loris bids importer package

Author: MaximeBICMTL

.github/labeler.yml

@@ -6,6 +6,10 @@
 - changed-files:
   - any-glob-to-any-file: '**/*.py'
 
+"Package: BIDS importer":
+- changed-files:
+  - any-glob-to-any-file: 'python/loris_bids_importer/**'
+
 "Package: BIDS reader":
 - changed-files:
   - any-glob-to-any-file: 'python/loris_bids_reader/**'

pyproject.toml

@@ -24,6 +24,7 @@ dependencies = [
     "scipy",
     "sqlalchemy>=2.0.0",
     "typing-extensions",
+    "loris-bids-importer  @ {root:uri}/python/loris_bids_importer",
     "loris-bids-reader    @ {root:uri}/python/loris_bids_reader",
     "loris-dicom-importer @ {root:uri}/python/loris_dicom_importer",
     "loris-ephys-chunker  @ {root:uri}/python/loris_ephys_chunker",
@@ -53,6 +54,7 @@ packages = [
 members = ["python/loris_*"]
 
 [tool.uv.sources]
+loris_bids_importer  = { workspace = true }
 loris_bids_reader    = { workspace = true }
 loris_dicom_importer = { workspace = true }
 loris_ephys_chunker  = { workspace = true }
@@ -83,21 +85,23 @@ include = [
     "python/tests",
     "python/lib/db",
     "python/lib/imaging_lib",
-    "python/lib/import_bids_dataset",
     "python/lib/physio",
     "python/lib/config.py",
     "python/lib/config_file.py",
     "python/lib/env.py",
     "python/lib/get_session_info.py",
     "python/lib/logging.py",
     "python/lib/make_env.py",
-    "python/scripts/import_bids_dataset.py",
     "python/loris_bids_reader",
+    "python/loris_bids_importer",
     "python/loris_dicom_importer",
     "python/loris_ephys_chunker",
     "python/loris_utils",
 ]
 exclude = [
+    # Legacy EEG BIDS import code.
+    "python/loris_bids_importer/src/loris_bids_importer/eeg",
+    # Generated protocol buffer code.
     "python/loris_ephys_chunker/src/loris_ephys_chunker/protocol_buffers",
 ]
 typeCheckingMode = "strict"

python/lib/dcm2bids_imaging_pipeline_lib/nifti_insertion_pipeline.py

@@ -6,6 +6,8 @@
 import sys
 from pathlib import Path
 
+from loris_bids_importer.file_type import get_check_bids_imaging_file_type_from_extension
+from loris_bids_importer.mri.sidecar import add_bids_mri_sidecar_file_parameters, get_bids_mri_sidecar_session_info
 from loris_bids_reader.mri.sidecar import BidsMriSidecarJsonFile
 from loris_utils.crypto import compute_file_blake2b_hash, compute_file_md5_hash
 
@@ -19,8 +21,6 @@
 from lib.imaging_lib.file_parameter import register_mri_file_parameter, register_mri_file_parameters
 from lib.imaging_lib.nifti import add_nifti_spatial_file_parameters
 from lib.imaging_lib.nifti_pic import create_nifti_preview_picture
-from lib.import_bids_dataset.file_type import get_check_bids_imaging_file_type_from_extension
-from lib.import_bids_dataset.mri_sidecar import add_bids_mri_sidecar_file_parameters, get_bids_mri_sidecar_session_info
 from lib.logging import log_error_exit, log_verbose
 
 

python/lib/imaging.py

@@ -76,7 +76,7 @@ def __init__(self, db, verbose, config_file=None):
         self.param_type_db_obj = ParameterType(db, verbose)
         self.param_file_db_obj = ParameterFile(db, verbose)
 
-    @deprecated('Use `lib.import_bids_dataset.file_type.get_check_bids_imaging_file_type_from_extension` instead.')
+    @deprecated('Use `loris_bids_importer.file_type.get_check_bids_imaging_file_type_from_extension` instead.')
     def determine_file_type(self, file):
         """
         Greps all file types defined in the ImagingFileTypes table and checks

python/loris_bids_importer/README.md

@@ -0,0 +1,52 @@
+# LORIS BIDS importer
+
+## Description
+
+The LORIS BIDS importer is a pipeline that allows to ingest an external BIDS dataset into LORIS, populating both the database and the file-system.
+
+The LORIS BIDS importer supports the MRI (NIfTI), EEG/iEEG (EDF/EEGLAB), and MEG (CTF) modalities.
+
+## Installation
+
+This package is installed by default with LORIS Python.
+
+## Script
+
+The LORIS BIDS importer can be ran with the following command:
+
+```sh
+import-bids-dataset -d /path/to/bids/dataset`
+```
+
+The directory passed as an argument should be a BIDS compliant dataset (see the [BIDS specification](https://bids-specification.readthedocs.io/en/stable/)).
+
+## Parameters
+
+### Subject and session validation
+
+To be imported into LORIS, a BIDS dataset must adhere to the following rules:
+- The subject labels of the BIDS dataset should map to LORIS candidate CandIDs or PSCIDs.
+- The session labels of the BIDS dataset should map to LORIS visit labels.
+
+If the candidates or sessions do not exist yet in LORIS, they can be created automatically from the BIDS dataset information using the following options:
+- `--create-candidate`: Create new LORIS candidates, in which case the subject label must be a PSCID (and not a CandID).
+- `--create-session`: Create new LORIS sessions.
+
+Note that these options may require additional information such as the candidate and session projects, sites, and cohorts from the `participants.tsv`, `sessions.tsv`, or `scans.tsv` BIDS files.
+
+### File copy
+
+By default, the files imported from the source BIDS dataset are copied in a new BIDS dataset in the LORIS data directory. The `--no-copy` option allows to re-use the original BIDS files without copy if the source BIDS dataset is already located in the LORIS data directory.
+
+### Other parameters
+
+To see all the CLI parameters of the LORIS BIDS importer, use `import-bids-dataset --help`.
+
+## Supported files
+
+The LORIS BIDS importer can import the following BIDS files:
+- Static dataset files: `dataset_description.json`, `README`.
+- Dataset structure files: `participants.tsv`, `scans.tsv`.
+- MRI acquisition files: NIfTI (`.nii`, `.nii.gz`) and their JSON sidecars.
+- EEG/iEEG/MEG acquisition files: EDF (`.edf`), EEGLAB (`.set`), CTF (`.ds` directories), and their JSON sidecars.
+- EEG/iEEG/MEG metadata files: `coordsystem.json`, `electrodes.tsv`, `channels.tsv`, `events.json`, `events.tsv`.

python/loris_bids_importer/pyproject.toml

@@ -0,0 +1,28 @@
+[project]
+name = "loris-bids-importer"
+version = "27.0.0"
+description = "The LORIS BIDS importer"
+readme = "README.md"
+license = "GPL-3.0-or-later"
+requires-python = ">= 3.11"
+dependencies = [
+    "loris-bids-reader",
+    "loris-utils",
+]
+
+[project.scripts]
+import-bids-dataset = "loris_bids_importer.scripts.import_bids_dataset:main"
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/loris_bids_importer"]
+
+[tool.ruff]
+extend = "../../pyproject.toml"
+src = ["src"]

…/lib/import_bids_dataset/acquisitions.py …/src/loris_bids_importer/acquisitions.pypython/lib/import_bids_dataset/acquisitions.py renamed to python/loris_bids_importer/src/loris_bids_importer/acquisitions.py python/lib/import_bids_dataset/acquisitions.py renamed to python/loris_bids_importer/src/loris_bids_importer/acquisitions.py

@@ -1,11 +1,11 @@
 from collections.abc import Callable
 from typing import TypeVar
 
-from loris_bids_reader.info import BidsAcquisitionInfo
-
 from lib.env import Env
-from lib.import_bids_dataset.env import BidsImportEnv
 from lib.logging import log, log_error
+from loris_bids_reader.info import BidsAcquisitionInfo
+
+from loris_bids_importer.env import BidsImportEnv
 
 T = TypeVar('T')
 

python/lib/import_bids_dataset/archive.py …orter/src/loris_bids_importer/archive.pypython/lib/import_bids_dataset/archive.py renamed to python/loris_bids_importer/src/loris_bids_importer/archive.py python/lib/import_bids_dataset/archive.py renamed to python/loris_bids_importer/src/loris_bids_importer/archive.py

@@ -1,14 +1,13 @@
 from pathlib import Path
 
-from loris_utils.archive import create_archive_with_files
-from loris_utils.crypto import compute_file_blake2b_hash
-from loris_utils.path import remove_path_extension
-
 from lib.config import get_data_dir_path_config, get_ephys_archive_dir_path_config
 from lib.db.models.physio_event_archive import DbPhysioEventArchive
 from lib.db.models.physio_file import DbPhysioFile
 from lib.db.models.physio_file_archive import DbPhysioFileArchive
 from lib.env import Env
+from loris_utils.archive import create_archive_with_files
+from loris_utils.crypto import compute_file_blake2b_hash
+from loris_utils.path import remove_path_extension
 
 
 def import_physio_file_archive(env: Env, physio_file: DbPhysioFile, file_paths: list[Path]):

python/lib/import_bids_dataset/args.py …importer/src/loris_bids_importer/args.pypython/lib/import_bids_dataset/args.py renamed to python/loris_bids_importer/src/loris_bids_importer/args.py python/lib/import_bids_dataset/args.py renamed to python/loris_bids_importer/src/loris_bids_importer/args.py

@@ -1,20 +1,20 @@
 from pathlib import Path
 
-from loris_bids_reader.eeg.channels import BidsEegChannelsTsvFile, BidsEegChannelTsvRow
-from loris_bids_reader.info import BidsAcquisitionInfo
-from loris_utils.crypto import compute_file_blake2b_hash
-from loris_utils.error import group_errors, group_errors_tuple
-
 from lib.db.models.physio_channel_type import DbPhysioChannelType
 from lib.db.models.physio_file import DbPhysioFile
 from lib.db.models.physio_status_type import DbPhysioStatusType
 from lib.db.models.session import DbSession
 from lib.db.queries.physio_channel import try_get_channel_type_with_name, try_get_status_type_with_name
 from lib.env import Env
-from lib.import_bids_dataset.copy_files import get_loris_bids_file_path
-from lib.import_bids_dataset.env import BidsImportEnv
 from lib.physio.channels import insert_physio_channel
 from lib.physio.parameters import insert_physio_file_parameter
+from loris_bids_reader.eeg.channels import BidsEegChannelsTsvFile, BidsEegChannelTsvRow
+from loris_bids_reader.info import BidsAcquisitionInfo
+from loris_utils.crypto import compute_file_blake2b_hash
+from loris_utils.error import group_errors, group_errors_tuple
+
+from loris_bids_importer.copy_files import get_loris_bids_file_path
+from loris_bids_importer.env import BidsImportEnv
 
 
 def insert_bids_channels_file(