Minor tweaks and fixes

Donders-Institute · Feb 4, 2025 · 09adde8 · 09adde8
1 parent bbf24a3
commit 09adde8
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Showing 4 changed files with 11 additions and 12 deletions.
diff --git a/bidscoin/bcoin.py b/bidscoin/bcoin.py
@@ -454,9 +454,6 @@ def test_bidscoin(bidsmapfile, options: dict=None, testplugins: bool=True, testg
     success = True
     if isinstance(bidsmapfile, (str, Path)):
         bidsmapfile = Path(bidsmapfile)
-        if not bidsmapfile.is_file():
-            LOGGER.info(f"Cannot find bidsmap-file: {bidsmapfile}")
-            return 1
         LOGGER.info(f"Running bidsmap checks:")
         try:            # Moving the import to the top of this module will cause circular import issues
             from bidscoin import bids

diff --git a/bidscoin/bids.py b/bidscoin/bids.py
@@ -1919,7 +1919,7 @@ def addmetadata(bidsses: Path):
                 for part in intendedfor:
                     pattern = part.split(':',1)[0].strip()          # part = 'pattern: [lowerlimit:upperlimit]'
                     limits  = part.split(':',1)[1].strip() if ':' in part else ''
-                    matches = [niifile.relative_to(bidsses).as_posix() for niifile in sorted(bidsses.rglob(f"*{pattern}*")) if pattern and '.nii' in niifile.suffixes]
+                    matches = [niifile.relative_to(bidsses).as_posix() for niifile in sorted(bidsses.rglob(f"*{pattern.strip('*')}*")) if pattern and '.nii' in niifile.suffixes]
                     limitmatches(fmap, matches, limits, niifiles, scans_table)
 
                 # Add the IntendedFor data. NB: The BIDS URI paths need to use forward slashes and be relative to the bids root folder

diff --git a/bidscoin/bidscoiner.py b/bidscoin/bidscoiner.py
@@ -278,7 +278,7 @@ def bidscoiner(sourcefolder: str, bidsfolder: str, participant: list=(), force:
                             has_run = False
                             for datatype in lsdirs(bidssession):                               # See what datatypes we already have in the bids session-folder
                                 if next(datatype.iterdir(), None) and datatype.name in bidsmap.dataformat(datasource.dataformat).datatypes:  # See if the plugin may add data for this datatype
-                                    LOGGER.info(f">>> Skipping processed session: {bidssession} already has {datatype.name} data (you can carefully use the -f option to overrule)")
+                                    LOGGER.info(f">>> Skipping {name} processing: {bidssession} already has {datatype.name} data (you can carefully use the -f option to overrule)")
                                     has_run = True
                             if has_run:
                                 continue

diff --git a/bidscoin/bidseditor.py b/bidscoin/bidseditor.py
@@ -1070,7 +1070,7 @@ def __init__(self, runitem: RunItem, bidsmap: BidsMap, template_bidsmap: BidsMap
         self.dataformat        = runitem.dataformat
         """The data format of the run-item being edited (bidsmap[dataformat][datatype][run-item])"""
         self.unknowndatatypes: list[str] = [datatype for datatype in bidsmap.options['unknowntypes'] if datatype in template_bidsmap.dataformat(self.dataformat).datatypes]
-        self.ignoredatatypes: list[str]  = [datatype for datatype in bidsmap.options['ignoretypes']  if datatype in template_bidsmap.dataformat(self.dataformat).datatypes]
+        self.ignoredatatypes:  list[str] = [datatype for datatype in bidsmap.options['ignoretypes']  if datatype in template_bidsmap.dataformat(self.dataformat).datatypes]
         self.bidsdatatypes     = [str(datatype) for datatype in template_bidsmap.dataformat(self.dataformat).datatypes if datatype not in self.unknowndatatypes + self.ignoredatatypes]
         self.bidsignore        = bidsmap.options['bidsignore']
         self.output_bidsmap    = bidsmap
@@ -1997,10 +1997,11 @@ def __init__(self, runitems: list[RunItem], subid: list[str], sesid: list[str]):
             bids_table.setToolTip('The BIDS entity that is used to construct the BIDS output filename')
 
             # Set up the meta table
-            meta_label = QLabel('Metadata')
-            meta_label.setToolTip('Key-value pairs that will be appended to the (e.g. dcm2niix-produced) json sidecar file')
-            meta_table = self.fill_table(meta_data, 'meta', minsize=False)
-            meta_table.setToolTip('The key-value pair that will be appended to the (e.g. dcm2niix-produced) json sidecar file')
+            if meta_data:
+                meta_label = QLabel('Metadata')
+                meta_label.setToolTip('Key-value pairs that will be appended to the (e.g. dcm2niix-produced) json sidecar file')
+                meta_table = self.fill_table(meta_data, 'meta', minsize=False)
+                meta_table.setToolTip('The key-value pair that will be appended to the (e.g. dcm2niix-produced) json sidecar file')
 
             # Set up the events table
             if events_data:
@@ -2018,8 +2019,9 @@ def __init__(self, runitems: list[RunItem], subid: list[str], sesid: list[str]):
             layout.addWidget(attributes_table)
             layout.addWidget(bids_label)
             layout.addWidget(bids_table)
-            layout.addWidget(meta_label)
-            layout.addWidget(meta_table)
+            if meta_data:
+                layout.addWidget(meta_label)
+                layout.addWidget(meta_table)
             if events_data:
                 layout.addWidget(events_label)
                 layout.addWidget(events_table)