Seal Phase4AF exact short fullgraph author GPU gate and APL integration audit

2026-09-30 08:14:16 +08:00
parent 1eb4c52cf7
commit 7dfe5d2d87
104 changed files with 11608 additions and 20 deletions
@@ -0,0 +1,71 @@
+"""Read-only canonical graph adaptation, before any neural trajectory."""
+from datetime import datetime, timezone
+import json
+import platform
+import shutil
+import subprocess
+import numpy as np
+import pandas as pd
+import yaml
+from context import ROOT, MODEL, EXP, AD, AE_MODEL, AE_EXP, CFG, save, digest, sources, integrity, budget_check
+
+def main():
+    assert not (EXP/'protocol').exists()
+    assert shutil.disk_usage(EXP.parent).free > 25*1024**3
+    for name in ('protocol','graph','cases','oracle','gpu','regression','audit','logs','extension-build'):
+        (EXP/name).mkdir(parents=True, exist_ok=False)
+    can = ROOT/'datasets/male-cns-v1.0/processed/neuron-only'
+    raw_paths = [can/'gpu/csr-indptr.int64.npy', can/'gpu/csr-indices.int32.npy',
+        can/'gpu/csr-weights.int64.npy', can/'neuron-index/unified-metadata.parquet',
+        ROOT/'models/male-cns-lif/runtime-v1/phase4c.yaml', AD/'external-resources/model.py',
+        AD/'manifest.json', AE_MODEL/'manifest.json', AE_EXP/'manifest.json',
+        AE_MODEL/'gpu_backend.py',AE_MODEL/'author_ext.cpp',AE_MODEL/'author_ext.cu',AE_MODEL/'oracle_stress.py']
+    save(EXP/'protocol/preregistered.json', dict(timestamp_utc=datetime.now(timezone.utc).isoformat(),
+        config=CFG, sources=sources(), before_model_execution=True,
+        inputs=[dict(path=str(p.relative_to(ROOT)),sha256=digest(p)) for p in raw_paths],
+        parent_commit=subprocess.check_output(['git','-C',str(ROOT),'rev-parse','HEAD'],text=True).strip()))
+    save(EXP/'regression/old-integrity-before.json',integrity())
+    ptr = np.load(raw_paths[0], mmap_mode='r'); dst = np.load(raw_paths[1], mmap_mode='r')
+    raw = np.load(raw_paths[2], mmap_mode='r'); meta = pd.read_parquet(raw_paths[3]).sort_values('neuron_idx').reset_index(drop=True)
+    n,e = CFG['neurons'],CFG['edges']
+    assert ptr.dtype == np.int64 and dst.dtype == np.int32 and raw.dtype == np.int64
+    assert len(meta)==n and np.array_equal(meta.neuron_idx,np.arange(n))
+    assert ptr.shape==(n+1,) and ptr[0]==0 and ptr[-1]==e and np.all(np.diff(ptr)>=0)
+    assert dst.shape == raw.shape == (e,) and dst.min()>=0 and dst.max()<n
+    assert raw.min()>0 and int(raw.sum())==CFG['raw_weight_sum']
+    policy = yaml.safe_load(raw_paths[4].read_text())['sign_policy']
+    signs=[]; nt_counts={}
+    for nt in meta.neurotransmitter:
+        s='' if pd.isna(nt) else str(nt).strip().lower()
+        signs.append(policy['unknown_sign'] if not s else policy['unclear_sign'] if s=='unclear' else policy['neurotransmitter_sign'][s])
+        nt_counts[s or 'NULL'] = nt_counts.get(s or 'NULL',0)+1
+    signs=np.asarray(signs,np.int8); assert set(signs).issubset({-1,0,1})
+    src=np.repeat(np.arange(n,dtype=np.int32),np.diff(ptr)); signed=raw*signs[src]
+    edge_id=np.arange(e,dtype=np.int64);graph=EXP/'graph'
+    for name,array in dict(nodes=np.arange(n,dtype=np.int32),edge_id=edge_id,src=src,dst=dst,
+                            signed_raw=signed,ptr=ptr,signs=signs).items():
+        with (graph/(name+'.npy')).open('xb') as f: np.save(f,array,allow_pickle=False)
+    pd.DataFrame({'local_index':np.arange(n,dtype=np.int32)},index=pd.Index(np.arange(n),name='global_neuron_idx')).to_csv(graph/'completeness.csv')
+    pd.DataFrame({'Presynaptic_Index':src,'Postsynaptic_Index':dst,
+                  'Excitatory x Connectivity':signed,'edge_id':edge_id},copy=False).to_parquet(graph/'connectivity.parquet',index=False)
+    idx=np.bincount(dst,minlength=n);out=np.diff(ptr)
+    assert int(np.count_nonzero(src==dst))==101 and int(np.count_nonzero((idx==0)&(out==0)))==217
+    save(graph/'audit.json',dict(neurons=n,edges=e,raw_weight_sum=int(raw.sum()),
+        self_loops=int(np.count_nonzero(src==dst)),isolates=int(np.count_nonzero((idx==0)&(out==0))),
+        signs={str(int(s)):int(np.count_nonzero(signs==s)) for s in np.unique(signs)},neurotransmitters=nt_counts,
+        canonical_edge_id='original CSR slot; source sorted; no reordering, filtering, normalization or new edge',
+        body_mapping_input=str(raw_paths[3]),original_weights_modified=False))
+    model=json.loads((AD/'protocol/preregistered.json').read_text())['config']['model']
+    for trial in CFG['trials']:
+        case=EXP/'cases'/trial['name'];case.mkdir()
+        save(case/'spec.json',dict(**trial,dt_ms=model['dt_ms'],duration_ms=trial['steps']*model['dt_ms'],model=model,
+             graph_dir=str(graph),precision=CFG['precision'],all_requests_at_tick=0,apl_overlay=False,training=False,
+             budget_root=str(EXP),output_budget_bytes=CFG['new_output_budget_bytes']))
+        meta.iloc[trial['seed_nodes']][['neuron_idx','body_id','annotation_type','neurotransmitter']].to_csv(case/'seed-identities.csv',index=False)
+    save(EXP/'protocol/environment.json',dict(python=platform.python_version(),platform=platform.platform(),
+        numpy=np.__version__,free_disk_bytes=shutil.disk_usage(EXP).free))
+    save(EXP/'protocol/graph-case-hashes.json',[dict(path=str(p.relative_to(EXP)),sha256=digest(p),bytes=p.stat().st_size)
+        for root in (graph,EXP/'cases') for p in sorted(root.rglob('*')) if p.is_file()])
+    budget_check();print('PREPARED full canonical graph and3 fixed trials; frozen integrity PASS',flush=True)
+
+if __name__=='__main__': main()