| import os |
| from concurrent.futures import ThreadPoolExecutor |
| from tqdm import tqdm |
|
|
| DATA_DIR = "/home/wenting/zr/Segmentation/data/lidc_TotalSeg" |
| EXPECTED_COUNT = 3000 |
|
|
| def check_patient(patient_folder): |
| patient_dir = os.path.join(DATA_DIR, patient_folder) |
| if not os.path.isdir(patient_dir): |
| return None |
| |
| img_dir = os.path.join(patient_dir, "04_drr_256", "cxr") |
| mask_dir = os.path.join(patient_dir, "04_drr_256", "mask_compact") |
| meta_path = os.path.join(patient_dir, "02_totalseg", "phase2_metadata.json") |
| |
| status = {"patient": patient_folder, "imgs": 0, "masks": 0, "has_meta": False, "issue": ""} |
| |
| |
| if os.path.exists(meta_path): |
| status["has_meta"] = True |
| else: |
| status["issue"] += "Missing metadata JSON. " |
| |
| |
| if os.path.exists(img_dir): |
| |
| status["imgs"] = len([f for f in os.scandir(img_dir) if f.name.endswith('.png')]) |
| else: |
| status["issue"] += "Missing cxr dir. " |
| |
| |
| if os.path.exists(mask_dir): |
| status["masks"] = len([f for f in os.scandir(mask_dir) if f.name.endswith('.npz')]) |
| else: |
| status["issue"] += "Missing mask dir. " |
| |
| if status["imgs"] != EXPECTED_COUNT or status["masks"] != EXPECTED_COUNT or not status["has_meta"]: |
| return status |
| return None |
|
|
| def main(): |
| patients = sorted([d for d in os.listdir(DATA_DIR) if d.startswith("LIDC-IDRI-")]) |
| print(f"[*] Scanning {len(patients)} patients in {DATA_DIR}...") |
| |
| anomalies =[] |
| |
| with ThreadPoolExecutor(max_workers=16) as executor: |
| results = list(tqdm(executor.map(check_patient, patients), total=len(patients))) |
| |
| for res in results: |
| if res is not None: |
| anomalies.append(res) |
| |
| print("\n" + "="*50) |
| print(f"[*] Found {len(anomalies)} patients with incomplete data:") |
| print("="*50) |
| |
| for a in anomalies: |
| issue_str = a["issue"] if a["issue"] else f"Incomplete pairs (Imgs: {a['imgs']}, Masks: {a['masks']})" |
| print(f"- {a['patient']}: {issue_str}") |
|
|
| if __name__ == "__main__": |
| main() |
