Skip sorting all report files, as they have a very limited DICOM header and bump version to 4.5.2.dev2

Author: marcelzwiers

bidscoin/heuristics/bidsmap_bids2bids.yaml

@@ -20,7 +20,7 @@ Options:
 # General BIDScoin and plugin options
 # --------------------------------------------------------------------------------
   bidscoin:
-    version: 4.5.2.dev1                  # BIDScoin version (should correspond with the version in pyproject.toml)
+    version: 4.5.2.dev2                  # BIDScoin version (should correspond with the version in pyproject.toml)
     subprefix: sub-                 # The subject prefix of the source data
     sesprefix: ses-                 # The session prefix of the source data
     bidsignore: [extra_data/, sub-*_ct.*]    # List of entries that are added to the .bidsignore file (for more info, see BIDS specifications), e.g. [extra_data/, pet/, myfile.txt, yourfile.csv]

bidscoin/heuristics/bidsmap_dccn.yaml

@@ -21,7 +21,7 @@ Options:
 # General BIDScoin and plugin options
 # -----------------------------------
   bidscoin:
-    version: 4.5.2.dev1                  # BIDScoin version (should correspond with the version in pyproject.toml)
+    version: 4.5.2.dev2                  # BIDScoin version (should correspond with the version in pyproject.toml)
     subprefix: sub-                 # The subject prefix of the source data
     sesprefix: ses-                 # The session prefix of the source data
     bidsignore: [extra_data/, sub-*_ct.*]   # List of entries that are added to the .bidsignore file (for more info, see BIDS specifications), e.g. [extra_data/, pet/, myfile.txt, yourfile.csv]
@@ -1016,6 +1016,12 @@ DICOM:
       <<: *leaveout_attributes_dicom
       ProtocolName: (?i).*(Scout|localizer|t2_haste_sag_ipat2).*
     bids: *leaveout_bids_dicom
+  - attributes:
+      <<: *leaveout_attributes_dicom
+      Modality: SR
+    bids:
+      <<: *leaveout_bids_dicom
+      rec: REPORT
   - attributes:
       <<: *leaveout_attributes_dicom
       ImageType: .*'CSA REPORT'.*

bidscoin/heuristics/bidsmap_sst.yaml

@@ -20,7 +20,7 @@ Options:
 # General BIDScoin and plugin options
 # -----------------------------------
   bidscoin:
-    version: 4.5.2.dev1                  # BIDScoin version (should correspond with the version in pyproject.toml)
+    version: 4.5.2.dev2                  # BIDScoin version (should correspond with the version in pyproject.toml)
     subprefix: sub-                 # The subject prefix of the source data
     sesprefix: ses-                 # The session prefix of the source data
     bidsignore: [extra_data/, sub-*_ct.*]   # List of entries that are added to the .bidsignore file (for more info, see BIDS specifications), e.g. [extra_data/, pet/, myfile.txt, yourfile.csv]
@@ -1015,6 +1015,12 @@ DICOM:
       <<: *leaveout_attributes_dicom
       ProtocolName: (?i).*(Scout|localizer|t2_haste_sag_ipat2).*
     bids: *leaveout_bids_dicom
+  - attributes:
+      <<: *leaveout_attributes_dicom
+      Modality: SR
+    bids:
+      <<: *leaveout_bids_dicom
+      rec: REPORT
   - attributes:
       <<: *leaveout_attributes_dicom
       ImageType: .*'CSA REPORT'.*

bidscoin/utilities/dicomsort.py

@@ -106,8 +106,8 @@ def sortsession(sessionfolder: Path, dicomfiles: list[Path], folderscheme: str,
             continue
 
         # Skip radiology reports, as they have a very limited DICOM header
-        if get_dicomfield('CodeMeaning', dicomfile) == 'Radiology Report':
-            LOGGER.info(f"Skipping radiology report '{dicomfile}'")
+        if get_dicomfield('Modality', dicomfile) == 'SR':
+            LOGGER.info(f"Skipping report file '{dicomfile}'")
             continue
 
         # Create a new subfolder if needed

docs/CHANGELOG.md

@@ -2,7 +2,7 @@
 
 *All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)*
 
-## [4.5.2.dev1]
+## [4.5.2.dev2]
 
 ## [4.5.0] - 2025-02-05
 

pyproject.toml

@@ -7,7 +7,7 @@ build-backend    = 'setuptools.build_meta'
 [project]
 name             = 'bidscoin'
 description      = 'Converts and organises raw MRI data-sets according to the Brain Imaging Data Structure (BIDS)'
-version          = '4.5.2.dev1'
+version          = '4.5.2.dev2'
 readme           = 'README.rst'
 requires-python  = '>= 3.9'
 license          = {file = 'LICENSE.txt'}

tests/test_data/bidsmap.yaml

@@ -19,7 +19,7 @@ $schema: schema.json
 
 Options:                            # =============================== General options and plugins =====================================
   bidscoin:
-    version: 4.5.2.dev1                  # BIDScoin version (should correspond with the version in pyproject.toml)
+    version: 4.5.2.dev2                  # BIDScoin version (should correspond with the version in pyproject.toml)
     bidsignore: extra_data/         # Semicolon-separated list of entries that are added to the .bidsignore file (for more info, see BIDS specifications), e.g. extra_data/;pet/;myfile.txt;yourfile.csv
     subprefix: sub-                 # The subject prefix of the source data
     sesprefix: ses-                 # The session prefix of the source data