Make the EEG chunker into a standalone Python package

.github/labeler.yml

@@ -5,3 +5,7 @@
 "Language: Python":
 - changed-files:
   - any-glob-to-any-file: '**/*.py'
+
+"Package: EEG chunker":
+- changed-files:
+  - any-glob-to-any-file: 'python/loris_eeg_chunker/**'

install/templates/environment_template

@@ -6,7 +6,7 @@ source ${MINC_TOOLKIT_DIR}/minc-toolkit-config.sh
 umask 0002
 
 # export PATH, PERL5LIB, TMPDIR and LORIS_CONFIG variables
-export PATH=/opt/${PROJECT}/bin/mri:/opt/${PROJECT}/bin/mri/uploadNeuroDB:/opt/${PROJECT}/bin/mri/uploadNeuroDB/bin:/opt/${PROJECT}/bin/mri/dicom-archive:/opt/${PROJECT}/bin/mri/python/scripts:/opt/${PROJECT}/bin/mri/tools:/opt/${PROJECT}/bin/mri/python/loris_eeg_chunker:${MINC_TOOLKIT_DIR}/bin:/usr/local/bin/tpcclib:$PATH
+export PATH=/opt/${PROJECT}/bin/mri:/opt/${PROJECT}/bin/mri/uploadNeuroDB:/opt/${PROJECT}/bin/mri/uploadNeuroDB/bin:/opt/${PROJECT}/bin/mri/dicom-archive:/opt/${PROJECT}/bin/mri/python/scripts:/opt/${PROJECT}/bin/mri/tools:${MINC_TOOLKIT_DIR}/bin:/usr/local/bin/tpcclib:$PATH
 export PERL5LIB=/opt/${PROJECT}/bin/mri/uploadNeuroDB:/opt/${PROJECT}/bin/mri/dicom-archive:$PERL5LIB
 export TMPDIR=/tmp
 export LORIS_CONFIG=/opt/${PROJECT}/bin/mri/config

pyproject.toml

@@ -12,24 +12,21 @@ license-files = ["LICENSE"]
 requires-python = ">= 3.11"
 dependencies = [
     "boto3==1.35.99",
-    "google",
     "mat73",
     "matplotlib",
-    "mne",
-    "mne-bids>=0.14",
     "mysqlclient",
     "nibabel",
     "nilearn",
     "nose",
     "numpy",
-    "protobuf>=3.0.0",
     "pybids==0.17.0",
     "pydicom",
     "python-dateutil",
     "scikit-learn",
     "scipy",
     "sqlalchemy>=2.0.0",
     "virtualenv",
+    "loris-eeg-chunker @ {root:uri}/python/loris_eeg_chunker",
 ]
 
 [project.optional-dependencies]
@@ -42,10 +39,12 @@ dev = [
 [project.urls]
 Homepage = "https://github.com/aces/loris-mri"
 
+[tool.hatch.metadata]
+allow-direct-references = true
+
 [tool.hatch.build.targets.wheel]
 packages = [
     "python/lib",
-    "python/loris_eeg_chunker",
     "python/tests",
 ]
 

python/lib/physiological.py

@@ -1234,12 +1234,13 @@ def create_chunks_for_visualization(self, physio_file_id, data_dir):
 
             # determine which script to run based on the file type
             file_type = self.grep_file_type_from_file_id(physio_file_id)
-            if file_type == 'set':
-                script = os.environ['LORIS_MRI'] + '/python/loris_eeg_chunker/eeglab_to_chunks.py'
-                command = 'python ' + script + ' ' + full_file_path + ' --destination ' + chunk_root_dir
-            elif file_type == 'edf':
-                script = os.environ['LORIS_MRI'] + '/python/loris_eeg_chunker/edf_to_chunks.py'
-                command = 'python ' + script + ' ' + full_file_path + ' --destination ' + chunk_root_dir
+            match file_type:
+                case 'set':
+                    script = 'eeglab-to-chunks'
+                case 'edf':
+                    script = 'edf-to-chunks'
+
+            command = script + ' ' + full_file_path + ' --destination ' + chunk_root_dir
 
             # chunk the electrophysiology dataset if a command was determined above
             try:

python/loris_eeg_chunker/README.md

@@ -1,3 +1,5 @@
+# LORIS EEG chunker
+
 Set of scripts to chunk EEG data in smaller bits for the React viewer of LORIS.
 
 These scripts were extracted on July 8th, 2019 from the master branch of the

python/loris_eeg_chunker/pyproject.toml

@@ -1,3 +1,31 @@
+[project]
+name = "loris-eeg-chunker"
+version = "27.0.0"
+description = "The LORIS EEG chunker"
+readme = "README.md"
+license = "GPL-3.0-or-later"
+requires-python = ">= 3.11"
+dependencies = [
+    "google",
+    "mne",
+    "mne-bids>=0.14",
+    "numpy",
+    "protobuf>=3.0.0",
+    "scipy",
+]
+
+[project.scripts]
+edf-to-chunks    = "loris_eeg_chunker.scripts.edf_to_chunks:main"
+eeglab-to-chunks = "loris_eeg_chunker.scripts.eeglab_to_chunks:main"
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/loris_eeg_chunker"]
+
 [tool.ruff]
 extend = "../../pyproject.toml"
+src = ["src"]
 exclude = ["protocol_buffers"]

python/loris_eeg_chunker/edf_to_chunks.py → python/loris_eeg_chunker/src/loris_eeg_chunker/scripts/edf_to_chunks.py

@@ -13,7 +13,7 @@ def load_channels(exclude):
     return lambda path : mne.io.read_raw_edf(path, exclude=exclude, preload=False)
 
 
-if __name__ == '__main__':
+def main():
     parser = argparse.ArgumentParser(
         description='Convert .edf files to chunks for browser based visualisation.')
     parser.add_argument('files', metavar='FILE', type=str, nargs='+',
@@ -87,3 +87,7 @@ def load_channels(exclude):
                 destination=args.destination,
                 prefix=args.prefix
             )
+
+
+if __name__ == '__main__':
+    main()

python/loris_eeg_chunker/eeglab_to_chunks.py → python/loris_eeg_chunker/src/loris_eeg_chunker/scripts/eeglab_to_chunks.py

@@ -13,7 +13,7 @@ def load_channels(path):
     return mne.io.read_raw_eeglab(path, preload=False)
 
 
-if __name__ == '__main__':
+def main():
     parser = argparse.ArgumentParser(
         description='Convert .set files to chunks for browser based visualisation.')
     parser.add_argument('files', metavar='FILE', type=str, nargs='+',
@@ -57,3 +57,7 @@ def load_channels(path):
             destination=args.destination,
             prefix=args.prefix
         )
+
+
+if __name__ == '__main__':
+    main()

test/mri.Dockerfile

@@ -86,7 +86,7 @@ RUN bash ./test/imaging_install_test.sh $DATABASE_NAME $DATABASE_USER $DATABASE_
 # Setup the LORIS-MRI environment variables
 ENV PROJECT=loris
 ENV MINC_TOOLKIT_DIR=/opt/minc/1.9.18
-ENV PATH=/opt/${PROJECT}/bin/mri:/opt/${PROJECT}/bin/mri/uploadNeuroDB:/opt/${PROJECT}/bin/mri/uploadNeuroDB/bin:/opt/${PROJECT}/bin/mri/dicom-archive:/opt/${PROJECT}/bin/mri/python/scripts:/opt/${PROJECT}/bin/mri/tools:/opt/${PROJECT}/bin/mri/python/loris_eeg_chunker:${MINC_TOOLKIT_DIR}/bin:/usr/local/bin/tpcclib:$PATH
+ENV PATH=/opt/${PROJECT}/bin/mri:/opt/${PROJECT}/bin/mri/uploadNeuroDB:/opt/${PROJECT}/bin/mri/uploadNeuroDB/bin:/opt/${PROJECT}/bin/mri/dicom-archive:/opt/${PROJECT}/bin/mri/python/scripts:/opt/${PROJECT}/bin/mri/tools:${MINC_TOOLKIT_DIR}/bin:/usr/local/bin/tpcclib:$PATH
 ENV PERL5LIB=/opt/${PROJECT}/bin/mri/uploadNeuroDB:/opt/${PROJECT}/bin/mri/dicom-archive:$PERL5LIB
 ENV TMPDIR=/tmp
 ENV LORIS_CONFIG=/opt/${PROJECT}/bin/mri/config