Bugfix for refactoring of IO helper functions (bidscoin.plugins -> …

…`bidscoin.utilities`) + minor tweaks

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)

bidscoin/utilities/dicomsort.py

@@ -41,7 +41,6 @@ def construct_name(scheme: str, dicomfile: Path, force: bool) -> str:
                 value = int(value.replace('.',''))      # Convert the SeriesInstanceUID to an int
         if not value and value != 0 and not force:
             LOGGER.error(f"Missing '{field}' DICOM field specified in the '{scheme}' folder/naming scheme, cannot find a safe name for: {dicomfile}\n")
-            trackusage('dicomsort_error')
             return ''
         else:
             schemevalues[field] = value
@@ -113,7 +112,6 @@ def sortsession(sessionfolder: Path, dicomfiles: list[Path], folderscheme: str,
             subfolder = construct_name(folderscheme, dicomfile, force)
             if not subfolder:
                 LOGGER.error('Cannot create subfolders, aborting dicomsort()...')
-                trackusage('dicomsort_error')
                 return
             destination = sessionfolder/subfolder
             if not destination.is_dir():

docs/installation.rst

@@ -61,6 +61,7 @@ Run your pip install command as before with the additional ``--upgrade`` or ``--
 .. caution::
    - The bidsmaps are not guaranteed to be compatible between different BIDScoin versions
    - After a successful BIDScoin installation or upgrade, it may be needed to (re)do any adjustments that were done on your `template bidsmap <./bidsmap.html#building-your-own-template-bidsmap>`__
+   - The code on GitHub does not always have a unique version number. Therefore, if you install the latest code from github, and then later re-install a newer BIDScoin with the same version number (e.g. the stable version from PyPi), then you need to actively delete your old user configuration. You can do this most easily by running ``bidscoin --reset``
 
 Dcm2niix installation
 ---------------------

docs/utilities.rst

@@ -110,7 +110,7 @@ The ``dicomsort`` command-line tool is a utility to move your flat- or DICOMDIR-
       dicomsort raw/sub-011/ses-mri01
       dicomsort raw --subprefix sub- --sesprefix ses-
       dicomsort myproject/raw/DICOMDIR --subprefix pat^ --sesprefix
-      dicomsort sub-011/ses-mri01/DICOMDIR -n {AcquisitionNumber:05d}_{InstanceNumber:05d}.dcm
+      dicomsort sub-011/ses-mri01/DICOMDIR -n '{AcquisitionNumber:05d}_{InstanceNumber:05d}.dcm'
 
 rawmapper
 ---------
@@ -140,8 +140,8 @@ Another command-line utility that can be helpful in organizing your source data
                             subid/sesid foldernames (default: ['PatientComments', 'ImageComments'])
       -w PATTERN, --wildcard PATTERN
                             The Unix style pathname pattern expansion that is used to select the series
-                            from which the dicomfield is being mapped (can contain wildcards) (default:
-                            *)
+                            folders from which the dicomfield is being mapped (can contain wildcards)
+                            (default: *)
       -o FOLDER, --outfolder FOLDER
                             The mapper-file is normally saved in sourcefolder or, when using this option,
                             in outfolder (default: None)