#!/usr/bin/env python3 """ regen_captions_v2.py — regenerate captions (v2, disease/lesion-centric) from an existing *_images_v1.parquet, WITHOUT re-running extraction. Works uniformly for the private / public-fundus / public-OCT manifests because caption_v2.caption_rows_for() is a pure function of the manifest row. Writes: {out_dir}/{out_name} unified captions_v2 parquet {out_dir}/{cohort}_captions_v2.parquet per-cohort (HF staging) if --per-cohort """ import argparse import time from pathlib import Path import pandas as pd import caption_v2 def main(): ap = argparse.ArgumentParser() ap.add_argument("--manifest", required=True, help="path to *_images_v1.parquet") ap.add_argument("--out-dir", required=True) ap.add_argument("--out-name", default="captions_v2.parquet") ap.add_argument("--per-cohort", action="store_true", help="also write one {cohort}_captions_v2.parquet per cohort") ap.add_argument("--lesion-sidecar", default=None, help="optional parquet (image_id, lesion_codes) to merge into " "lesion_tags before captioning (from enrich_lesion_tags.py)") args = ap.parse_args() out_dir = Path(args.out_dir) out_dir.mkdir(parents=True, exist_ok=True) print(f"loading manifest: {args.manifest}") df = pd.read_parquet(args.manifest) print(f" {len(df)} image rows, {df.cohort.nunique()} cohort(s)") sidecar = {} if args.lesion_sidecar: sc = pd.read_parquet(args.lesion_sidecar) sidecar = {r["image_id"]: list(r["lesion_codes"]) for _, r in sc.iterrows()} print(f" merged lesion sidecar: {len(sidecar)} images with extra lesion tags") t0 = time.time() records = df.to_dict("records") all_caps, per_cohort = [], {} for i, row in enumerate(records): if sidecar: extra = sidecar.get(row.get("image_id")) if extra: cur = caption_v2._as_list(row.get("lesion_tags")) row["lesion_tags"] = list(dict.fromkeys(cur + extra)) caps = caption_v2.caption_rows_for(row) all_caps.extend(caps) if args.per_cohort: per_cohort.setdefault(row.get("cohort"), []).extend(caps) if (i + 1) % 100000 == 0: dt = time.time() - t0 print(f" ... {i+1}/{len(records)} ({dt:.0f}s, {(i+1)/dt:.0f} img/s)") dt = time.time() - t0 print(f" done in {dt:.0f}s: {len(all_caps)} caption rows " f"({len(all_caps)/max(len(records),1):.2f} per image)") cap_df = pd.DataFrame(all_caps, columns=caption_v2.CAP_COLS) uni = out_dir / args.out_name cap_df.to_parquet(uni, index=False) print(f"\n wrote unified: {uni} ({len(cap_df)} rows)") print(" level distribution:") print(cap_df["level"].value_counts().to_string()) if args.per_cohort: for cohort, caps in per_cohort.items(): cp = out_dir / f"{cohort}_captions_v2.parquet" pd.DataFrame(caps, columns=caption_v2.CAP_COLS).to_parquet(cp, index=False) print(f" wrote {len(per_cohort)} per-cohort caption parquets") # peek a few print("\n sample captions:") for t in cap_df["prompt_text"].drop_duplicates().head(12): print(f" {t}") if __name__ == "__main__": main()