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[FIX] ADNI-to-BIDS fmap conversion : delete real/imaginary files prop…
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…erly, enable converting to the same folder for fmap (#1198)

* Adapt for mod_to_update and already renamed cases

* Add sessions to conversion errors

* Adapt unit tests

* Suggestions + conversion_errors list updated

* Add same logic for wrong suffixes

* Change variable name

* Add helper functions

* Add unit test 1

* Modify helper functions and add unit tests

* Small fixes
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@AliceJoubert
AliceJoubert authored Jun 5, 2024
1 parent b142b96 commit a2c7d06
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Showing 4 changed files with 300 additions and 108 deletions.
60 changes: 48 additions & 12 deletions clinica/iotools/converters/adni_to_bids/adni_modalities/adni_fmap.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -168,20 +168,43 @@ def compute_fmap_path(
# Exceptions
# ==========
conversion_errors = [
("006_S_4485", "m84"),
("123_S_4127", "m96"),
# Eq_1
("094_S_4503", "m24"),
("009_S_4388", "m72"),
("036_S_6088", "bl"),
("036_S_6134", "bl"),
("016_S_6802", "bl"),
("016_S_6816", "bl"),
("126_S_4891", "m84"),
("177_S_6448", "m24"),
("023_S_4115", "m126"),
# Multiple images
("029_S_2395", "m72"),
# Real/Imaginary
("002_S_1261", "m60"),
("002_S_1261", "m72"),
("002_S_1261", "m84"),
("002_S_1261", "m96"),
("006_S_4485", "bl"),
("006_S_4485", "m03"),
("006_S_4485", "m06"),
("006_S_4485", "m12"),
("006_S_4485", "m24"),
("006_S_4485", "m48"),
# Unrecognized BIDSCase
("006_S_4485", "m78"),
("009_S_4388", "m03"),
("009_S_4388", "m06"),
("009_S_4388", "m12"),
("009_S_4388", "m24"),
("009_S_4388", "m48"),
("023_S_4115", "bl"),
("023_S_4115", "m03"),
("023_S_4115", "m06"),
("023_S_4115", "m12"),
("023_S_4115", "m24"),
("023_S_4115", "m48"),
("123_S_4127", "bl"),
("123_S_4127", "m12"),
("123_S_4127", "m24"),
("123_S_4127", "m36"),
# Missing EchoTime Keys
("006_S_4485", "m90"),
("036_S_6088", "m12"),
("123_S_4127", "m84"),
# Missing DICOMS
("023_S_4115", "m126"),
("177_S_6448", "m24"),
]

# Removing known exceptions from images to convert
Expand Down Expand Up @@ -250,6 +273,7 @@ def fmap_image(


class BIDSFMAPCase(str, Enum):
ALREADY_RENAMED = "already_renamed"
EMPTY_FOLDER = "empty_folder"
ONE_PHASE_TWO_MAGNITUDES = "one_phase_two_magnitudes"
TWO_PHASES_TWO_MAGNITUDES = "two_phases_two_magnitudes"
Expand Down Expand Up @@ -295,6 +319,8 @@ def rename_files(fmap_path: Path, case: BIDSFMAPCase):


def fmap_case_handler_factory(case: BIDSFMAPCase) -> Callable:
if case == BIDSFMAPCase.ALREADY_RENAMED:
return already_renamed_handler
if case == BIDSFMAPCase.EMPTY_FOLDER:
return empty_folder_handler
if case == BIDSFMAPCase.ONE_PHASE_TWO_MAGNITUDES:
Expand Down Expand Up @@ -333,6 +359,14 @@ def check_json_contains_keys(json_file: Path, keys: Iterable[str]) -> bool:
return True


def already_renamed_handler(fmap_path: Path):
cprint(
f"Files for subject {fmap_path.parent.parent.name},"
f"session {fmap_path.parent.name} were already renamed.",
lvl="info",
)


def empty_folder_handler(fmap_path: Path):
cprint(
f"Folder for subject {fmap_path.parent.parent.name},"
Expand Down Expand Up @@ -409,6 +443,8 @@ def infer_case_fmap(fmap_path: Path) -> BIDSFMAPCase:

if nb_files == 0:
return BIDSFMAPCase.EMPTY_FOLDER
elif all([re.search(r"magnitude|phase", f) for f in files]):
return BIDSFMAPCase.ALREADY_RENAMED
elif nb_files == 4:
if extensions == {""}:
return BIDSFMAPCase.DIRECT_FIELDMAPS
Expand Down
108 changes: 68 additions & 40 deletions clinica/iotools/converters/adni_to_bids/adni_utils.py
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
from enum import Enum, auto
from pathlib import Path
from typing import List, Optional, Tuple, Union
from typing import Iterable, List, Optional, Tuple, Union

import pandas as pd

Expand Down Expand Up @@ -1365,10 +1365,64 @@ def paths_to_bids(
return [create_file_(image) for image in images_list]
with Pool(processes=n_procs) as pool:
output_file_treated = pool.map(create_file_, images_list)

return output_file_treated


def _get_images_with_suffix(
folder: Path,
suffixes: Iterable[str],
) -> Iterable[Path]:
import re

if suffixes:
rgx = re.compile(r"|".join(suffixes))
images = list(filter(rgx.search, [f.name for f in folder.iterdir()]))
return [folder / image for image in images]
return []


def _remove_existing_images_if_necessary(
folder: Path,
suffixes: Iterable[str],
mod_to_update: bool = False,
) -> bool:
"""Returns whether it was possible to delete the existing images or not."""
from clinica.utils.stream import cprint

images_to_remove = _get_images_with_suffix(folder, suffixes)
if not images_to_remove:
return True
elif mod_to_update:
cprint(f"Removing old images : {images_to_remove}", lvl="info")
for path_to_unlink in images_to_remove:
(path_to_unlink).unlink()
return True
cprint(
f"There already exist images : {images_to_remove}. "
"The parameter 'mod_to_update' is set to False so that "
"they cannot be overwritten.",
lvl="warning",
)
return False


def _remove_files_with_unsupported_suffixes(
folder: Path, suffixes: Iterable[str]
) -> Iterable[Path]:
from clinica.utils.stream import cprint

invalid_suffix_images = _get_images_with_suffix(folder, suffixes)
for image_to_remove in invalid_suffix_images:
cprint(
f"Image with bad suffix {', '.join(suffixes)} was generated by dcm2nix. These are not"
f"supported by Clinica so the image will NOT be converted.",
lvl="warning",
)
cprint(f"Removing image {folder / image_to_remove}", lvl="info")
(folder / image_to_remove).unlink()
return [folder / image for image in invalid_suffix_images]


def create_file(
image: pd.Series, modality: str, bids_dir: Path, mod_to_update: bool
) -> Optional[Path]:
Expand Down Expand Up @@ -1495,6 +1549,7 @@ def create_file(
modality = image.Tracer.lower()

if not image.Path:
# todo : check for message redundancy
cprint(
f"[{modality.upper()}] No path specified for {subject} in session {viscode}",
lvl="info",
Expand Down Expand Up @@ -1524,18 +1579,13 @@ def create_file(
)
output_path.mkdir(parents=True, exist_ok=True)

# If updated mode is selected, check if an old image is existing and remove it
for image_to_remove in output_path.glob(f"{output_filename}*"):
if not mod_to_update:
cprint(
f"There exists already an image at {image_to_remove}. "
"The parameter 'mod_to_update' is set to False such that "
"images cannot be overwritten.",
lvl="warning",
)
return None
cprint(f"Removing old image {image_to_remove}...", lvl="info")
image_to_remove.unlink()
# Check if old images exist and if updated mode is set to TRUE remove them
if not _remove_existing_images_if_necessary(
output_path,
(modality_specific[modality]["output_filename"], "magnitude", "phase"),
mod_to_update,
):
return None

try:
os.makedirs(output_path)
Expand Down Expand Up @@ -1571,32 +1621,10 @@ def create_file(
os.rename(trigger_time, no_trigger_time)

# Removing images with unsupported suffixes if generated by dcm2niix
for suffix in (
"ADC",
"real",
"imaginary",
"e1_real",
"e1_imaginary",
"e2_real",
"e2_imaginary",
):
file_with_bad_suffix = output_path / f"{output_filename}_{suffix}"
if any(
[
file_with_bad_suffix.with_suffix(s).exists()
for s in (".nii", ".nii.gz")
]
):
cprint(
f"Image with bad suffix {suffix} was generated by dcm2niix "
f"for subject {subject} and session {session} : "
f"{file_with_bad_suffix.with_suffix('.nii.gz')}. This image will NOT "
"be converted as the suffix is not supported by Clinica.",
lvl="warning",
)
for file_to_delete in output_path.glob(f"{output_filename}_{suffix}*"):
cprint(f"Deleting file {file_to_delete}.", lvl="info")
os.remove(file_to_delete)
# todo : maybe later use output to remind user what failed
_remove_files_with_unsupported_suffixes(
output_path, ("ADC", "real", "imaginary")
)

# Conditions to check if output NIFTI files exists,
# and, if DWI, if .bvec and .bval files are also present
Expand Down
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