Dataloader/deal_with_json.py

import os, sys
ROOT_DIR = os.path.dirname(os.path.abspath(__file__))
sys.path.append(ROOT_DIR)
import json

# CORRECT_DATA_PATH = os.path.join(ROOT_DIR, '../..')
# CORRECT_DATA_PATH = os.path.join('/hy-tmp')
CORRECT_DATA_PATH = '/home/dn-zhen2/rds/rds-airr-p51-TWhPgQVLKbA/Data/Omini3D'


def traverse_and_print(data, path=()):
    for key, value in data.items():
        current_path = path + (key,)

        if isinstance(key, str) and 'DATASETS' in key:
            print(f"KEY (str): {key}")

        if isinstance(value, str) and 'DATASETS' in value:
            print(f"  VALUE (str): {value}")
        elif isinstance(value, dict):
            traverse_and_print(value, current_path)

def traverse_and_check(data, path=()):
    failed_files = []
    for key, value in data.items():
        current_path = path + (key,)

        if isinstance(key, str) and 'DATASETS_processed' in key:
            if os.path.isfile(key):
                print(f'\rCheck pass: {key}', end='')
            else:
                print(f'\rCheck fail ! : {key}')
                failed_files.append(key)

        if isinstance(value, str) and 'DATASETS_processed' in value:
            if os.path.isfile(value):
                print(f'\rCheck pass: {value}', end='')
            else:
                print(f'\rCheck fail ! : {value}')
                failed_files.append(value)
        elif isinstance(value, dict):
            traverse_and_check(value, current_path)
    
    if failed_files != []:
        print(f'\nCheck finished. Failed files: {failed_files}')
        return False
    else:
        print('\nAll files check passed!')
        return True

def traverse_and_revise(data, path=()):
    what_need_change = [
        '/home/jachin/data/Github/data/data_gen_def',
        '/home/data/Github/data/data_gen_def',
    ]
    for key, value in list(data.items()):
        current_path = path + (key,)

        new_key = key
        if isinstance(key, str) and 'data_gen_def' in key:
            for wnc in what_need_change:
                if wnc in key:
                    new_key = key.replace(wnc, CORRECT_DATA_PATH)
            
            # change keys
            data[new_key] = data.pop(key)
            value = data[new_key]
            current_path = path + (new_key,)

        if isinstance(value, str) and 'data_gen_def' in value:
            for wnc in what_need_change:
                if wnc in value:
                    data[new_key] = value.replace(wnc, CORRECT_DATA_PATH)

        elif isinstance(value, dict):
            traverse_and_revise(value, current_path)
    
    return data

def traverse_and_rename_label(data, old_label, new_label, task_keys=("segmentation", "registration")):
    """Rename a label key inside Label_path -> segmentation/registration for every entry.

    Example: rename "brain" -> "brain_tumour" to fix the BraTS mislabel.
    """
    count = 0
    for key, value in data.items():
        if not isinstance(value, dict):
            continue
        label_path = value.get("Label_path")
        if isinstance(label_path, dict):
            for tk in task_keys:
                task_dict = label_path.get(tk)
                if isinstance(task_dict, dict) and old_label in task_dict:
                    task_dict[new_label] = task_dict.pop(old_label)
                    count += 1
        else:
            # recurse into nested dicts
            count += traverse_and_rename_label(value, old_label, new_label, task_keys)
    return count


mapping_files = {
    'MSD': 'nifty_mappings/MSD_mappings.json',
    'TotalSegmentor': 'nifty_mappings/TotalSegmentorCT_MRI_mappings.json',
    'Kaggle_osic': 'nifty_mappings/Kaggle_osic_mappings.json',
    'CancerImageArchive': 'nifty_mappings/CIA_mappings.json',
    'MnMs': 'nifty_mappings/MnMs_mappings.json',
    'Brats2019': 'nifty_mappings/Brats2019_mappings.json',
    'Brats2020': 'nifty_mappings/Brats2020_mappings.json',
    'Brats2021': 'nifty_mappings/Brats2021_mappings.json',
    'OASIS_1': 'nifty_mappings/OASIS_1_mappings.json',
    'OASIS_2': 'nifty_mappings/OASIS_2_mappings.json',
    'PSMA-FDG-PET-CT-LESION':'nifty_mappings/PSMA-FDG-PET-CT-LESION_mappings.json',
    'PSMA-CT':'nifty_mappings/PSMA-CT-Longitud_mappings.json',
    'AbdomenAtlas':'nifty_mappings/AbdomenAtlas_mappings.json',
    'AbdomenCT1k':'nifty_mappings/AbdomenCT1k_mappings.json',
}
for k,v in mapping_files.items():
    mapping_files[k] = os.path.join(ROOT_DIR, v)


if __name__ == "__main__":
    # --- Fix BraTS / MSD mislabel: "brain" -> "brain_tumour" ---
    rename_datasets = ['Brats2019', 'Brats2020', 'Brats2021', 'MSD']
    for ds_name in rename_datasets:
        if ds_name not in mapping_files:
            continue
        v = mapping_files[ds_name]
        with open(v, 'r') as f:
            mappings_tmp = json.load(f)
        n = traverse_and_rename_label(mappings_tmp, 'brain', 'brain_tumour')
        if n > 0:
            with open(v, 'w') as f:
                json.dump(mappings_tmp, f, indent=4)
            print(f'[{ds_name}] Renamed "brain" -> "brain_tumour" in {n} entries, saved to {v}')
        else:
            print(f'[{ds_name}] No "brain" labels found (already renamed?)')

    # --- Path revision (uncomment to run) ---
    # for k,v in mapping_files.items():
    #     with open(v, 'r') as f:
    #         mappings_tmp = json.load(f)
    #         new_mappings_tmp = traverse_and_revise(mappings_tmp)
    #         # traverse_and_print(new_mappings_tmp)
    #         # all_good = traverse_and_check(new_mappings_tmp)
    #     # save in-place
    #     with open(v, 'w') as f:
    #         json.dump(new_mappings_tmp, f, indent=4)
    #     print(f'Saved revised mapping to {v}')