Minor tweaks

Author: marcelzwiers

bidscoin/bcoin.py

@@ -275,11 +275,11 @@ def install_plugins(filenames: List[str]=()) -> None:
             continue
 
         # Add the Options and data format section of the plugin to the default template bidsmap
-        if 'OPTIONS' in dir(module) or 'BIDSMAP' in dir(module):
-            if 'OPTIONS' in dir(module):
+        if hasattr(module, 'OPTIONS') or hasattr(module, 'BIDSMAP'):
+            if hasattr(module, 'OPTIONS'):
                 LOGGER.info(f"Adding default {file.name} bidsmap options to the {bidsmap_template.stem} template")
                 template['Options']['plugins'][file.stem] = module.OPTIONS
-            if 'BIDSMAP' in dir(module):
+            if hasattr(module, 'BIDSMAP'):
                 for key, value in module.BIDSMAP.items():
                     LOGGER.info(f"Adding default {key} bidsmappings to the {bidsmap_template.stem} template")
                     template[key] = value
@@ -331,11 +331,11 @@ def uninstall_plugins(filenames: List[str]=(), wipe: bool=True) -> None:
         if not module:
             LOGGER.warning(f"Cannot remove any {file.stem} bidsmap options from the {bidsmap_template.stem} template")
             continue
-        if 'OPTIONS' in dir(module) or 'BIDSMAP' in dir(module):
-            if 'OPTIONS' in dir(module):
+        if hasattr(module, 'OPTIONS') or hasattr(module, 'BIDSMAP'):
+            if hasattr(module, 'OPTIONS'):
                 LOGGER.info(f"Removing default {file.stem} bidsmap options from the {bidsmap_template.stem} template")
                 template['Options']['plugins'].pop(file.stem, None)
-            if wipe and 'BIDSMAP' in dir(module):
+            if wipe and hasattr(module, 'BIDSMAP'):
                 for key, value in module.BIDSMAP.items():
                     LOGGER.info(f"Removing default {key} bidsmappings from the {bidsmap_template.stem} template")
                     template.pop(key, None)
@@ -376,7 +376,7 @@ def import_plugin(plugin: Union[Path,str], functions: tuple=()) -> Union[types.M
 
         functionsfound = []
         for function in functions:
-            if function not in dir(module):
+            if not hasattr(module, function):
                 LOGGER.verbose(f"Could not find '{function}' in the '{plugin}' plugin")
             elif not callable(getattr(module, function)):
                 LOGGER.error(f"'The {function}' attribute in the '{plugin}' plugin is not callable")
@@ -405,13 +405,13 @@ def test_plugin(plugin: Union[Path,str], options: dict) -> int:
 
     LOGGER.info(f"--------- Testing the '{plugin}' plugin ---------")
 
-    # First test to see if we can import the plugin
+    # First test to see if we can import the core plugin methods
     module = import_plugin(plugin, ('bidsmapper_plugin','bidscoiner_plugin'))
     if module is None:
         return 1
 
     # Then run the plugin's own 'test' routine (if implemented)
-    if 'test' in dir(module) and callable(getattr(module, 'test')):
+    if hasattr(module, 'test') and callable(getattr(module, 'test')):
         try:
             returncode = module.test(options)
             if returncode == 0:

bidscoin/bids.py

@@ -122,7 +122,6 @@ def eventstable(self) -> pd.DataFrame:
 
         # Loop over the row groups to filter/edit the rows
         rows = pd.Series([len(self.rows) == 0] * len(df)).astype(bool)  # Series with True values if no row expressions were specified
-        rows.index = df.index                                           # Make sure the indices align
         for group in self.rows:
 
             for column, regex in group['include'].items():

bidscoin/bidseditor.py

@@ -820,7 +820,7 @@ def add_plugin(self):
             LOGGER.error(f"Cannot add the '{plugin}' plugin as it already exists in the bidsmap")
             return
         module  = bcoin.import_plugin(plugin)
-        options = self.input_bidsmap.plugins.get(plugin, self.template_bidsmap.plugins.get(plugin, module.OPTIONS if 'OPTIONS' in dir(module) else {}))
+        options = self.input_bidsmap.plugins.get(plugin, self.template_bidsmap.plugins.get(plugin, getattr(module, 'OPTIONS', {})))
 
         # Insert the selected plugin in the options_layout
         LOGGER.info(f"Adding the '{plugin}' plugin to bidsmap")
@@ -1256,8 +1256,6 @@ def fill_table(self, table: MyQTable, data: list):
         table.clearContents()
         table.setRowCount(len(data + extrarow) - header)
         table.setColumnCount(ncols)
-        table.horizontalHeader().setSectionResizeMode(QHeaderView.ResizeMode.ResizeToContents)
-        table.horizontalHeader().setSectionResizeMode(ncols - 1, QHeaderView.ResizeMode.Stretch)
 
         for i, row in enumerate(data + extrarow):
 
@@ -1314,6 +1312,8 @@ def fill_table(self, table: MyQTable, data: list):
                         myitem.setToolTip(get_eventshelp(itemvalue))
                     table.setItem(i, j, myitem)
 
+        table.horizontalHeader().setSectionResizeMode(QHeaderView.ResizeMode.ResizeToContents)
+        table.horizontalHeader().setSectionResizeMode(ncols - 1, QHeaderView.ResizeMode.Stretch)
         table.show()
         table.blockSignals(False)
 
@@ -2267,7 +2267,7 @@ def bidseditor(bidsfolder: str, bidsmap: str='', template: str=bidsmap_template)
 
     # Start the Qt-application
     app = QApplication(sys.argv)
-    app.setApplicationName(f"{bidsmapfile} - BIDS editor {__version__}")
+    app.setApplicationName(f"{input_bidsmap.filepath} - BIDS editor {__version__}")
     mainwin = MainWindow(bidsfolder, input_bidsmap, template_bidsmap, datasaved=True)
     mainwin.show()
     app.exec()

bidscoin/plugins/dcm2niix2bids.py

@@ -46,7 +46,7 @@ def test(options: Plugin=OPTIONS) -> int:
 
     LOGGER.info('Testing the dcm2niix2bids installation:')
 
-    if 'readphysio' not in dir(physio) or 'physio2tsv' not in dir(physio):
+    if not hasattr(physio, 'readphysio') or not hasattr(physio, 'physio2tsv'):
         LOGGER.error("Could not import the expected 'readphysio' and/or 'physio2tsv' from the physio.py utility")
         return 1
     if 'command' not in {**OPTIONS, **options}:

bidscoin/plugins/events2bids.py

@@ -242,28 +242,35 @@ def __init__(self, sourcefile: Path, _data: dict, options: dict):
         # Read the log-tables from the Presentation logfile
         self._sourcetable = pd.read_csv(self.sourcefile, sep='\t', skiprows=3, skip_blank_lines=True)
         """The Presentation log-tables (https://www.neurobs.com/pres_docs/html/03_presentation/07_data_reporting/01_logfiles/index.html)"""
+        self._columns     = self._sourcetable.columns
+        """Store the original column names"""
 
     @property
     def logtable(self) -> pd.DataFrame:
         """Returns a Presentation log-table"""
 
-        nrows          = len(self._sourcetable)
-        stimulus_start = (self._sourcetable.iloc[:, 0] == 'Event Type').idxmax() or nrows
-        video_start    = (self._sourcetable.iloc[:, 0] == 'filename').idxmax() or nrows
-        survey_start   = (self._sourcetable.iloc[:, 0] == 'Time').idxmax() or nrows
+        nrows           = len(self._sourcetable)
+        stimulus_header = (self._sourcetable.iloc[:, 0] == 'Event Type').idxmax() or nrows
+        video_header    = (self._sourcetable.iloc[:, 0] == 'filename').idxmax() or nrows
+        survey_header   = (self._sourcetable.iloc[:, 0] == 'Time').idxmax() or nrows
 
-        # Drop the stimulus, video and survey tables
+        # Keep only the event, stimulus, video or survey table
+        self._sourcetable.columns = self._columns
         if self.options['table'] == 'event':
             begin = 0
-            end   = min(stimulus_start, video_start, survey_start)
+            end   = min(stimulus_header, video_header, survey_header)
         elif self.options['table'] == 'stimulus':
-            self._sourcetable.columns = self._sourcetable.iloc[stimulus_start]
-            begin = stimulus_start + 1
-            end   = min(video_start, survey_start)
+            self._sourcetable.columns = self._sourcetable.iloc[stimulus_header]
+            begin = stimulus_header + 1
+            end   = min(video_header, survey_header)
         elif self.options['table'] == 'video':
-            self._sourcetable.columns = self._sourcetable.iloc[video_start]
-            begin = video_start + 1
-            end   = survey_start
+            self._sourcetable.columns = self._sourcetable.iloc[video_header]
+            begin = video_header + 1
+            end   = survey_header
+        elif self.options['table'] == 'survey':
+            self._sourcetable.columns = self._sourcetable.iloc[survey_header]
+            begin = survey_header + 1
+            end   = nrows
         else:
             begin = 0
             end   = nrows

bidscoin/plugins/spec2nii2bids.py

@@ -33,7 +33,7 @@ def test(options: Plugin=OPTIONS) -> int:
 
     LOGGER.info('Testing the spec2nii2bids installation:')
 
-    if 'get_twixfield' not in dir(bids) or 'get_sparfield' not in dir(bids) or 'get_p7field' not in dir(bids):
+    if not all(hasattr(bids, name) for name in ('get_twixfield', 'get_sparfield', 'get_p7field')):
         LOGGER.error("Could not import the expected 'get_twixfield', 'get_sparfield' and/or 'get_p7field' from the bids.py library")
         return 1
     if 'command' not in {**OPTIONS, **options}: