Minor tweaks / cleanups

Author: marcelzwiers

bidscoin/bidseditor.py

@@ -206,9 +206,11 @@ def show_contextmenu(self, pos):
         menu    = QtWidgets.QMenu(self)
         compare = menu.addAction('Compare')
         compare.setEnabled(len(rowindex) > 1)
+        compare.setToolTip('Compare the BIDS mappings of multiple run-items')
         edit    = menu.addAction('Edit')
-        edit.setToolTip('Edit individual items in detail or change the data type')
+        edit.setToolTip('Edit a single run-item in detail or edit the data type of multiple run-items')
         delete  = menu.addAction('Remove')
+        delete.setToolTip('Delete run-items from the bidsmap (expert usage)')
         action  = menu.exec(table.viewport().mapToGlobal(pos))
 
         if action == delete:

bidscoin/plugins/dcm2niix2bids.py

@@ -215,14 +215,9 @@ def bidscoiner_plugin(session: Path, bidsmap: Bidsmap, bidsses: Path) -> Union[N
     """
 
     # Get the subject identifiers and the BIDS root folder from the bidsses folder
-    if bidsses.name.startswith('ses-'):
-        bidsfolder = bidsses.parent.parent
-        subid      = bidsses.parent.name
-        sesid      = bidsses.name
-    else:
-        bidsfolder = bidsses.parent
-        subid      = bidsses.name
-        sesid      = ''
+    subid      = bidsses.name if bidsses.name.startswith('sub-') else bidsses.parent.name
+    sesid      = bidsses.name if bidsses.name.startswith('ses-') else ''
+    bidsfolder = bidsses.parent.parent if sesid else bidsses.parent
 
     # Get started and see what dataformat we have
     options: Plugin  = bidsmap['Options']['plugins']['dcm2niix2bids']

bidscoin/plugins/nibabel2bids.py

@@ -169,13 +169,9 @@ def bidscoiner_plugin(session: Path, bidsmap: Bidsmap, bidsses: Path) -> None:
     :return:            Nothing
     """
 
-    # Get the subject identifiers and the BIDS root folder from the bidsses folder
-    if bidsses.name.startswith('ses-'):
-        subid = bidsses.parent.name
-        sesid = bidsses.name
-    else:
-        subid = bidsses.name
-        sesid = ''
+    # Get the subject identifiers from the bidsses folder
+    subid = bidsses.name if bidsses.name.startswith('sub-') else bidsses.parent.name
+    sesid = bidsses.name if bidsses.name.startswith('ses-') else ''
 
     # Get started
     options     = bidsmap['Options']['plugins']['nibabel2bids']

bidscoin/plugins/spec2nii2bids.py

@@ -177,13 +177,9 @@ def bidscoiner_plugin(session: Path, bidsmap: Bidsmap, bidsses: Path) -> Union[N
     :return:            A dictionary with personal data for the participants.tsv file (such as sex or age)
     """
 
-    # Get the subject identifiers and the BIDS root folder from the bidsses folder
-    if bidsses.name.startswith('ses-'):
-        subid = bidsses.parent.name
-        sesid = bidsses.name
-    else:
-        subid = bidsses.name
-        sesid = ''
+    # Get the subject identifiers from the bidsses folder
+    subid = bidsses.name if bidsses.name.startswith('sub-') else bidsses.parent.name
+    sesid = bidsses.name if bidsses.name.startswith('ses-') else ''
 
     # Get started and see what dataformat we have
     options     = bidsmap['Options']['plugins']['spec2nii2bids']

docs/troubleshooting.rst

@@ -53,7 +53,7 @@ Normally the list of items in the bidsmap is a shortlist that represents the dif
 
 I have duplicate run-items in my bidsmap
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-There shouldn't be exact duplicates, i.e. there is probably a small difference in the properties or attributes that identify your run-items. To investigate this, you can compare these run-items by selecting their BIDS output names (use shift-/control-click), then right-click them and choose ``compare`` from the context menu
+Exact duplicates should not exist, i.e. there is probably a small difference in the properties or attributes that identify your run-items. To investigate this, you can compare these run-items by selecting their BIDS output names (use shift-/control-click), then right-click them and choose ``compare`` from the context menu
 
 My subject/session labels are wrong
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

tests/test_bids.py

@@ -11,7 +11,7 @@
 from nibabel.testing import data_path
 from pydicom.data import get_testdata_file
 from bidscoin import bcoin, bids, bidsmap_template
-from bidscoin.bids import Run, Plugin
+from bidscoin.bids import Run, Plugin, Meta
 
 bcoin.setup_logging()
 
@@ -614,10 +614,10 @@ def test_updatemetadata(dcm_file, tmp_path):
         json.dump({'PatientName': 'SidecarTest'}, fid)
 
     # Create the user metadata
-    usermeta = {'PatientName':       'UserTest',
-                'DynamicName':       '<<(0010, 0010)>>',
-                'B0FieldSource':     'Source<<session:[-2:2]>>',
-                'B0FieldIdentifier': ['Identifier<<session>>', 'Identifier']}
+    usermeta = Meta({'PatientName':       'UserTest',
+                     'DynamicName':       '<<(0010, 0010)>>',
+                     'B0FieldSource':     'Source<<session:[-2:2]>>',
+                     'B0FieldIdentifier': ['Identifier<<session>>', 'Identifier']})
 
     # Test if the user metadata takes precedence
     metadata = bids.updatemetadata(extdatasource, sidecar, usermeta, ['.json'])
@@ -628,10 +628,10 @@ def test_updatemetadata(dcm_file, tmp_path):
     assert not (outfolder/sourcefile.with_suffix('.jsn').name).is_file()
 
     # Test if the source metadata takes precedence
-    metadata = bids.updatemetadata(extdatasource, sidecar, {}, ['.jsn', '.json'], sourcefile)
+    metadata = bids.updatemetadata(extdatasource, sidecar, Meta({}), ['.jsn', '.json'], sourcefile)
     assert metadata['PatientName'] == 'SourceTest'
     assert (outfolder/sourcefile.with_suffix('.jsn').name).is_file()
 
     # Test if the sidecar metadata takes precedence
-    metadata = bids.updatemetadata(extdatasource, sidecar, {}, [])
+    metadata = bids.updatemetadata(extdatasource, sidecar, Meta({}), [])
     assert metadata['PatientName'] == 'SidecarTest'