code/adapter_messidor2.py

#!/usr/bin/env python3
"""
Messidor-2 adapter — DR grading + DME + gradability multi-task fundus dataset.

Inputs:
    {input_root}/messidor-2/messidor-2/preprocess/{id_code}    (1744 PNG files)
    {input_root}/messidor_data.csv                              (id_code, diagnosis, adjudicated_dme, adjudicated_gradable)

Outputs (under {output_root}):
    extracted/public_messidor2_dr/{hash[:2]}/{hash}/
        fundus_color.jpg
        meta.json
    manifest/public_messidor2_dr_images.parquet
    captions/public_messidor2_dr_captions.parquet

Label mapping:
    diagnosis 0..4  -> severity {none, mild, moderate, severe, proliferative}, diagnosis_group += [DR] if >0
    adjudicated_dme 0/1                    -> diagnosis_group += [DME], lesion_tags += [macular_edema]
    adjudicated_gradable 0                 -> image_quality_band = "ungradable", is_valid = False
"""
import argparse
import json
from pathlib import Path

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_messidor2_dr"
COHORT_PHRASE = "Messidor-2 diabetic retinopathy screening dataset"

DR_SEVERITY = {0: "none", 1: "mild", 2: "moderate", 3: "severe", 4: "proliferative"}


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"])

    dr = meta.get("dr_grade")
    dme = bool(meta.get("dme"))
    gradable = bool(meta.get("gradable"))

    dx, lesions = [], []
    if dr is not None and dr > 0:
        dx.append("DR")
    if dme:
        dx.append("DME")
        lesions.append("macular_edema")
    row["diagnosis_group"] = dx
    row["lesion_tags"] = lesions
    row["severity"] = DR_SEVERITY.get(dr, "unknown")
    row["diagnosis_source"] = "adjudicated_label" if dr is not None else "none"
    row["label_confidence"] = "adjudicated" if dr is not None else None
    row["image_quality_band"] = "unknown" if gradable else "ungradable"

    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": False,
        "n_layers_visible": 0,
        "is_valid": gradable,
    })

    caps = caption_l1_public(image_id, COHORT_PHRASE, "fundus_color", meta["eye"])
    parts = ["A color fundus photograph from the Messidor-2 dataset"]
    if dr is not None:
        parts.append(f"diabetic retinopathy grade {dr} ({DR_SEVERITY[dr]})")
    if dme:
        parts.append("diabetic macular edema present")
    if not gradable:
        parts.append("flagged as ungradable")
    l3 = ", ".join(parts) + "."
    caps.append(caption_l3_public(image_id, l3, "manifest_fields+csv_labels"))
    return row, caps


def process_one(image_path: Path, labels: dict, out_root: Path, force: bool):
    basename = image_path.stem
    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)

    meta = {
        "status": "ok",
        "cohort": COHORT,
        "study_hash": sh,
        "source_basename": basename,
        "image_height_px": int(h),
        "image_width_px": int(w),
        "eye": "unknown",
        "dr_grade": labels.get("diagnosis"),
        "dme": int(labels.get("adjudicated_dme", 0)),
        "gradable": int(labels.get("adjudicated_gradable", 1)),
    }
    write_meta(sdir, meta)
    return _row_and_caps(meta)


def main():
    ap = argparse.ArgumentParser()
    ap.add_argument("--input-root", required=True,
                    help="Path to .../Generation/Messidor2 (contains messidor_data.csv and messidor-2/messidor-2/preprocess/)")
    ap.add_argument("--output-root", required=True)
    ap.add_argument("--force", action="store_true")
    ap.add_argument("--limit", type=int, default=None)
    args = ap.parse_args()

    in_root = Path(args.input_root)
    out_root = Path(args.output_root)
    csv_path = in_root / "messidor_data.csv"
    img_dir = in_root / "messidor-2" / "messidor-2" / "preprocess"

    df = pd.read_csv(csv_path)
    print(f"[{COHORT}] CSV rows: {len(df)}, image dir: {img_dir}")
    if args.limit:
        df = df.head(args.limit)

    rows, caps = [], []
    missing = 0
    for _, lab in df.iterrows():
        fname = lab["id_code"]
        ip = img_dir / fname
        if not ip.exists():
            missing += 1
            continue
        row, cap = process_one(ip, lab.to_dict(), out_root, args.force)
        rows.append(row)
        caps.extend(cap)

    if missing:
        print(f"[{COHORT}] WARN: {missing} CSV rows have no matching image file")
    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)} images, {len(caps_df)} captions")
    print(imgs_df.groupby(["severity"]).size().to_string())


if __name__ == "__main__":
    main()