import ast import csv import json import os import random from collections import defaultdict from multiprocessing import Pool from PIL import Image BASE_DIR = "./VindrMammo" CSV_PATH = os.path.join(BASE_DIR, "vindr_detection_v1_folds.csv") IMG_DIR = os.path.join(BASE_DIR, "images_png") CROP_DIR = os.path.join(BASE_DIR, "crop") OUTPUT_TRAIN_JSON = os.path.join(BASE_DIR, "VinDr-Mammo_train.json") OUTPUT_TEST_JSON = os.path.join(BASE_DIR, "VinDr-Mammo_test.json") MIN_SIZE = 28 IOU_THR = 0.5 CONTAIN_THR = 0.7 NUM_WORKERS = 8 MAX_TEST_SAMPLES = 1000 RANDOM_SEED = 42 def area(b): return max(0, b[2] - b[0]) * max(0, b[3] - b[1]) def intersect_area(a, b): ix1 = max(a[0], b[0]); iy1 = max(a[1], b[1]) ix2 = min(a[2], b[2]); iy2 = min(a[3], b[3]) return max(0, ix2 - ix1) * max(0, iy2 - iy1) def should_merge(a, b): inter = intersect_area(a, b) if inter == 0: return False iou = inter / (area(a) + area(b) - inter) contain = inter / min(area(a), area(b)) return iou >= IOU_THR or contain >= CONTAIN_THR def union_box(boxes): return (min(b[0] for b in boxes), min(b[1] for b in boxes), max(b[2] for b in boxes), max(b[3] for b in boxes)) def merge_boxes(boxes): boxes = list(boxes) changed = True while changed: changed = False for i in range(len(boxes)): for j in range(i + 1, len(boxes)): if should_merge(boxes[i], boxes[j]): merged = union_box([boxes[i], boxes[j]]) boxes = [boxes[k] for k in range(len(boxes)) if k not in (i, j)] boxes.append(merged) changed = True break if changed: break return boxes def crop_with_min_size(img, x_min, y_min, x_max, y_max, min_size=MIN_SIZE): cx = (x_min + x_max) // 2 cy = (y_min + y_max) // 2 w = max(x_max - x_min, min_size) h = max(y_max - y_min, min_size) x_min = max(0, cx - w // 2); x_max = min(img.width, x_min + w); x_min = max(0, x_max - w) y_min = max(0, cy - h // 2); y_max = min(img.height, y_min + h); y_min = max(0, y_max - h) return img.crop((x_min, y_min, x_max, y_max)) def normalize_path(path): return str(path).replace("\\", "/") def remove_root_prefix(path, root): path = normalize_path(path) root = normalize_path(root).rstrip("/") if path.startswith(root + "/"): return path[len(root) + 1:] elif path == root: return "" return path def process_group(args): key, before_boxes, class_id, patient_id, split = args image_id, class_name = key img_path = os.path.join(IMG_DIR, patient_id, image_id + ".png") try: img = Image.open(img_path) except Exception as e: return None, f"open {image_id}: {e}" after_boxes = merge_boxes(before_boxes) crop_paths = [] for idx, box in enumerate(after_boxes): crop_name = f"{image_id}_{class_id}_{idx}.png" crop_path = os.path.join(CROP_DIR, crop_name) try: crop = crop_with_min_size(img, *box) crop.save(crop_path) crop_paths.append(crop_path) except Exception as e: return None, f"crop {image_id} box{idx}: {e}" if not crop_paths: return None, None return { "image_path": img_path, "class_name": class_name, "split": split, "crop_image_paths": crop_paths, }, None def convert_record(record): img_path_rel = remove_root_prefix(record["image_path"], BASE_DIR) crop_paths_rel = [remove_root_prefix(p, BASE_DIR) for p in record["crop_image_paths"]] tgt_img_path = crop_paths_rel if len(crop_paths_rel) <= 1 else [crop_paths_rel] return { "qry_inst": "<|image_1|> Locate the specific region that corresponds to the provided text description.", "qry_text": record["class_name"], "qry_img_path": img_path_rel, "tgt_inst": "Match the target", "tgt_text": ["<|image_1|>\n"], "tgt_img_path": tgt_img_path, } def sample_test_data(data, max_samples, seed=RANDOM_SEED): if len(data) <= max_samples: return data rng = random.Random(seed) path_to_samples = {} for s in data: path_to_samples.setdefault(s["qry_img_path"], []).append(s) unique_paths = list(path_to_samples.keys()) rng.shuffle(unique_paths) sampled = [] for path in unique_paths: sampled.append(rng.choice(path_to_samples[path])) if len(sampled) >= max_samples: break if len(sampled) < max_samples: selected_ids = {id(x) for x in sampled} remaining = [x for x in data if id(x) not in selected_ids] rng.shuffle(remaining) sampled.extend(remaining[:max_samples - len(sampled)]) rng.shuffle(sampled) return sampled def main(): os.makedirs(CROP_DIR, exist_ok=True) with open(CSV_PATH, newline="") as f: rows = list(csv.DictReader(f)) print(f"Raw rows: {len(rows)}") groups = defaultdict(list) patient_id_map = {} img_split = {} all_categories = set() for row in rows: if not row.get("resized_xmin", "").strip(): continue categories = ast.literal_eval(row["finding_categories"]) if categories == ["No Finding"]: continue bbox = ( max(0, int(float(row["resized_xmin"]))), max(0, int(float(row["resized_ymin"]))), max(0, int(float(row["resized_xmax"]))), max(0, int(float(row["resized_ymax"]))), ) image_id = row["image_id"].replace(".png", "") patient_id_map[image_id] = row["patient_id"] img_split[image_id] = row["split"] for cat in categories: if cat == "No Finding": continue groups[(image_id, cat)].append(bbox) all_categories.add(cat) cat_to_id = {cat: idx for idx, cat in enumerate(sorted(all_categories))} print(f"Categories ({len(cat_to_id)}): {cat_to_id}") tasks = [ (key, boxes, cat_to_id[key[1]], patient_id_map[key[0]], img_split[key[0]]) for key, boxes in groups.items() ] print(f"Total groups: {len(tasks)} Workers: {NUM_WORKERS}") train_records = [] test_records = [] errors = 0 with Pool(NUM_WORKERS) as pool: for i, (record, err) in enumerate( pool.imap_unordered(process_group, tasks, chunksize=16), start=1 ): if err: print(f" ERROR: {err}") errors += 1 elif record: entry = convert_record(record) if record["split"] == "training": train_records.append(entry) else: test_records.append(entry) if i % 500 == 0: print(f" [{i}/{len(tasks)}] errors={errors}") print(f"\nProcessing complete. errors={errors}") print(f" training samples : {len(train_records)}") print(f" test samples (before sampling): {len(test_records)}") test_records = sample_test_data(test_records, MAX_TEST_SAMPLES, RANDOM_SEED) print(f" test samples (after sampling): {len(test_records)}") for path, data in [(OUTPUT_TRAIN_JSON, train_records), (OUTPUT_TEST_JSON, test_records)]: os.makedirs(os.path.dirname(path), exist_ok=True) with open(path, "w", encoding="utf-8") as f: json.dump(data, f, ensure_ascii=False, indent=2) print(f" Saved: {path}") if __name__ == "__main__": main()