Merge pull request Open-Minds-Lab#34 from sinhaharsh/main

Skipping physiological continuous recordings
sinhaharsh · Mar 8, 2024 · 8f9cb96 · 8f9cb96
2 parents 6a2ff66 + 5a0e19c
commit 8f9cb96
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Showing 2 changed files with 14 additions and 5 deletions.
diff --git a/MRdataset/bids.py b/MRdataset/bids.py
@@ -131,11 +131,11 @@ def _process(self, folder):
                 sequences.append(seq)
             else:
                 if name not in SUPPORTED_BIDS_DATATYPES:
-                    logger.error(f'MRdataset primarily supports '
-                                 f'{SUPPORTED_BIDS_DATATYPES}'
-                                 f'It seems the parameters in '
-                                 f'this sequence are invalid or '
-                                 f'not supported yet. Skipping it.')
+                    logger.warning(f'MRdataset primarily supports '
+                                   f'{SUPPORTED_BIDS_DATATYPES} .'
+                                   f'It seems the parameters in '
+                                   f'this sequence are invalid or '
+                                   f'not supported yet. Skipping it.')
         return sequences
 
     @staticmethod

diff --git a/MRdataset/dicom_utils.py b/MRdataset/dicom_utils.py
@@ -33,6 +33,15 @@ def is_bids_file(filename: Union[str, Path]):
         return False
     if 'sourcedata' in str(filename):
         return False
+
+    # TODO: Add support for physiological and other continuous
+    #  recordings. Skip for now.
+    #  See : https://bids-specification.readthedocs.io/en/stable/modality-specific-files/physiological-and-other-continuous-recordings.html # noqa
+    #  Example dataset on OpenNeuro : ds002785
+    if '_physio.' in str(filename):
+        return False
+    if '_stim.' in str(filename):
+        return False
     # Regular expression pattern
     pattern = r'sub-[^_]+'
     # Extracting substring using regex