Add option to select a Presentation source table

Author: marcelzwiers

bidscoin/bids.py

@@ -62,17 +62,18 @@
 class EventsParser(ABC):
     """Parser for stimulus presentation logfiles"""
 
-    def __init__(self, sourcefile: Path, eventsdata: dict):
+    def __init__(self, sourcefile: Path, eventsdata: dict, options: dict):
         """
         Reads the events table from the events logfile
 
         :param sourcefile:  The full filepath of the raw logfile
         :param eventsdata:  The run['events'] data (from a bidsmap)
+        :param options:     The plugin options
         """
 
         self.sourcefile = sourcefile
         self._data      = eventsdata
-        # TODO: Check if edits in self.start/timecols propagate back to the bidsmap data
+        self.options    = options
 
     def __repr__(self):
 
@@ -121,6 +122,7 @@ 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():
@@ -822,7 +824,7 @@ def eventsparser(self) -> EventsParser:
 
         for name in self.plugins:
             if plugin := bcoin.import_plugin(name, (f"{self.dataformat}Events",)):
-                return getattr(plugin, f"{self.dataformat}Events")(self.provenance, self.events)
+                return getattr(plugin, f"{self.dataformat}Events")(self.provenance, self.events, self.plugins[name])
 
 
 class DataType:

bidscoin/bidseditor.py

@@ -1281,7 +1281,7 @@ def fill_table(self, table: MyQTable, data: list):
 
             elif header:
                 if i == 0:              # The first/header row of the data has the column names
-                    table.setHorizontalHeaderLabels(item.get('value') for item in row)
+                    table.setHorizontalHeaderLabels(str(item.get('value')) for item in row)
                     continue
                 i -= 1                  # Account for the header row
 
@@ -1310,7 +1310,7 @@ def fill_table(self, table: MyQTable, data: list):
                         myitem.setToolTip(get_entityhelp(key))
                     elif tablename == 'meta' and j == 0:
                         myitem.setToolTip(get_metahelp(key))
-                    elif tablename == 'events_columns' and i == 1:
+                    elif tablename == 'events_columns' and j == 1:
                         myitem.setToolTip(get_eventshelp(itemvalue))
                     table.setItem(i, j, myitem)
 
@@ -1423,18 +1423,18 @@ def run2data(self) -> tuple:
         events_data['columns'] = [[{'value': 'input', 'editable': False}, {'value': 'output', 'editable': False}]]
         for mapping in runitem.events.get('columns') or []:
             for key, value in mapping.items():
-                events_data['columns'].append([{'value': value, 'editable': True}, {'value': key, 'editable': True}])
+                events_data['columns'].append([{'value': value, 'editable': True}, {'value': key, 'editable': key not in ('onset','duration')}])
 
         # Set up the data for the events table
         parser = runitem.eventsparser()
         if parser:
             df = parser.logtable
-            events_data['log_table'] = [[{'value': name, 'editable': False} for name in df.columns]]
+            events_data['log_table'] = [[{'value': name, 'editable': False} for name in df.columns]] if len(df) else []
             for i in range(len(df)):
                 events_data['log_table'].append([{'value': value, 'editable': False} for value in df.iloc[i]])
 
             df = parser.eventstable
-            events_data['table'] = [[{'value': name, 'editable': False} for name in df.columns]]
+            events_data['table'] = [[{'value': name, 'editable': False} for name in df.columns]] if len(df) else []
             for i in range(len(df)):
                 events_data['table'].append([{'value': value, 'editable': False} for value in df.iloc[i]])
         else:

bidscoin/heuristics/bidsmap_dccn.yaml

@@ -39,7 +39,8 @@ Options:
       meta: [.json, .tsv, .tsv.gz]  # The file extensions of the equally named metadata sourcefiles that are copied over to the BIDS sidecar files
       fallback: y                   # Appends unhandled dcm2niix suffixes to the `acq` label if 'y' (recommended, else the suffix data is discarded)
     events2bids:
-      meta: [.json, .tsv, .tsv.gz]
+      table: event                  # The table that is used to generate the output table (https://www.neurobs.com/pres_docs/html/03_presentation/07_data_reporting/01_logfiles/index.html)
+      meta: [.json, .tsv]
 
 
 DICOM:

bidscoin/plugins/events2bids.py

@@ -13,7 +13,7 @@
 LOGGER = logging.getLogger(__name__)
 
 # The default/fallback options that are set when installing/using the plugin
-OPTIONS = Plugin({'meta': ['.json', '.tsv']})  # The file extensions of the equally named metadata sourcefiles that are copied over as BIDS sidecar files
+OPTIONS = Plugin({'table': 'event', 'meta': ['.json', '.tsv']})  # The file extensions of the equally named metadata sourcefiles that are copied over as BIDS sidecar files
 
 
 def test(options: Plugin=OPTIONS) -> int:
@@ -228,28 +228,47 @@ def bidscoiner_plugin(session: Path, bidsmap: BidsMap, bidsses: Path) -> None:
 class PresentationEvents(EventsParser):
     """Parser for Presentation (Neurobs) logfiles"""
 
-    def __init__(self, sourcefile: Path, _data):
+    def __init__(self, sourcefile: Path, _data: dict, options: dict):
         """
         Reads the event table from the Presentation logfile
 
         :param sourcefile:  The full filepath of the logfile
         :param data:        The run['events'] data (from a bidsmap)
+        :param options:     The plugin options
         """
 
-        super().__init__(sourcefile, _data)
+        super().__init__(sourcefile, _data, options)
 
-        # Read the event table from the Presentation logfile
-        self.sourcetable = df = pd.read_csv(self.sourcefile, sep='\t', skiprows=3, skip_blank_lines=True)
-        """The Presentation event table (https://www.neurobs.com/pres_docs/html/03_presentation/07_data_reporting/01_logfiles/index.html)"""
-
-        # Drop the stimulus, video and survey tables
-        endoftable = df['Subject'].isin(['Event Type', 'filename', 'Time']).idxmax()
-        if endoftable:
-            LOGGER.bcdebug(f"Dropping sourcetable data at row: {endoftable}")
-            self.sourcetable = df.iloc[:endoftable]
+        # 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)"""
 
     @property
     def logtable(self) -> pd.DataFrame:
-        """Returns the source logging data"""
+        """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
+
+        # Drop the stimulus, video and survey tables
+        if self.options['table'] == 'event':
+            begin = 0
+            end   = min(stimulus_start, video_start, survey_start)
+        elif self.options['table'] == 'stimulus':
+            self._sourcetable.columns = self._sourcetable.iloc[stimulus_start]
+            begin = stimulus_start + 1
+            end   = min(video_start, survey_start)
+        elif self.options['table'] == 'video':
+            self._sourcetable.columns = self._sourcetable.iloc[video_start]
+            begin = video_start + 1
+            end   = survey_start
+        else:
+            begin = 0
+            end   = nrows
+            LOGGER.error(f"NOT IMPLEMENTED TABLE: {self.options['table']}")
+
+        LOGGER.bcdebug(f"Slicing '{self.options['table']}' sourcetable[{begin}:{end}]")
 
-        return self.sourcetable
+        return self._sourcetable.iloc[begin:end]