feat(bids.dataset): add methods to support the creation of an initial BIDS dataset (8b95bcc0) · Commits · HIP / DataHIPy

bids_tools/bids/dataset.py

+80 −0

Original line number	Diff line number	Diff line
		@@ -27,6 +27,86 @@ from bids_tools.bids.version import determine_bids_schema_version
		NUM_THREADS = os.cpu_count() - 1 if os.cpu_count() > 1 else 1


		def create_initial_bids_readme(bids_dir, dataset_desc):
		"""Create an initial `README` file for a BIDS dataset.

		Parameters
		----------
		bids_dir : str
		Path to the BIDS dataset.

		dataset_desc : dict
		Dictionary with the content of the dataset_description.json file.
		"""
		with open(os.path.join(bids_dir, "README"), "w") as f:
		f.writelines(
		[
		f'# {dataset_desc["Name"]}\n\n',
		f"To be completed...\n\n",
		f"Use it as the dataset landing page, "
		"which should provide enough information "
		"about the dataset and its creation context.",
		]
		)


		def create_initial_bids_changes(bids_dir):
		"""Create an initial `CHANGES` file for a BIDS dataset.

		Parameters
		----------
		bids_dir : str
		Path to the BIDS dataset.
		"""
		with open(os.path.join(bids_dir, "CHANGES"), "w") as f:
		f.writelines(
		[
		f"0.0.0 {date.today().strftime('%Y-%m-%d')}\n",
		"\t- Creation of the dataset.",
		]
		)


		def create_initial_participants_tsv(bids_dir):
		"""Create an initial `participants.tsv` file for a BIDS dataset.

		Parameters
		----------
		bids_dir : str
		Path to the BIDS dataset.
		"""
		with open(os.path.join(bids_dir, "participants.tsv"), "w") as f:
		f.write("participant_id\tage\tsex\tgroup")


		def create_empty_bids_dataset(bids_dir=None, dataset_desc=None):
		"""Create an empty BIDS dataset.

		Parameters
		----------
		bids_dir : str
		Path to the BIDS dataset.

		dataset_desc : dict
		Dictionary with the content of the dataset_description.json file.
		"""
		print("> Creating an empty BIDS dataset at: ", bids_dir, "...")
		# Create the BIDS dataset directory
		os.makedirs(bids_dir, exist_ok=True)
		# Create the dataset_description.json file
		with open(os.path.join(bids_dir, "dataset_description.json"), "w") as f:
		json.dump(dataset_desc, f, indent=4)
		# Create initial README file
		create_initial_bids_readme(bids_dir, dataset_desc)
		# Create initial CHANGES file
		create_initial_bids_changes(bids_dir)
		# Create the .bidsignore file and add the line to ignore CT files
		# (not yet supported by the validator)
		add_bidsignore_validation_rule(bids_dir, "*/_ct.*")
		# Create an initial participants.tsv file
		create_initial_participants_tsv(bids_dir)


		def create_bids_layout(bids_dir=None, **kwargs):
		"""Create a pybids representation of a BIDS dataset.