correct_ilastik_abspath.py

from os.path import relpath
from pathlib import Path
import shutil

import h5py

def make_abspath_to_relpath(ilp_filename: str, my_root: Path, their_root: Path):
    pa_ilp_old = my_root / ilp_filename
    assert pa_ilp_old.exists()
    pa_ilp_new = pa_ilp_old.parent / f'relpath_{pa_ilp_old.name}'
    with h5py.File(shutil.copy(pa_ilp_old, pa_ilp_new), 'r+') as h5:
        infos = h5['Input Data/infos']
        for lane in infos.keys():
            for role in infos[lane].keys():
                if len(infos[lane][role]) == 0:
                    continue
                pa_img_abs = Path(infos[lane][role]['filePath'][()].decode())
                my_ilp_dir = (my_root / ilp_filename).parent
                their_ilp_dir = (their_root / ilp_filename).parent
                pa_img_rel = Path(relpath(pa_img_abs, their_ilp_dir))
                if pa_img_rel.parts[-2].upper().endswith('.H5'):
                    assert (my_ilp_dir / Path(*pa_img_rel.parts[0:-1])).exists()
                else:
                    assert (my_ilp_dir / pa_img_rel).exists()
                del infos[lane][role]['filePath']
                infos[lane][role]['filePath'] = str(pa_img_rel)
    return pa_ilp_new




if __name__ == '__main__':
    files = [
        '01_ilastik_files/240301_LSM900_DNA_PC.ilp',
        '01_ilastik_files/240320_LSM900_DNA_OC_new.ilp',
        '01_ilastik_files/240301_LSM900_TM_PC.ilp',
        '01_ilastik_files/240320_LSM900_TM_OC_new.ilp'
    ]
    for f in files:
        new_ilp = make_abspath_to_relpath(
            f,
            Path('w:/03_analysis/Trial3_LSM900'),
            Path('/g/cuylen/01_Share/Filemaker/01_Experiments/Experiments_1100/1156/03_analysis/Trial3_LSM900')
        )
        print(f'Finished converting {new_ilp}')