Bugfix for refactoring of IO helper functions (bidscoin.plugins -> bidscoin.utilities) + minor tweaks

Author: marcelzwiers

bidscoin/bcoin.py

@@ -26,7 +26,7 @@
 from importlib.util import find_spec
 if find_spec('bidscoin') is None:
     sys.path.append(str(Path(__file__).parents[1]))
-from bidscoin import templatefolder, pluginfolder, bidsmap_template, tutorialurl, trackusage, tracking, configfile, config, DEBUG
+from bidscoin import templatefolder, pluginfolder, bidsmap_template, tutorialurl, trackusage, tracking, configdir, configfile, config, DEBUG
 
 yaml = YAML()
 yaml.representer.ignore_aliases = lambda *data: True                         # Expand aliases (https://stackoverflow.com/questions/58091449/disabling-alias-for-yaml-file-in-python)
@@ -625,6 +625,19 @@ def reportcredits(args: list) -> None:
             LOGGER.info(f"No DueCredit citation files found in {Path(args[0]).resolve()} and {report.parent}")
 
 
+def reset(delete: bool) -> None:
+    """
+    Resets the configuration directory by deleting it if the `delete` parameter is set to True
+
+    :param delete: If set to True, the configuration directory will be removed
+    :return: None
+    """
+
+    if not delete: return
+
+    shutil.rmtree(configdir)
+
+
 def settracking(value: str) -> None:
     """
     Set or show usage tracking
@@ -677,6 +690,7 @@ def main():
         pulltutorialdata(tutorialfolder=args.download)
         test_bidscoin(bidsmapfile=args.test)
         test_bidsmap(bidsmapfile=args.bidsmaptest)
+        reset(delete=args.reset)
         settracking(value=args.tracking)
         reportcredits(args=args.credits)
 

bidscoin/bids.py

@@ -1262,7 +1262,7 @@ def exist_run(self, runitem: RunItem, datatype: Union[str, DataType]='') -> bool
 
         return False
 
-    def get_matching_run(self, sourcefile: Union[str, Path], dataformat, runtime=False) -> tuple[RunItem, str]:
+    def get_matching_run(self, sourcefile: Union[str, Path], dataformat: str='', runtime: bool=False) -> tuple[RunItem, str]:
         """
         Find the first run in the bidsmap with properties and attributes that match with the data source. Only non-empty
         properties and attributes are matched, except when runtime is True, then the empty attributes are also matched.
@@ -1271,20 +1271,29 @@ def get_matching_run(self, sourcefile: Union[str, Path], dataformat, runtime=Fal
         ignoredatatypes (e.g. 'exclude') -> normal datatypes (e.g. 'anat') -> unknowndatatypes (e.g. 'extra_data')
 
         :param sourcefile:  The full filepath of the data source for which to get a run-item
-        :param dataformat:  The dataformat section in the bidsmap in which a matching run is searched for, e.g. 'DICOM'
+        :param dataformat:  The dataformat section in the bidsmap in which a matching run is searched for, e.g. 'DICOM'. Leave empty to recursively search through all dataformats
         :param runtime:     Dynamic <<values>> are expanded if True
         :return:            (run, provenance) A vanilla run that has all its attributes populated with the source file attributes.
                             If there is a match, the provenance of the bidsmap entry is returned, otherwise it will be ''
         """
 
+        # Iterate over all dataformats if dataformat is not given
+        if not dataformat:
+            runitem, provenance = RunItem(), ''
+            for dformat in self.dataformats:
+                runitem, provenance = self.get_matching_run(sourcefile, dformat.dataformat, runtime)
+                if provenance: break
+            return runitem, provenance
+
+        # Defaults
         datasource       = DataSource(sourcefile, self.plugins, dataformat, options=self.options)
         unknowndatatypes = self.options.get('unknowntypes') or ['unknown_data']
         ignoredatatypes  = self.options.get('ignoretypes') or []
         normaldatatypes  = [dtype.datatype for dtype in self.dataformat(dataformat).datatypes if dtype not in unknowndatatypes + ignoredatatypes]
         rundata          = {'provenance': str(sourcefile), 'properties': {}, 'attributes': {}, 'bids': {}, 'meta': {}, 'events': {}}
         """The a run-item data structure. NB: Keep in sync with the RunItem() data attributes"""
 
-        # Loop through all datatypes and runs; all info goes cleanly into runitem (to avoid formatting problem of the CommentedMap)
+        # Iterate over all datatypes and runs; all info goes cleanly into runitem (to avoid formatting problem of the CommentedMap)
         if 'fmap' in normaldatatypes:
             normaldatatypes.insert(0, normaldatatypes.pop(normaldatatypes.index('fmap')))   # Put fmap at the front (to catch inverted polarity scans first
         for datatype in ignoredatatypes + normaldatatypes + unknowndatatypes:                      # The ordered datatypes in which a matching run is searched for

bidscoin/bidscoiner.py

@@ -101,7 +101,7 @@ def bidscoiner(sourcefolder: str, bidsfolder: str, participant: list=(), force:
     # Load the data conversion plugins
     plugins = [plugin for name in bidsmap.plugins if (plugin := bcoin.import_plugin(name))]
     if not plugins:
-        LOGGER.warning(f"The plugins listed in your bidsmap['Options'] did not have a usable `bidscoiner_plugin` function, nothing to do")
+        LOGGER.warning(f"The {bidsmap.plugins.keys()} plugins listed in your bidsmap['Options'] did not have a usable `bidscoiner` interface, nothing to do")
         LOGGER.info('-------------- FINISHED! ------------')
         LOGGER.info('')
         return

bidscoin/bidseditor.py

@@ -24,6 +24,7 @@
     sys.path.append(str(Path(__file__).parents[1]))
 from bidscoin import bcoin, bids, bidsversion, check_version, trackusage, bidsmap_template, __version__
 from bidscoin.bids import BidsMap, RunItem, DataType
+from bidscoin.utilities import is_dicomfile, is_parfile
 config.INVALID_KEY_BEHAVIOR = 'IGNORE'
 
 ROW_HEIGHT       = 22
@@ -958,7 +959,7 @@ def open_inspectwindow(self, index: int):
         datafile = Path(self.filesystem.fileInfo(index).absoluteFilePath())
         if datafile.is_file():
             ext = ''.join(datafile.suffixes).lower()
-            if bids.is_dicomfile(datafile) or bids.is_parfile(datafile) or ext in sum((klass.valid_exts for klass in nib.imageclasses.all_image_classes), ('.nii.gz',)):
+            if is_dicomfile(datafile) or is_parfile(datafile) or ext in sum((klass.valid_exts for klass in nib.imageclasses.all_image_classes), ('.nii.gz',)):
                 self.popup = InspectWindow(datafile)
                 self.popup.show()
                 self.popup.scrollbar.setValue(0)  # This can only be done after self.popup.show()
@@ -2041,11 +2042,11 @@ def __init__(self, filename: Path):
         super().__init__()
 
         ext = ''.join(filename.suffixes).lower()
-        if bids.is_dicomfile(filename):
+        if is_dicomfile(filename):
             if filename.name == 'DICOMDIR':
                 LOGGER.bcdebug(f"Getting DICOM fields from {filename} will raise dcmread error below if pydicom => v3.0")
             text = str(dcmread(filename, force=True))
-        elif bids.is_parfile(filename) or ext in ('.spar', '.txt', '.text', '.log'):
+        elif is_parfile(filename) or ext in ('.spar', '.txt', '.text', '.log'):
             text = filename.read_text()
         elif ext == '.7':
             try:

bidscoin/bidsmapper.py

@@ -103,7 +103,7 @@ def bidsmapper(sourcefolder: str, bidsfolder: str, bidsmap: str, template: str,
     # Import the data scanning plugins
     plugins = [plugin for name in bidsmap_new.plugins if (plugin := bcoin.import_plugin(name))]
     if not plugins:
-        LOGGER.warning(f"The plugins listed in your bidsmap['Options'] did not have a usable `bidsmapper_plugin` function, nothing to do")
+        LOGGER.warning(f"The {bidsmap_new.plugins.keys()} plugins listed in your bidsmap['Options'] did not have a usable `bidsmapper` interface, nothing to do")
         LOGGER.info('-------------- FINISHED! ------------')
         LOGGER.info('')
         return bidsmap_new

bidscoin/cli/_bcoin.py

@@ -54,6 +54,7 @@ def get_parser() -> argparse.ArgumentParser:
     parser.add_argument('-t', '--test',        help='Test the bidscoin installation and template bidsmap', nargs='?', metavar='TEMPLATE', const=bidsmap_template)
     parser.add_argument('-b', '--bidsmaptest', help='Test the run-items and their bidsnames of all normal runs in the study bidsmap. Provide the bids-folder or the bidsmap filepath', metavar='BIDSMAP')
     parser.add_argument('-c', '--credits',     help='Show duecredit citations for your BIDS repository. You can also add duecredit summary arguments (without dashes), e.g. `style {apa,harvard1}` or `format {text,bibtex}`.', metavar='OPTIONS', nargs='+')
+    parser.add_argument('-r', '--reset',       help='Restore the settings, plugins and template bidsmaps in your home directory to their default values', action='store_true')
     parser.add_argument(      '--tracking',    help='Show the usage tracking info {show}, or set usage tracking to {yes} or {no}', choices=['yes','no','show'])
     parser.add_argument('-v', '--version',     help='Show the installed version and check for updates', action='version', version=f"BIDS-version:\t\t{bidsversion()}\nBIDScoin-version:\t{__version__}, {versionmessage}")
 

bidscoin/cli/_dicomsort.py

@@ -22,7 +22,7 @@ class CustomFormatter(argparse.ArgumentDefaultsHelpFormatter, argparse.RawDescri
                                             '  dicomsort raw/sub-011/ses-mri01\n'
                                             '  dicomsort raw --subprefix sub- --sesprefix ses-\n'
                                             '  dicomsort myproject/raw/DICOMDIR --subprefix pat^ --sesprefix\n'
-                                            '  dicomsort sub-011/ses-mri01/DICOMDIR -n {AcquisitionNumber:05d}_{InstanceNumber:05d}.dcm\n ')
+                                            "  dicomsort sub-011/ses-mri01/DICOMDIR -n '{AcquisitionNumber:05d}_{InstanceNumber:05d}.dcm'\n ")
     parser.add_argument('sourcefolder',         help='The root folder containing the [sub/][ses/] dicomfiles or the DICOMDIR file')
     parser.add_argument('-i','--subprefix',     help='Provide a prefix string to recursively sort sourcefolder/subject subfolders (e.g. "sub-" or "S_")', metavar='PREFIX')
     parser.add_argument('-j','--sesprefix',     help='Provide a prefix string to recursively sort sourcefolder/subject/session subfolders (e.g. "ses-" or "T_")', metavar='PREFIX')

bidscoin/cli/_rawmapper.py

@@ -29,7 +29,7 @@ class CustomFormatter(argparse.ArgumentDefaultsHelpFormatter, argparse.RawDescri
     parser.add_argument('sourcefolder',     help='The source folder with the raw data in sub-#/ses-#/series organization', metavar='FOLDER')
     parser.add_argument('-s','--sessions',  help='Space separated list of selected sub-#/ses-# names/folders to be processed. Otherwise all sessions in the bidsfolder will be processed', nargs='+', metavar='SESSION')
     parser.add_argument('-f','--field',     help='The fieldname(s) of the DICOM attribute(s) used to rename or map the subid/sesid foldernames', default=['PatientComments', 'ImageComments'], nargs='+', metavar='NAME')
-    parser.add_argument('-w','--wildcard',  help='The Unix style pathname pattern expansion that is used to select the series from which the dicomfield is being mapped (can contain wildcards)', default='*', metavar='PATTERN')
+    parser.add_argument('-w','--wildcard',  help='The Unix style pathname pattern expansion that is used to select the series folders from which the dicomfield is being mapped (can contain wildcards)', default='*', metavar='PATTERN')
     parser.add_argument('-o','--outfolder', help='The mapper-file is normally saved in sourcefolder or, when using this option, in outfolder', metavar='FOLDER')
     parser.add_argument('-r','--rename',    help='Rename sub-subid/ses-sesid directories in the sourcefolder to sub-dcmval/ses-dcmval', action='store_true')
     parser.add_argument('-c','--clobber',   help='Rename the sub/ses directories, even if the target-directory already exists', action='store_true')

bidscoin/plugins/__init__.py

@@ -63,7 +63,10 @@ def bidsmapper(self, session: Path, bidsmap_new: 'BidsMap', bidsmap_old: 'BidsMa
         """
 
         # See for every source file in the session if we already discovered it or not
-        for sourcefile in session.rglob('*'):
+        sourcefiles = session.rglob('*')
+        if not sourcefiles:
+            LOGGER.info(f"No {__name__} sourcedata found in: {session}")
+        for sourcefile in sourcefiles:
 
             # Check if the sourcefile is of a supported dataformat
             if is_hidden(sourcefile.relative_to(session)) or not (dataformat := self.has_support(sourcefile, dataformat='')):

bidscoin/plugins/dcm2niix2bids.py

@@ -140,6 +140,8 @@ def bidsmapper(self, session: Path, bidsmap_new: BidsMap, bidsmap_old: BidsMap,
             LOGGER.error(f"Unsupported dataformat '{dataformat}'")
 
         # See for every data source in the session if we already discovered it or not
+        if not sourcefiles:
+            LOGGER.info(f"No {__name__} sourcedata found in: {session}")
         for sourcefile in sourcefiles:
 
             # Check if the source files all have approximately the same size (difference < 50kB)