def generate_readme(self):
"""
It is recommended by BIDS specifications to have a README file at the
base of our project, so we create a blank one for further usage.
"""
bids_dir = get_bids_dir()
bids_dir.mkdir(exist_ok=True, parents=True)
readme = bids_dir / "README"
if not readme.is_file():
readme_template = TEMPLATES_DIR / "README"
shutil.copy(str(readme_template), str(readme))
def generate_bidsignore(self):
"""
Some acquisitions do not conform to BIDS specification (mainly
localizers), so we generate a .bidsignore file, pointing to them.
References
----------
* `BIDS validator specifications`_
.. _BIDS validator specifications:
https://neuroimaging-core-docs.readthedocs.io/en/latest/pages/bids-validator.html
"""
bids_dir = get_bids_dir()
bids_dir.mkdir(exist_ok=True, parents=True)
bidsignore = bids_dir / ".bidsignore"
with open(bidsignore, "w+") as in_file:
in_file.write("**/*ignore-bids*\n")
def set_participant_tsv_and_json(self, scan):
"""
Generates recommended "participants.tsv" by either copying the
template from TEMPLATES_DiR or editing an existing one under {parent}
directory.
Parameters
----------
parent : Path
BIDS-compatible directory, underwhich there are "sub-x" directories
subject_dict : dict
Subject's parameters dictionary, containing "participant_id",
"handedness","age","sex" fields
References
----------
* `BIDS complementary files`_
.. _BIDS complementary files:
https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html
"""
bids_dir = get_bids_dir()
bids_dir.mkdir(exist_ok=True, parents=True)
subject_dict = self.get_subject_data(scan)
participants_tsv = bids_dir / self.PARTICIPANTS_FILE_NAME
participants_json = participants_tsv.with_suffix(".json")
for participants_file in [participants_tsv, participants_json]:
if not participants_file.is_file():
participants_template = TEMPLATES_DIR / participants_file.name
shutil.copy(str(participants_template), str(participants_file))
participants_df = pd.read_csv(participants_tsv, sep="\t")
subject_dict[
"participant_id"
] = f"sub-{subject_dict['participant_id']}"
if (
not subject_dict["participant_id"]
in participants_df["participant_id"].values
):
participants_df = participants_df.append(
pd.DataFrame(subject_dict, index=[0]), ignore_index=True
)
participants_df.to_csv(participants_tsv, sep="\t", index=False)
else:
pass
def set_description_json(self):
"""
Generates required "dataset_description.json" file, as stated by BIDS
structure.
References
----------
* `BIDS complementary files`_
.. _BIDS complementary files:
https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html
"""
bids_dir = get_bids_dir()
bids_dir.mkdir(exist_ok=True, parents=True)
description_file = bids_dir / self.DATASET_DESCRIPTION_FILE_NAME
if not description_file.is_file():
description_template = TEMPLATES_DIR / description_file.name
description_file.parent.mkdir(exist_ok=True)
shutil.copy(str(description_template), str(description_file))
def build_bids_path(self, scan):
"""
Uses parameters extracted by :func:`get_subject_data` to update BIDS-
compatible file path derived from *dicom_parser*
Returns
-------
pathlib.Path
Full path to an updated BIDS-compatible file, according to scan's
parameters.
"""
self._logger.debug(
f"Building BIDS-compatible path for scan #{scan.id}"
)
subject_id = scan.session.subject.id
sample_header = scan.dicom.get_sample_header()
default_bids_path = sample_header.build_bids_path()
if default_bids_path is None:
raise ValueError(
"BIDS path could not be derived from scan parameters."
)
self._logger.debug(
f"Default relative path generated by dicom_parser based on DICOM metadata:\n{default_bids_path}" # noqa: E501
)
self._logger.debug("Replacing Patient ID with subject primary key...")
default_subject_id = sample_header.get("PatientID")
fixed_relative_path = default_bids_path.replace(
f"sub-{default_subject_id}", f"sub-{subject_id}"
)
self._logger.debug(f"Result: {fixed_relative_path}")
bids_path = get_bids_dir() / fixed_relative_path
self._logger.debug(f"Checking for an existing file at {bids_path}")
path_with_suffix = {
bids_path.with_suffix(".nii"),
bids_path.with_suffix(".nii.gz"),
}
try:
existing = NIfTI.objects.get(path__in=path_with_suffix)
except NIfTI.DoesNotExist:
self._logger.debug("No existing NIfTI file found! All done.")
return bids_path
else:
self._logger.debug(f"Existing NIfTI (#{existing.id}) found!")
if scan._nifti == existing:
self._logger.debug(
"Existing NIfTI instance belongs to queried scan!"
)
path = Path(existing.path)
return path.parent / path.name.split(".")[0]
self._logger.debug(
f"Checking for an existing run label in scan #{scan.id}."
)
try:
existing_run_label = re.findall(
self.RUN_PATTERN, str(bids_path)
)[0]
except IndexError:
self._logger.debug("No existing run label found.")
self._logger.debug(f"Renaming {scan.id} to include run label.")
existing_run_label = self.RUN_LABEL_TEMPLATE.format(index=1)
name_parts = Path(existing.path).name.split("_")
name_parts.insert(-1, existing_run_label)
name_with_run = "_".join(name_parts)
updated_path = bids_path.parent / name_with_run
existing.rename(updated_path)
self._logger.debug(
f"Scan #{scan.id} successfully moved to {bids_path}"
)
new_run_label = self.RUN_LABEL_TEMPLATE.format(index=2)
bids_path = (
updated_path.parent / updated_path.name.split(".")[0]
)
else:
self._logger.debug(
f"Existing run label found: {existing_run_label}"
)
existing_run_index = int(existing_run_label.split("-"))
index = existing_run_index + 1
new_run_label = self.RUN_LABEL_TEMPLATE.format(index=index)
self._logger.debug(f"New run label: {new_run_label}")
return Path(
str(bids_path).replace(existing_run_label, new_run_label)
)