Minor tweaks

Author: marcelzwiers

bidscoin/bids.py

@@ -2075,7 +2075,7 @@ def poolmetadata(datasource: DataSource, targetmeta: Path, usermeta: Meta, metae
             LOGGER.bcdebug(f"Adding '{metakey}: {metaval}' to: {targetmeta}")
         metapool[metakey] = metaval or None
 
-    # Update <<session_id>> in B0FieldIdentifiers/Sources. NB: Leave range specifiers (<<session_id:[-2:2]>>) untouched (-> bidscoiner)
+    # Update <<session_id>> in B0FieldIdentifiers/Sources. NB: Leave range specifiers (<<session_id:[-2:2]>>) untouched until all data is present (-> bidscoiner -> addmetadata)
     sesid = get_bidsvalue(targetmeta, 'ses')
     for key in ('B0FieldSource', 'B0FieldIdentifier'):
 

bidscoin/heuristics/bidsmap_dccn.yaml

@@ -57,7 +57,7 @@ DICOM:
     age<<session_id>>: &age
       value: <<PatientAge>>
       meta:
-        Description: Age of the participant
+        Description: Age of the participant at the time of the acquired session
         Units: year
     sex: &sex
       value: <<PatientSex>>

bidscoin/heuristics/bidsmap_sst.yaml

@@ -46,17 +46,17 @@ DICOM:
 # ------------------------------------------------------------------
   participant:                      # Attributes or properties to populate the participants tsv/json files
     participant_id: &participant_id
-      value: <<filepath:/sub-(.*?)/>>                 # This filesystem property extracts the subject label from the source directory. NB: Any property or attribute can be used as subject-label, e.g. <PatientID>
-      meta:                                           # All data in "meta" is stored in the participants json sidecar-file
+      value: <<filepath:/sub-(.*?)/>>           # This filesystem property extracts the subject label from the source directory. NB: Any property or attribute can be used as subject-label, e.g. <PatientID>
+      meta:                                     # All data in "meta" is stored in the participants json sidecar-file
         Description: The unique participant identifier of the form sub-<label>, matching a participant entity found in the dataset
     session_id: &session_id
       value: <<filepath:/sub-.*?/ses-\.\.\.(.*?)/>>   # This filesystem property extracts the session label from the source directory. NB: Any property or attribute can be used as session-label, e.g. <StudyID>
       meta:
         Description: The session identifier of the form ses-<label>, matching a session found in the dataset
-    age: &age
+    age<<session_id>>: &age
       value: <<PatientAge>>
       meta:
-        Description: Age of the participant
+        Description: Age of the participant at the time of the acquired session
         Units: year
     sex: &sex
       value: <<PatientSex>>

bidscoin/utilities/dicomsort.py

@@ -98,7 +98,7 @@ def sortsession(sessionfolder: Path, dicomfiles: list[Path], folderscheme: str,
         sessionfolder.mkdir(parents=True, exist_ok=True)
 
     # Sort the dicomfiles in (e.g. DICOM Series) subfolders
-    for dicomfile in dicomfiles:
+    for n, dicomfile in enumerate(dicomfiles):
 
         # Check if the DICOM file exists (e.g. in case of DICOMDIRs this may not be the case)
         if not dicomfile.is_file():
@@ -120,7 +120,8 @@ def sortsession(sessionfolder: Path, dicomfiles: list[Path], folderscheme: str,
                 return
             destination = sessionfolder/subfolder
             if not destination.is_dir():
-                LOGGER.verbose(f"   Creating:  {destination}")
+                sorted = int(100 * n / len(dicomfiles))
+                LOGGER.verbose(f"[{sorted}%]   Creating:  {destination}")
                 if not dryrun:
                     destination.mkdir(parents=True)