in the SpikeGenerator, we need to reset the\n # lastindex when the period has passed\n if _lastindex_before > 0 and _array_zz_external_sources__timebins[_lastindex_before - 1] >= _timebin:\n _lastindex_before = 0\n _n_spikes = _numpy.searchsorted(_array_zz_external_sources__timebins[_lastindex_before:],\n _timebin, side='right')\n _array_zz_external_sources__lastindex[0] = _lastindex_before + _n_spikes\n _indices = _array_zz_external_sources_neuron_index[_lastindex_before:_lastindex_before+_n_spikes]\n _array_zz_external_sources__spikespace[:_n_spikes] = _indices\n _array_zz_external_sources__spikespace[-1] = _n_spikes\n", + "name": "zz_external_sources_codeobject", + "type": "CallableProxyType" + } + ], + "name": "zz_external_sources", + "order": 0, + "type": "SpikeGeneratorGroup", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_1", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "g_post += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "zz_external_arrivals_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g_post += w\n _postsynaptic_idx = _array_zz_external_arrivals__synaptic_post[_idx]\n w = _array_zz_external_arrivals_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "zz_external_arrivals_pre_codeobject", + "type": "CallableProxyType" + } + ], + "name": "zz_external_arrivals_pre", + "order": 0, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_1", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/independent-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/independent-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/run-spec.json new file mode 100644 index 0000000..a61837e --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/run-spec.json @@ -0,0 +1,120 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 20.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + -1 + ], + "external_arrivals": { + "actual_weights_mv": [ + 1.0 + ], + "events": 1, + "ordering": "after default_synapses.pre", + "pathway_order": 0 + }, + "internal_voltage_unit": "volt", + "nodes": [ + -1 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float64", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float64", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null + }, + "steps": 200, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/schedule.json new file mode 100644 index 0000000..2ca6fb3 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+-------------------------------------------+----------------------+------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nzz_external_sources (SpikeGeneratorGroup) | zz_external_sources (SpikeGeneratorGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \nzz_external_arrivals_pre (SynapticPathway) | zz_external_arrivals (Synapses) | 100. us (every step) | synapses | 0 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/seed.json new file mode 100644 index 0000000..f164c97 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-weak_excitation-float64/seed.json @@ -0,0 +1,5 @@ +{ + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/actual-weights.json new file mode 100644 index 0000000..14b16bb --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/actual-weights.json @@ -0,0 +1,11 @@ +{ + "edge_id": [ + -1 + ], + "weights_mv": [ + 0.0 + ], + "weights_volt": [ + 0.0 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/brian-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/brian-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/comparison.json new file mode 100644 index 0000000..a9e3395 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 1.0728836059570312e-06, + "mean_abs_mv": 5.364418029785156e-07, + "same_event_prefix_max_abs_mv": 1.0728836059570312e-06, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/completeness.csv new file mode 100644 index 0000000..f05fab6 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/completeness.csv @@ -0,0 +1,2 @@ +global_neuron_idx,local_index +-1,0 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/external-arrivals.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/external-arrivals.csv new file mode 100644 index 0000000..1d42707 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/external-arrivals.csv @@ -0,0 +1 @@ +tick,neuron_idx,requested_mv diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/generated-code.json new file mode 100644 index 0000000..7a5e47b --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/generated-code.json @@ -0,0 +1,119 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject_4", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject_4", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject_4", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject_4", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/independent-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/independent-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/run-spec.json new file mode 100644 index 0000000..1e659f8 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/run-spec.json @@ -0,0 +1,116 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 20.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + -1 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + -1 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float32", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float32", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null + }, + "steps": 200, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/schedule.json new file mode 100644 index 0000000..cd48c36 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/seed.json new file mode 100644 index 0000000..f164c97 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float32/seed.json @@ -0,0 +1,5 @@ +{ + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/actual-weights.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/actual-weights.json new file mode 100644 index 0000000..14b16bb --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/actual-weights.json @@ -0,0 +1,11 @@ +{ + "edge_id": [ + -1 + ], + "weights_mv": [ + 0.0 + ], + "weights_volt": [ + 0.0 + ] +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/brian-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/brian-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/brian-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/comparison.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/comparison.json new file mode 100644 index 0000000..9ae07c7 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/comparison.json @@ -0,0 +1,11 @@ +{ + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 7.105427357601002e-15, + "mean_abs_mv": 3.552713678800501e-15, + "same_event_prefix_max_abs_mv": 7.105427357601002e-15, + "first_event_divergence_step": null, + "tolerance_mv": 1e-08, + "pass_oracle": true +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/completeness.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/completeness.csv new file mode 100644 index 0000000..f05fab6 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/completeness.csv @@ -0,0 +1,2 @@ +global_neuron_idx,local_index +-1,0 diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/environment.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/environment.json new file mode 100644 index 0000000..a598de4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/environment.json @@ -0,0 +1,102 @@ +{ + "all_package_pins_match": true, + "author_platform": "Windows", + "author_python": "3.10.11", + "binary_identical_author_environment_claimed": false, + "packages": { + "brian2": { + "actual": "2.5.1", + "expected": "2.5.1", + "matches": true + }, + "cython": { + "actual": "0.29.33", + "expected": "0.29.33", + "matches": true + }, + "jinja2": { + "actual": "2.11.3", + "expected": "2.11.3", + "matches": true + }, + "joblib": { + "actual": "1.2.0", + "expected": "1.2.0", + "matches": true + }, + "markupsafe": { + "actual": "1.1.1", + "expected": "1.1.1", + "matches": true + }, + "mpmath": { + "actual": "1.3.0", + "expected": "1.3.0", + "matches": true + }, + "numpy": { + "actual": "1.22.3", + "expected": "1.22.3", + "matches": true + }, + "packaging": { + "actual": "23.1", + "expected": "23.1", + "matches": true + }, + "pandas": { + "actual": "1.4.3", + "expected": "1.4.3", + "matches": true + }, + "pyarrow": { + "actual": "11.0.0", + "expected": "11.0.0", + "matches": true + }, + "pyparsing": { + "actual": "3.0.9", + "expected": "3.0.9", + "matches": true + }, + "python-dateutil": { + "actual": "2.8.2", + "expected": "2.8.2", + "matches": true + }, + "pytz": { + "actual": "2023.3", + "expected": "2023.3", + "matches": true + }, + "scipy": { + "actual": "1.8.1", + "expected": "1.8.1", + "matches": true + }, + "setuptools": { + "actual": "67.8.0", + "expected": "67.8.0", + "matches": true + }, + "six": { + "actual": "1.16.0", + "expected": "1.16.0", + "matches": true + }, + "sympy": { + "actual": "1.12", + "expected": "1.12", + "matches": true + }, + "wheel": { + "actual": "0.38.4", + "expected": "0.38.4", + "matches": true + } + }, + "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35", + "python": "3.10.12", + "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python", + "python_patch_matches": false +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/external-arrivals.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/external-arrivals.csv new file mode 100644 index 0000000..1d42707 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/external-arrivals.csv @@ -0,0 +1 @@ +tick,neuron_idx,requested_mv diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/generated-code.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/generated-code.json new file mode 100644 index 0000000..cf2b019 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/generated-code.json @@ -0,0 +1,119 @@ +[ + { + "active": true, + "code_objects": [], + "name": "default_neurons", + "order": 0, + "type": "NeuronGroup", + "when": "start" + }, + { + "active": true, + "code_objects": [], + "name": "default_synapses", + "order": 0, + "type": "Synapses", + "when": "start" + }, + { + "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n dt = _array_defaultclock_dt[0]\n _lio_1 = (- dt) / tau\n _lio_2 = exp(_lio_1)\n _lio_3 = tau / (t_mbr - tau)\n _lio_4 = dt / t_mbr\n _lio_5 = dt / tau\n _lio_6 = (- dt) / t_mbr\n _lio_7 = v_0 - v_0\n _lio_8 = v_0 - (v_0 * exp(_lio_6))\n _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n _lio_10 = exp(_lio_6)\n # vector code\n _vectorisation_idx = LazyArange(N)\n g = _array_default_neurons_g.copy()\n t = _array_defaultclock_t[0]\n dt = _array_defaultclock_dt[0]\n rfc = _array_default_neurons_rfc\n v = _array_default_neurons_v.copy()\n lastspike = _array_default_neurons_lastspike\n not_refractory = _array_default_neurons_not_refractory.copy()\n not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n _g = _numpy.where(not_refractory, _lio_2 * g, g)\n _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n g[not_refractory] = _g[not_refractory]\n v[not_refractory] = _v[not_refractory]\n _array_default_neurons_g[:] = g\n _array_default_neurons_v[:] = v\n _array_default_neurons_not_refractory[:] = not_refractory\n", + "name": "default_neurons_stateupdater_codeobject", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_stateupdater", + "order": 0, + "type": "StateUpdater", + "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr", + "when": "groups" + }, + { + "abstract_code": "_cond = (v > v_th) and not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n numpy_True = _numpy.bool_(True)\n numpy_False = _numpy.bool_(False)\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = LazyArange(N)\n v = _array_default_neurons_v\n not_refractory = _array_default_neurons_not_refractory\n _cond = (v > v_th) & not_refractory\n if _cond is True or _cond is numpy_True:\n _events = _numpy.arange(N)\n elif _cond is False or _cond is numpy_False:\n _events = _numpy.array([])\n else:\n _events, = _cond.nonzero()\n _array_default_neurons__spikespace[-1] = len(_events)\n _array_default_neurons__spikespace[:len(_events)] = _events\n # Set the neuron to refractory\n _array_default_neurons_not_refractory[_events] = False\n _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n", + "name": "default_neurons_spike_thresholder_codeobject", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_thresholder", + "order": 0, + "type": "Thresholder", + "user_code": "_cond = v > v_th", + "when": "thresholds" + }, + { + "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _n_events = _array_default_neurons__spikespace[-1]\n if _n_events > 0:\n _events = _array_default_neurons__spikespace[:_n_events]\n # Take subgroups into account\n if _source_start != 0 or _source_stop != _source_N:\n _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n _n_events = len(_events)\n if _n_events > 0:\n _vectorisation_idx = 1\n _curlen = _array_spikemonitor_N[0]\n _newlen = _curlen + _n_events\n _owner.resize(_newlen)\n _array_spikemonitor_N[0] = _newlen\n _vectorisation_idx = _events\n _idx = _events\n _source_i = _array_default_neurons_i[_idx]\n _source_t = _array_defaultclock_t[0]\n _to_record_i = _source_i\n _to_record_t = _source_t\n _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n _array_spikemonitor_count[_events - _source_start] += 1\n", + "name": "spikemonitor_codeobject", + "type": "CallableProxyType" + } + ], + "name": "spikemonitor", + "order": 1, + "type": "SpikeMonitor", + "user_code": "None", + "when": "thresholds" + }, + { + "abstract_code": "g += w\n", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.initialise_queue()\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _owner.push_spikes()\n", + "name": "default_synapses_pre_push_spikes", + "type": "CallableProxyType" + }, + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n _spiking_synapses = _queue.peek()\n if len(_spiking_synapses):\n # scalar code\n # vector code\n _idx = _spiking_synapses\n _vectorisation_idx = _idx\n # Abstract code: g += w\n _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n w = _array_default_synapses_w[_idx]\n not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n # Advance the spike queue\n _queue.advance()\n", + "name": "default_synapses_pre_codeobject", + "type": "CallableProxyType" + } + ], + "name": "default_synapses_pre", + "order": -1, + "type": "SynapticPathway", + "user_code": "None", + "when": "synapses" + }, + { + "abstract_code": "v = v_rst; w = 0; g = 0 * mV", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # scalar code\n _vectorisation_idx = 1\n w = 0\n # vector code\n _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n _vectorisation_idx = _idx\n v = v_rst\n g = 0.0\n _array_default_neurons_g[_idx] = g\n _array_default_neurons_v[_idx] = v\n", + "name": "default_neurons_spike_resetter_codeobject", + "type": "CallableProxyType" + } + ], + "name": "default_neurons_spike_resetter", + "order": 0, + "type": "Resetter", + "user_code": "None", + "when": "resets" + }, + { + "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory", + "active": true, + "code_objects": [ + { + "generated_code": "after_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nbefore_run:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # EMPTY_CODE_BLOCK -- overwrite in child template\nrun:\n import numpy as _numpy\n from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n # Resize dynamic arrays\n _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n _owner.resize(_new_len)\n # Store values\n _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n # scalar code\n _vectorisation_idx = 1\n # vector code\n _vectorisation_idx = _array_oracle_end_state__indices\n _idx = _array_oracle_end_state__indices\n _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n _source_g = _array_default_neurons_g[_idx]\n _source_v = _array_default_neurons_v[_idx]\n _source_lastspike = _array_default_neurons_lastspike[_idx]\n _to_record_v = _source_v\n _to_record_g = _source_g\n _to_record_lastspike = _source_lastspike\n _to_record_not_refractory = _source_not_refractory\n _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n", + "name": "oracle_end_state_codeobject", + "type": "CallableProxyType" + } + ], + "name": "oracle_end_state", + "order": 0, + "type": "StateMonitor", + "user_code": "None", + "when": "end" + } +] diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/independent-output/events.csv b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/independent-output/events.csv new file mode 100644 index 0000000..256e1e4 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/independent-output/events.csv @@ -0,0 +1 @@ +step,neuron_idx diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/run-spec.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/run-spec.json new file mode 100644 index 0000000..7fb293c --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/run-spec.json @@ -0,0 +1,116 @@ +{ + "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960", + "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e", + "config": { + "author_precisions": [ + "float64", + "float32" + ], + "comparison": { + "exact_spike_events_required_for_oracle_validation": true, + "float32_state_max_abs_tolerance_mv": 0.001, + "float64_state_max_abs_tolerance_mv": 1e-08, + "precision_cross_comparison_may_diverge_but_must_be_reported": true + }, + "component_policies": [ + "frozen", + "reset_g_only", + "refractory_gate_only", + "reset_and_refractory" + ], + "dt_ms": 0.1, + "duration_ms": 20.0, + "experiment": "experiments/phase4ad-author-semantics", + "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe", + "late_start_ms": 500.0, + "model": { + "dt_ms": 0.1, + "membrane_tau_ms": 20.0, + "refractory_ms": 2.2, + "reset_potential_mv": -52.0, + "resting_potential_mv": -52.0, + "synaptic_delay_ms": 1.8, + "synaptic_tau_ms": 5.0, + "threshold_mv": -45.0, + "w_syn_mv_per_anatomical_synapse": 0.275 + }, + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "motifs": [ + "pair", + "trio", + "five", + "feedforward", + "no_input" + ], + "name": "author-semantics-lab-v1", + "no_training_or_candidate": true, + "phase": "4AD", + "prior_experiment": "experiments/phase4ac-lif-semantics", + "prior_model": "models/male-cns-lif/lif-semantics-audit-v1", + "root": "/data/digital-drosophila", + "seed_margin_mv": 1.0, + "seed_node": 1381 + }, + "delay_steps": 18, + "dt_ms": 0.1, + "edge_ids": [ + -1 + ], + "external_arrivals": { + "events": 0, + "ordering": "after default_synapses.pre" + }, + "internal_voltage_unit": "volt", + "nodes": [ + -1 + ], + "parameter_checks": { + "membrane_tau_ms": { + "author": 20.0, + "config": 20.0 + }, + "refractory_ms": { + "author": 2.2, + "config": 2.2 + }, + "reset_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "resting_potential_mv": { + "author": -52.0, + "config": -52.0 + }, + "synaptic_delay_ms": { + "author": 1.8, + "config": 1.8 + }, + "synaptic_tau_ms": { + "author": 5.0, + "config": 5.0 + }, + "threshold_mv": { + "author": -45.0, + "config": -45.0 + }, + "w_syn_mv_per_anatomical_synapse": { + "author": 0.275, + "config": 0.275 + } + }, + "precision": "float64", + "preferences": { + "codegen.target": "numpy", + "core.default_float_dtype": "float64", + "legacy.refractory_timing": false + }, + "refractory_steps": 22, + "returned_voltage_unit": "mV", + "seed": { + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null + }, + "steps": 200, + "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference" +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/schedule.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/schedule.json new file mode 100644 index 0000000..cd48c36 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/schedule.json @@ -0,0 +1,11 @@ +{ + "schedule": [ + "start", + "groups", + "thresholds", + "synapses", + "resets", + "end" + ], + "summary": " object | part of | Clock dt | when | order | active\n------------------------------------------------+---------------------------------+----------------------+------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater) | default_neurons (NeuronGroup) | 100. us (every step) | groups | 0 | yes \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup) | 100. us (every step) | thresholds | 0 | yes \nspikemonitor (SpikeMonitor) | spikemonitor (SpikeMonitor) | 100. us (every step) | thresholds | 1 | yes \ndefault_synapses_pre (SynapticPathway) | default_synapses (Synapses) | 100. us (every step) | synapses | -1 | yes \ndefault_neurons_spike_resetter (Resetter) | default_neurons (NeuronGroup) | 100. us (every step) | resets | 0 | yes \noracle_end_state (StateMonitor) | oracle_end_state (StateMonitor) | 100. us (every step) | end | 0 | yes " +} diff --git a/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/seed.json b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/seed.json new file mode 100644 index 0000000..f164c97 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/oracle/unit-zero-float64/seed.json @@ -0,0 +1,5 @@ +{ + "injections": 0, + "margin_mv": 1.0, + "requested_global_node": null +} diff --git a/registry/phase4ad-author-semantics/evidence/performance/summary.json b/registry/phase4ad-author-semantics/evidence/performance/summary.json new file mode 100644 index 0000000..c991fed --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/performance/summary.json @@ -0,0 +1,5 @@ +{ + "wall_seconds": 45.55126182100025, + "backend": "CPU NumPy + Brian2", + "not_runtime_benchmark": true +} diff --git a/registry/phase4ad-author-semantics/evidence/protocol/preregistered.json b/registry/phase4ad-author-semantics/evidence/protocol/preregistered.json new file mode 100644 index 0000000..4024fcc --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/protocol/preregistered.json @@ -0,0 +1,175 @@ +{ + "config": { + "name": "author-semantics-lab-v1", + "phase": "4AD", + "root": "/data/digital-drosophila", + "experiment": "experiments/phase4ad-author-semantics", + "model_directory": "models/male-cns-lif/author-semantics-lab-v1", + "prior_experiment": 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"first_event_divergence_step": null, + "tolerance_mv": 1e-08, + "pass_oracle": true + } + }, + { + "fixture": "zero", + "precision": "float32", + "checks": { + "no_events": true, + "g_zero": true, + "rest_stationary": true + }, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 1.0728836059570312e-06, + "mean_abs_mv": 5.364418029785156e-07, + "same_event_prefix_max_abs_mv": 1.0728836059570312e-06, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true + } + }, + { + "fixture": "weak_excitation", + "precision": "float32", + "checks": { + "no_events": true, + "arrival_at_zero": true, + "integration_next_step": true + }, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.00012701749801635742, + "mean_abs_mv": 3.341285439091735e-05, + "same_event_prefix_max_abs_mv": 0.00012701749801635742, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true + } + }, + { + "fixture": "inhibition", + "precision": "float32", + "checks": { + "no_events": true, + "arrival_at_zero": true, + "integration_next_step": true + }, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.00011596083641052246, + "mean_abs_mv": 3.622157426434569e-05, + "same_event_prefix_max_abs_mv": 0.00011596083641052246, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true + } + }, + { + "fixture": "refractory_boundary", + "precision": "float32", + "checks": { + "one_seed": true, + "reject_through_21": true, + "accept_at_22": true, + "release_at_22": true, + "reset_g_at_zero": true + }, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.00010353326797485352, + "mean_abs_mv": 2.6278293235009186e-05, + "same_event_prefix_max_abs_mv": 0.00010353326797485352, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true + } + }, + { + "fixture": "equal_threshold", + "precision": "float32", + "checks": { + "strict_threshold_no_event": true + }, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.00012242794036865234, + "mean_abs_mv": 3.6822035908699036e-05, + "same_event_prefix_max_abs_mv": 0.00012242794036865234, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true + } + }, + { + "fixture": "above_threshold", + "precision": "float32", + "checks": { + "single_seed": true, + "reset_g": true + }, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 1.0728836059570312e-06, + "mean_abs_mv": 5.364418029785156e-07, + "same_event_prefix_max_abs_mv": 1.0728836059570312e-06, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true + } + }, + { + "fixture": "nonzero_g_reset", + "precision": "float32", + "checks": { + "natural_spike_at_1": true, + "nonzero_g_before_spike": true, + "zero_g_after_spike": true + }, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.0001220703125, + "mean_abs_mv": 8.416175842285156e-07, + "same_event_prefix_max_abs_mv": 0.0001220703125, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true + } + }, + { + "fixture": "delay_18", + "precision": "float32", + "checks": { + "one_seed": true, + "zero_before_arrival": true, + "arrival_at_18": true, + "first_voltage_effect_at_19": true + }, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.0001220405101776123, + "mean_abs_mv": 1.6799908344182768e-05, + "same_event_prefix_max_abs_mv": 0.0001220405101776123, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true + } + } +] diff --git a/registry/phase4ad-author-semantics/evidence/regression/unit-inhibition-float32.json b/registry/phase4ad-author-semantics/evidence/regression/unit-inhibition-float32.json new file mode 100644 index 0000000..2c68c94 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/regression/unit-inhibition-float32.json @@ -0,0 +1,20 @@ +{ + "fixture": "inhibition", + "precision": "float32", + "checks": { + "no_events": true, + "arrival_at_zero": true, + "integration_next_step": true + }, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.00011596083641052246, + "mean_abs_mv": 3.622157426434569e-05, + "same_event_prefix_max_abs_mv": 0.00011596083641052246, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true + } +} diff --git a/registry/phase4ad-author-semantics/evidence/regression/unit-inhibition-float64.json b/registry/phase4ad-author-semantics/evidence/regression/unit-inhibition-float64.json new file mode 100644 index 0000000..010b1bd --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/regression/unit-inhibition-float64.json @@ -0,0 +1,20 @@ +{ + "fixture": "inhibition", + "precision": "float64", + "checks": { + "no_events": true, + "arrival_at_zero": true, + "integration_next_step": true + }, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 2.4158453015843406e-13, + "mean_abs_mv": 7.103867841196099e-14, + "same_event_prefix_max_abs_mv": 2.4158453015843406e-13, + "first_event_divergence_step": null, + "tolerance_mv": 1e-08, + "pass_oracle": true + } +} diff --git a/registry/phase4ad-author-semantics/evidence/regression/unit-nonzero_g_reset-float32.json b/registry/phase4ad-author-semantics/evidence/regression/unit-nonzero_g_reset-float32.json new file mode 100644 index 0000000..1a5f50b --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/regression/unit-nonzero_g_reset-float32.json @@ -0,0 +1,20 @@ +{ + "fixture": "nonzero_g_reset", + "precision": "float32", + "checks": { + "natural_spike_at_1": true, + "nonzero_g_before_spike": true, + "zero_g_after_spike": true + }, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.0001220703125, + "mean_abs_mv": 8.416175842285156e-07, + "same_event_prefix_max_abs_mv": 0.0001220703125, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true + } +} diff --git a/registry/phase4ad-author-semantics/evidence/regression/unit-nonzero_g_reset-float64.json b/registry/phase4ad-author-semantics/evidence/regression/unit-nonzero_g_reset-float64.json new file mode 100644 index 0000000..b52a015 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/regression/unit-nonzero_g_reset-float64.json @@ -0,0 +1,20 @@ +{ + "fixture": "nonzero_g_reset", + "precision": "float64", + "checks": { + "natural_spike_at_1": true, + "nonzero_g_before_spike": true, + "zero_g_after_spike": true + }, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 7.105427357601002e-15, + "mean_abs_mv": 3.552713678800501e-15, + "same_event_prefix_max_abs_mv": 7.105427357601002e-15, + "first_event_divergence_step": null, + "tolerance_mv": 1e-08, + "pass_oracle": true + } +} diff --git a/registry/phase4ad-author-semantics/evidence/regression/unit-refractory_boundary-float32.json b/registry/phase4ad-author-semantics/evidence/regression/unit-refractory_boundary-float32.json new file mode 100644 index 0000000..09949be --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/regression/unit-refractory_boundary-float32.json @@ -0,0 +1,22 @@ +{ + "fixture": "refractory_boundary", + "precision": "float32", + "checks": { + "one_seed": true, + "reject_through_21": true, + "accept_at_22": true, + "release_at_22": true, + "reset_g_at_zero": true + }, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.00010353326797485352, + "mean_abs_mv": 2.6278293235009186e-05, + "same_event_prefix_max_abs_mv": 0.00010353326797485352, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true + } +} diff --git a/registry/phase4ad-author-semantics/evidence/regression/unit-refractory_boundary-float64.json b/registry/phase4ad-author-semantics/evidence/regression/unit-refractory_boundary-float64.json new file mode 100644 index 0000000..bd623b9 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/regression/unit-refractory_boundary-float64.json @@ -0,0 +1,22 @@ +{ + "fixture": "refractory_boundary", + "precision": "float64", + "checks": { + "one_seed": true, + "reject_through_21": true, + "accept_at_22": true, + "release_at_22": true, + "reset_g_at_zero": true + }, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 1.9184653865522705e-13, + "mean_abs_mv": 4.753580341854136e-14, + "same_event_prefix_max_abs_mv": 1.9184653865522705e-13, + "first_event_divergence_step": null, + "tolerance_mv": 1e-08, + "pass_oracle": true + } +} diff --git a/registry/phase4ad-author-semantics/evidence/regression/unit-weak_excitation-float32.json b/registry/phase4ad-author-semantics/evidence/regression/unit-weak_excitation-float32.json new file mode 100644 index 0000000..ce9e9f9 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/regression/unit-weak_excitation-float32.json @@ -0,0 +1,20 @@ +{ + "fixture": "weak_excitation", + "precision": "float32", + "checks": { + "no_events": true, + "arrival_at_zero": true, + "integration_next_step": true + }, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 0.00012701749801635742, + "mean_abs_mv": 3.341285439091735e-05, + "same_event_prefix_max_abs_mv": 0.00012701749801635742, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true + } +} diff --git a/registry/phase4ad-author-semantics/evidence/regression/unit-weak_excitation-float64.json b/registry/phase4ad-author-semantics/evidence/regression/unit-weak_excitation-float64.json new file mode 100644 index 0000000..7f76108 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/regression/unit-weak_excitation-float64.json @@ -0,0 +1,20 @@ +{ + "fixture": "weak_excitation", + "precision": "float64", + "checks": { + "no_events": true, + "arrival_at_zero": true, + "integration_next_step": true + }, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 2.3447910280083306e-13, + "mean_abs_mv": 7.853490427423005e-14, + "same_event_prefix_max_abs_mv": 2.3447910280083306e-13, + "first_event_divergence_step": null, + "tolerance_mv": 1e-08, + "pass_oracle": true + } +} diff --git a/registry/phase4ad-author-semantics/evidence/regression/unit-zero-float32.json b/registry/phase4ad-author-semantics/evidence/regression/unit-zero-float32.json new file mode 100644 index 0000000..0e36196 --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/regression/unit-zero-float32.json @@ -0,0 +1,20 @@ +{ + "fixture": "zero", + "precision": "float32", + "checks": { + "no_events": true, + "g_zero": true, + "rest_stationary": true + }, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 1.0728836059570312e-06, + "mean_abs_mv": 5.364418029785156e-07, + "same_event_prefix_max_abs_mv": 1.0728836059570312e-06, + "first_event_divergence_step": null, + "tolerance_mv": 0.001, + "pass_oracle": true + } +} diff --git a/registry/phase4ad-author-semantics/evidence/regression/unit-zero-float64.json b/registry/phase4ad-author-semantics/evidence/regression/unit-zero-float64.json new file mode 100644 index 0000000..342917f --- /dev/null +++ b/registry/phase4ad-author-semantics/evidence/regression/unit-zero-float64.json @@ -0,0 +1,20 @@ +{ + "fixture": "zero", + "precision": "float64", + "checks": { + "no_events": true, + "g_zero": true, + "rest_stationary": true + }, + "comparison": { + "exact_events": true, + "exact_counts": true, + "ref_exact": true, + "max_abs_mv": 7.105427357601002e-15, + "mean_abs_mv": 3.552713678800501e-15, + "same_event_prefix_max_abs_mv": 7.105427357601002e-15, + "first_event_divergence_step": null, + "tolerance_mv": 1e-08, + "pass_oracle": true + } +} diff --git a/registry/phase4ad-author-semantics/seal-verification.json b/registry/phase4ad-author-semantics/seal-verification.json new file mode 100644 index 0000000..0dcdc27 --- /dev/null +++ b/registry/phase4ad-author-semantics/seal-verification.json @@ -0,0 +1,16 @@ +{ + "models/male-cns-lif/author-semantics-lab-v1": { + "pass": true, + "checked": 11, + "mismatches": [], + "manifest_sha256": "07a22bade4892adca3a4585656aa3ecce5219790b0dc8a851a12bfd7248d3769", + "checksums_sha256": "a632c04e62d8072caacfa680e0da7ad785a1d0db604cf5900853fd0b01c70ee7" + }, + "experiments/phase4ad-author-semantics": { + "pass": true, + "checked": 565, + "mismatches": [], + "manifest_sha256": "c939d3977a1883e86108c1e3edd25619118cec61e5c7712ae4dfa2893a73c0ca", + "checksums_sha256": "89ca0f11877dadb901bd2bd5d469d7bd145de980fc6b203b79daeec640a1b72c" + } +} diff --git a/tools/publish_phase4ad.py b/tools/publish_phase4ad.py new file mode 100644 index 0000000..f6f8e11 --- /dev/null +++ b/tools/publish_phase4ad.py @@ -0,0 +1,35 @@ +"""Publish sealed new-branch evidence only; never copy environment or bulk states.""" +import json +from pathlib import Path +import shutil +import sys + +ROOT=Path('/data/digital-drosophila') +MODEL=ROOT/'models/male-cns-lif/author-semantics-lab-v1' +EXP=ROOT/'experiments/phase4ad-author-semantics' +sys.path.insert(0,str(MODEL)) +from context import digest,save,check_prereg +sys.path.insert(0,str(ROOT/'models/male-cns-lif/terminal-scope-diagnostic-v1')) +from diagnostic import manifest_check + +check_prereg() +verification={str(p.relative_to(ROOT)):manifest_check(p,digest) for p in (MODEL,EXP)} +assert all(v['pass'] for v in verification.values()) +registry=ROOT/'registry/phase4ad-author-semantics';registry.mkdir(exist_ok=False) +records=[] +manifest=json.loads((EXP/'manifest.json').read_text()) +paths=[EXP/row['path'] for row in manifest['files']]+[EXP/'manifest.json',EXP/'checksums.sha256'] +for p in paths: + assert '.venv' not in p.parts and '__pycache__' not in p.parts + external=p.parent==EXP/'external-resources' + if p.stat().st_size>4*1024**2:continue + if p.suffix not in ('.json','.csv','.md','.sha256') and not external:continue + dst=registry/'evidence'/p.relative_to(EXP);dst.parent.mkdir(parents=True,exist_ok=True) + with p.open('rb') as src,dst.open('xb') as out:shutil.copyfileobj(src,out) + assert digest(p)==digest(dst) + records.append(dict(source=str(p.relative_to(ROOT)),copy=str(dst.relative_to(registry)),sha256=digest(p),bytes=p.stat().st_size)) +save(registry/'evidence-index.json',records) +save(registry/'seal-verification.json',verification) +target=ROOT/'docs/progress/phase4ad-author-semantics.md' +with (EXP/'REPORT.md').open('rb') as src,target.open('xb') as out:shutil.copyfileobj(src,out) +print('Published',len(records),'small evidence records; no bulk states, datasets or environment copied')