#!/usr/bin/env python3 """ DRIVE adapter — vessel segmentation public dataset. Inputs: {input_root}/DRIVE/training/images/NN_training.tif (20 files) {input_root}/DRIVE/training/1st_manual/NN_manual1.gif (vessel GT) {input_root}/DRIVE/training/mask/NN_training_mask.gif (FOV mask) Outputs (under {output_root}): extracted/public_drive_vessel/{hash[:2]}/{hash}/ fundus_color.jpg (re-encoded from .tif) vessel_mask.png (binary 0/255, from 1st_manual) fov_mask.png (binary 0/255, from mask/) meta.json manifest/public_drive_vessel_images.parquet captions/public_drive_vessel_captions.parquet Test split (also 20 images) intentionally skipped — it lacks vessel GT, only FOV mask. """ import argparse import json from pathlib import Path import numpy as np import pandas as pd from PIL import Image from public_common import ( IMAGE_SCHEMA_COLUMNS, CAPTION_SCHEMA_COLUMNS, study_hash_for, default_base_fields, caption_l1_public, caption_l3_public, study_dir_for, rel_file_path, write_meta, coerce_image_row, ) COHORT = "public_drive_vessel" COHORT_PHRASE = "DRIVE retinal vessel segmentation dataset" def _binarize(p: Path) -> np.ndarray: arr = np.array(Image.open(p).convert("L")) return ((arr > 127).astype(np.uint8) * 255) def process_one(image_path: Path, vessel_path: Path, fov_path: Path, out_root: Path, force: bool): basename = image_path.stem # "21_training" sh = study_hash_for(COHORT, basename) sdir = study_dir_for(out_root, COHORT, sh) sdir.mkdir(parents=True, exist_ok=True) meta_path = sdir / "meta.json" if meta_path.exists() and not force: try: meta = json.loads(meta_path.read_text()) if meta.get("status") == "ok": return _row_and_caps(meta) except Exception: pass img = Image.open(image_path).convert("RGB") w, h = img.size img.save(sdir / "fundus_color.jpg", "JPEG", quality=95) Image.fromarray(_binarize(vessel_path), mode="L").save( sdir / "vessel_mask.png", "PNG", optimize=True) Image.fromarray(_binarize(fov_path), mode="L").save( sdir / "fov_mask.png", "PNG", optimize=True) meta = { "status": "ok", "cohort": COHORT, "study_hash": sh, "source_basename": basename, "image_height_px": int(h), "image_width_px": int(w), "has_vessel_mask": True, "has_fov_mask": True, "eye": "unknown", } write_meta(sdir, meta) return _row_and_caps(meta) def _row_and_caps(meta: dict): sh = meta["study_hash"] image_id = f"{COHORT}_{sh}_fundus_color" row = default_base_fields(COHORT, sh, eye=meta["eye"]) row.update({ "image_id": image_id, "file_path": rel_file_path(COHORT, sh, "fundus_color.jpg"), "file_format": "jpg", "modality": "fundus_color", "anatomy": "macula", "device_technology": "fundus_camera", "scan_protocol": "single_shot", "image_height_px": int(meta["image_height_px"]), "image_width_px": int(meta["image_width_px"]), "has_segmentation": True, "n_layers_visible": 0, "is_valid": True, }) caps = caption_l1_public(image_id, COHORT_PHRASE, "fundus_color", meta["eye"]) l3 = ("A color fundus photograph from the DRIVE dataset, " "with manually annotated retinal vessel segmentation mask and field-of-view mask.") caps.append(caption_l3_public(image_id, l3, "manifest_fields+vessel_mask")) return row, caps def main(): ap = argparse.ArgumentParser() ap.add_argument("--input-root", required=True, help="Path to .../Generation/DRIVE (contains DRIVE/training/...)") ap.add_argument("--output-root", required=True, help="Public manifest root, e.g. .../c3/public_eye_pretrain") ap.add_argument("--force", action="store_true") args = ap.parse_args() in_root = Path(args.input_root) out_root = Path(args.output_root) train_dir = in_root / "DRIVE" / "training" img_dir = train_dir / "images" vessel_dir = train_dir / "1st_manual" fov_dir = train_dir / "mask" img_files = sorted(img_dir.glob("*_training.tif")) print(f"[{COHORT}] {len(img_files)} training images under {img_dir}") rows, caps = [], [] for ip in img_files: stem = ip.stem.replace("_training", "") vp = vessel_dir / f"{stem}_manual1.gif" fp = fov_dir / f"{stem}_training_mask.gif" if not (vp.exists() and fp.exists()): print(f" skip {ip.name}: vessel={vp.exists()}, fov={fp.exists()}") continue row, cap = process_one(ip, vp, fp, out_root, args.force) rows.append(row) caps.extend(cap) if not rows: print(f"[{COHORT}] no rows produced, aborting") return manifest_dir = out_root / "manifest" captions_dir = out_root / "captions" manifest_dir.mkdir(parents=True, exist_ok=True) captions_dir.mkdir(parents=True, exist_ok=True) imgs_df = pd.DataFrame([coerce_image_row(r) for r in rows])[IMAGE_SCHEMA_COLUMNS] imgs_df.to_parquet(manifest_dir / f"{COHORT}_images.parquet", index=False) caps_df = pd.DataFrame(caps)[CAPTION_SCHEMA_COLUMNS] caps_df.to_parquet(captions_dir / f"{COHORT}_captions.parquet", index=False) print(f"[{COHORT}] wrote {len(imgs_df)} image rows, {len(caps_df)} caption rows") if __name__ == "__main__": main()