Minor tweaks

Author: marcelzwiers

bidscoin/__init__.py

@@ -41,7 +41,7 @@
         __version__ = tomllib.load(fid)['project']['version']
 
 # Add license metadata
-__license__    = 'GNU General Public License v3 or later (GPLv3+)'
+__license__    = 'GNU General Public License v3.0 or later (GPLv3+)'
 __copyright__  = f"2018-{datetime.date.today().year}, Marcel Zwiers"
 __disclaimer__ = """\
 This module and all modules in this package are part of BIDScoin (https://github.com/Donders-Institute/bidscoin).

bidscoin/bcoin.py

@@ -537,7 +537,7 @@ def test_bidscoin(bidsmapfile: Union[Path,dict], options: dict=None, testplugins
     except ModuleNotFoundError:
         pass
 
-    # Show an overview of the bidscoin tools. TODO: test the entry points?
+    # Show an overview of the bidscoin tools
     list_executables(True)
 
     # Test the plugins

bidscoin/bids.py

@@ -627,8 +627,7 @@ def get_dicomfield(tagname: str, dicomfile: Path) -> Union[str, int]:
 
                         if find_spec('dicom_parser'):
                             from dicom_parser import Image
-
-                            LOGGER.bcdebug(f"Parsing {tagname} using `dicom_parser`")
+                            LOGGER.bcdebug(f"Parsing {tagname} from the CSA header using `dicom_parser`")
                             for csa in ('CSASeriesHeaderInfo', 'CSAImageHeaderInfo'):
                                 value = value if (value or value==0) else Image(dicomfile).header.get(csa)
                                 for csatag in tagname.split('.'):           # E.g. CSA tagname = 'SliceArray.Slice.instance_number.Position.Tra'
@@ -640,8 +639,7 @@ def get_dicomfield(tagname: str, dicomfile: Path) -> Union[str, int]:
                                     value = str(value or '')
 
                         else:
-
-                            LOGGER.bcdebug(f"Parsing {tagname} using `nibabel`")
+                            LOGGER.bcdebug(f"Parsing {tagname} from the CSA header using `nibabel`")
                             for modality in ('Series', 'Image'):
                                 value = value if (value or value==0) else csareader.get_csa_header(dicomdata, modality)['tags']
                                 for csatag in tagname.split('.'):           # NB: Currently MrPhoenixProtocol is not supported
@@ -902,7 +900,7 @@ def get_p7field(tagname: str, p7file: Path) -> Union[str, int]:
         return str(value)  # If it's a MultiValue type then flatten it
 
 
-# ---------------- All function below this point are bidsmap related. TODO: make a class out of them -------------------
+# TODO: A number of functions below this point are bidsmap related. Make a class out of them
 
 
 def load_bidsmap(yamlfile: Path=Path(), folder: Path=templatefolder, plugins:Iterable[Union[Path,str]]=(), checks: Tuple[bool, bool, bool]=(True, True, True)) -> Tuple[Bidsmap, Path]:

bidscoin/bidseditor.py

@@ -193,9 +193,9 @@ def show_contextmenu(self, pos):
         rowindex   = [index.row() for index in table.selectedIndexes() if index.column() == colindex]
         if colindex in (-1, 0, 4):      # User clicked the index, the edit-button or elsewhere (i.e. not on an activated widget)
             return
-        runs       = []
-        subid      = []
-        sesid      = []
+        runs  = []
+        subid = []
+        sesid = []
         for index in rowindex:
             datatype   = table.item(index, 2).text()
             provenance = table.item(index, 5).text()
@@ -216,7 +216,7 @@ def show_contextmenu(self, pos):
 
         if action == delete:
             answer = QMessageBox.question(self, f"Remove {dataformat} mapping",
-                                          f'Only delete mappings for obsolete data (unless you are an expert user). Do you really want to remove this mapping"?',
+                                          'Only delete mappings for obsolete data (unless you are an expert user). Do you want to continue?',
                                           QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.Cancel, QMessageBox.StandardButton.Cancel)
             if answer == QMessageBox.StandardButton.Yes:
                 for index in rowindex:

bidscoin/plugins/dcm2niix2bids.py

@@ -380,10 +380,10 @@ def bidscoiner_plugin(session: Path, bidsmap: Bidsmap, bidsses: Path) -> Union[N
                 # Strip each dcm2niix postfix and assign it to the proper bids entity in the new bidsname (else assign it to the fallback entity)
                 ext         = ''.join(dcm2niixfile.suffixes)
                 postfixes   = dcm2niixfile.name.split(bidsname)[1].rsplit(ext)[0].split('_')[1:]
-                newbidsname = bids.insert_bidskeyval(dcm2niixfile.name, 'run', runindex, ignore)        # Restart the run-index. NB: Unlike bidsname, newbidsname has a file extension
+                newbidsname = bids.insert_bidskeyval(dcm2niixfile.name, 'run', runindex, ignore)            # Restart the run-index. NB: Unlike bidsname, newbidsname has a file extension
                 for postfix in postfixes:
 
-                    # Patch the echo entity in the newbidsname with the dcm2niix echo info                     # NB: We can't rely on the bids-entity info here because manufacturers can e.g. put multiple echos in one series / run-folder
+                    # Patch the echo entity in the newbidsname with the dcm2niix echo info                      # NB: We can't rely on the bids-entity info here because manufacturers can e.g. put multiple echos in one series / run-folder
                     if 'echo' in run['bids'] and postfix.startswith('e'):
                         echonr = f"_{postfix}".replace('_e','')                                                 # E.g. postfix='e1'
                         if not echonr:
@@ -393,10 +393,10 @@ def bidscoiner_plugin(session: Path, bidsmap: Bidsmap, bidsses: Path) -> Union[N
                         elif echonr[0:-1].isdecimal():
                             LOGGER.verbose(f"Splitting off echo-number {echonr[0:-1]} from the '{postfix}' postfix")
                             newbidsname = bids.insert_bidskeyval(newbidsname, 'echo', echonr[0:-1].lstrip('0'), ignore) # Strip of the 'a', 'b', etc. from `e1a`, `e1b`, etc
-                            newbidsname = bids.get_bidsvalue(newbidsname, fallback, echonr[-1])        # Append the 'a' to the fallback-label
+                            newbidsname = bids.get_bidsvalue(newbidsname, fallback, echonr[-1])                 # Append the 'a' to the fallback-label
                         else:
                             LOGGER.error(f"Unexpected postix '{postfix}' found in {dcm2niixfile}")
-                            newbidsname = bids.get_bidsvalue(newbidsname, fallback, postfix)           # Append the unknown postfix to the fallback-label
+                            newbidsname = bids.get_bidsvalue(newbidsname, fallback, postfix)                    # Append the unknown postfix to the fallback-label
 
                     # Patch the phase entity in the newbidsname with the dcm2niix mag/phase info
                     elif 'part' in run['bids'] and postfix in ('ph','real','imaginary'):                        # e.g. part: ['', 'mag', 'phase', 'real', 'imag', 0]