Merge branch 'psychopy'

# Conflicts:
#	bidscoin/plugins/events2bids.py

Author: marcelzwiers

CONTRIBUTING.rst

@@ -26,7 +26,7 @@ The preferred way to contribute to the BIDScoin code base or documentation is to
 
 1. Set up a clone of the repository on your local machine and connect it to both the “official” and your copy of the repository on GitHub::
 
-    git clone git://github.com/Donders-Institute/bidscoin
+    git clone https://github.com/Donders-Institute/bidscoin.git
     cd bidscoin
     git remote rename origin official
     git remote add origin git://github.com/[YOUR_GITHUB_USERNAME]/bidscoin
@@ -35,15 +35,14 @@ The preferred way to contribute to the BIDScoin code base or documentation is to
 
     python -m venv venv         # Or use any other tool (such as conda)
     source venv/bin/activate    # On Linux, see the documentation for other operating systems
-    pip install bidscoin[dev]   # Unfortunately pyproject.toml has no way to install BIDScoin's dependencies only
-    pip uninstall bidscoin      # Hence we need to retrospectively remove BIDScoin from site-packages
+    pip install -e .[dev]
     # NB: Install dcm2niix yourself (see the online installation instructions)
 
-3. When you wish to start a new contribution, create a new branch::
+3. When you wish to start working on your contribution, create a new branch::
 
     git checkout -b [topic_of_your_contribution]
 
-4. When you are done making the changes you wish to contribute, test, commit and push them to GitHub::
+4. When you are done with coding, you should then test, commit and push your work to GitHub::
 
     tox                                                  # Run this command from the bidscoin directory (make sure the venv is activated)
     git commit -am "A SHORT DESCRIPTION OF THE CHANGES"  # Run this command every time you have made a set of changes that belong together

bidscoin/bids.py

@@ -57,7 +57,7 @@ def ignore_aliases(self, data):
 
 
 class DataSource:
-    """Reads properties, attributes and BIDS-related features to sourcefiles of a supported dataformat (e.g. DICOM or PAR)"""
+    """Reads properties, attributes and BIDS-related features to source files of a supported dataformat (e.g. DICOM or PAR)"""
 
     def __init__(self, sourcefile: Union[str, Path]='', plugins: Plugins=None, dataformat: str='', options: Options=None):
         """
@@ -669,7 +669,7 @@ 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, self.plugins[name])
+                return getattr(plugin, f"{self.dataformat}Events")(Path(self.provenance), self.events, self.plugins[name])
 
 
 class DataType:
@@ -815,7 +815,7 @@ def __hash__(self):
     def participant(self) -> dict:
         """The data to populate the participants.tsv table"""
 
-        return self._data['participant']
+        return self._data.get('participant', {})
 
     @participant.setter
     def participant(self, value: dict):
@@ -1040,14 +1040,14 @@ def plugins(self, plugins: Plugins):
 
     @property
     def dataformats(self):
-        """Gets a list of the DataFormat objects in the bidsmap (e.g. DICOM)"""
+        """Gets a list of the non-empty DataFormat objects in the bidsmap (e.g. DICOM)"""
 
         return [DataFormat(dataformat, self._data[dataformat], self.options, self.plugins) for dataformat in self._data if dataformat not in ('$schema', 'Options')]
 
     def dataformat(self, dataformat: str) -> DataFormat:
         """Gets the DataFormat object from the bidsmap"""
 
-        return DataFormat(dataformat, self._data[dataformat], self.options, self.plugins)
+        return DataFormat(dataformat, self._data.get(dataformat,''), self.options, self.plugins)
 
     def add_dataformat(self, dataformat: Union[str, DataFormat]):
         """Adds a DataFormat to the bidsmap"""
@@ -1311,6 +1311,11 @@ def get_matching_run(self, sourcefile: Union[str, Path], dataformat: str='', run
                 if provenance: break
             return runitem, provenance
 
+        # Check if the dataformat is present
+        if dataformat not in self.dataformats:
+            LOGGER.error(f"Cannot find a matching run-item for {sourcefile} due to a missing '{dataformat}' section in {self}")
+            return RunItem(), ''
+
         # Defaults
         datasource       = DataSource(sourcefile, self.plugins, dataformat, options=self.options)
         unknowndatatypes = self.options.get('unknowntypes') or ['unknown_data']

bidscoin/bidseditor.py

@@ -71,7 +71,7 @@
 args: Argument string that is passed to dcm2niix. Click [Test] and see the terminal output for usage
     Tip: SPM users may want to use '-z n', which produces unzipped NIfTI's
     
-meta: The file extensions of the associated / equally named (meta)data sourcefiles that are copied over as
+meta: The file extensions of the associated / equally named (meta)data source files that are copied over as
     BIDS (sidecar) files, such as ['.json', '.tsv', '.tsv.gz']. You can use this to enrich json sidecar files,
     or add data that is not supported by this plugin
 
@@ -91,7 +91,6 @@ def __init__(self, minsize: bool=True, ncols: int=0, nrows: int=0):
         self.horizontalHeader().setVisible(False)
         self.verticalHeader().setVisible(False)
         self.verticalHeader().setDefaultSectionSize(ROW_HEIGHT)
-        self.setMinimumHeight(2 * (ROW_HEIGHT + 8))
         self.setSizeAdjustPolicy(QtWidgets.QAbstractScrollArea.SizeAdjustPolicy.AdjustToContents)
         if minsize:
             self.setSizePolicy(QtWidgets.QSizePolicy.Policy.Expanding, QtWidgets.QSizePolicy.Policy.Minimum)
@@ -101,6 +100,7 @@ def __init__(self, minsize: bool=True, ncols: int=0, nrows: int=0):
             self.setColumnCount(ncols)
         if nrows:
             self.setRowCount(nrows)
+        self.resizeRowsToContents()
 
 
 class MyQTableItem(QTableWidgetItem):
@@ -168,7 +168,7 @@ def __init__(self, bidsfolder: Path, input_bidsmap: BidsMap, template_bidsmap: B
         """The bidsmap from which new data type run-items are taken"""
         self.datasaved                   = datasaved
         """True if data has been saved on disk"""
-        self.dataformats                 = [dataformat.dataformat for dataformat in input_bidsmap.dataformats if input_bidsmap.dir(dataformat)]
+        self.dataformats                 = [dataformat.dataformat for dataformat in input_bidsmap.dataformats if input_bidsmap.dir(dataformat) and dataformat.dataformat]
         self.bidsignore: list[str]       = input_bidsmap.options['bidsignore']
         self.unknowndatatypes: list[str] = input_bidsmap.options['unknowntypes']
         self.ignoredatatypes: list[str]  = input_bidsmap.options['ignoretypes']
@@ -1146,6 +1146,10 @@ def __init__(self, runitem: RunItem, bidsmap: BidsMap, template_bidsmap: BidsMap
         meta_table.setToolTip(f"The key-value pair that will be appended to the (e.g. dcm2niix-produced) json sidecar file")
 
         # Set up the events tables
+        self.events_settings = events_settings = self.setup_table(events_data.get('settings', []), 'events_settings')
+        events_settings.cellChanged.connect(self.events_settings2run)
+        events_settings.setToolTip(f"Settings for parsing the input table from the source file")
+        events_settings.setStyleSheet('QTableView::item {border-right: 1px solid #d6d9dc;}')
         inspect_button = QPushButton('Source')
         inspect_button.setToolTip('TODO')
         inspect_button.clicked.connect(self.inspect_sourcefile)
@@ -1174,7 +1178,7 @@ def __init__(self, runitem: RunItem, bidsmap: BidsMap, template_bidsmap: BidsMap
         events_columns.horizontalHeader().setVisible(True)
         events_columns.setStyleSheet('QTableView::item {border-right: 1px solid #d6d9dc;}')
         log_table_label = QLabel('Log data')
-        log_table = self.setup_table(events_data.get('log_table',[]), 'log_table', minsize=False)
+        self.log_table = log_table = self.setup_table(events_data.get('log_table',[]), 'log_table', minsize=False)
         log_table.setShowGrid(True)
         log_table.horizontalHeader().setVisible(True)
         log_table.setToolTip(f"The raw stimulus presentation data that is parsed from the log file")
@@ -1197,12 +1201,16 @@ def __init__(self, runitem: RunItem, bidsmap: BidsMap, template_bidsmap: BidsMap
         sourcebox.setLayout(layout1)
 
         layout1_ = QVBoxLayout()
-        layout1_.addWidget(inspect_button, alignment=QtCore.Qt.AlignmentFlag.AlignRight)
+        layout1_header = QHBoxLayout()
+        layout1_header.addWidget(events_settings)
+        layout1_header.addStretch()
+        layout1_header.addWidget(inspect_button)
+        layout1_.addLayout(layout1_header)
         layout1_.addWidget(log_table_label)
         layout1_.addWidget(log_table)
-        self.events_inbox = events_inbox = QGroupBox(f"{self.dataformat} input data")
-        events_inbox.setSizePolicy(sizepolicy)
-        events_inbox.setLayout(layout1_)
+        self.events_inputbox = events_inputbox = QGroupBox(f"{self.dataformat} input data")
+        events_inputbox.setSizePolicy(sizepolicy)
+        events_inputbox.setLayout(layout1_)
 
         self.arrow = arrow = QLabel()
         arrow.setPixmap(QtGui.QPixmap(str(RIGHTARROW)).scaled(30, 30, QtCore.Qt.AspectRatioMode.KeepAspectRatio, QtCore.Qt.TransformationMode.SmoothTransformation))
@@ -1251,10 +1259,10 @@ def __init__(self, runitem: RunItem, bidsmap: BidsMap, template_bidsmap: BidsMap
         layout_tables.addWidget(arrow)
         layout_tables.addWidget(bidsbox)
         if events_data:
-            layout_tables.addWidget(events_inbox)
+            layout_tables.addWidget(events_inputbox)
             layout_tables.addWidget(events_editbox)
             layout_tables.addWidget(eventsbox)
-            events_inbox.hide()
+            events_inputbox.hide()
             events_editbox.hide()
 
         # Set-up buttons
@@ -1354,12 +1362,12 @@ def fill_table(self, table: MyQTable, data: list):
             for j, item in enumerate(row):
                 itemvalue = item['value']
 
-                if tablename == 'bids' and isinstance(itemvalue, list):
+                if tablename in ('bids', 'events_settings') and isinstance(itemvalue, list):
                     dropdown = QComboBox()
                     dropdown.addItems(itemvalue[0:-1])
                     dropdown.setCurrentIndex(itemvalue[-1])
-                    dropdown.currentIndexChanged.connect(partial(self.bids2run, i, j))
-                    if j == 0:
+                    dropdown.currentIndexChanged.connect(partial(self.bids2run if tablename=='bids' else self.events_settings2run, i, j))
+                    if tablename=='bids' and j == 0:
                         dropdown.setToolTip(get_entityhelp(key))
                     table.setCellWidget(i, j, self.spacedwidget(dropdown))
 
@@ -1482,6 +1490,11 @@ def run2data(self) -> tuple:
                                    [{'value': 'units/sec', 'editable': False}, {'value': runitem.events['time']['unit'],  'editable': True}],
                                    [{'value': 'start',     'editable': False}, {'value': runitem.events['time']['start'], 'editable': True}]]
 
+        # Set up the data for the events settings
+        events_data['settings'] = []
+        for key, value in runitem.events.get('settings', {}).items():
+            events_data['settings'].append([{'value': key, 'editable': True}, {'value': value, 'editable': True}])
+
         # Set up the data for the events conditions / row groups
         events_data['rows'] = [[{'value': 'condition', 'editable': False}, {'value': 'output column', 'editable': False}]]
         for condition in runitem.events.get('rows') or []:
@@ -1517,8 +1530,7 @@ def properties2run(self, rowindex: int, colindex: int):
         if colindex == 1:
             key      = self.properties_table.item(rowindex, 0).text().strip()
             value    = self.properties_table.item(rowindex, 1).text().strip()
-            oldvalue = self.target_run.properties.get(key)
-            if oldvalue is None:
+            if (oldvalue := self.target_run.properties.get(key)) is None:
                 oldvalue = ''
 
             # Only if cell was changed, update
@@ -1541,8 +1553,7 @@ def attributes2run(self, rowindex: int, colindex: int):
         if colindex == 1:
             key      = self.attributes_table.item(rowindex, 0).text().strip()
             value    = self.attributes_table.item(rowindex, 1).text()
-            oldvalue = self.target_run.attributes.get(key)
-            if oldvalue is None:
+            if (oldvalue := self.target_run.attributes.get(key)) is None:
                 oldvalue = ''
 
             # Only if cell was changed, update
@@ -1567,11 +1578,9 @@ def bids2run(self, rowindex: int, colindex: int):
             if hasattr(self.bids_table.cellWidget(rowindex, 1), 'spacedwidget'):
                 dropdown = self.bids_table.cellWidget(rowindex, 1).spacedwidget
                 value    = [dropdown.itemText(n) for n in range(len(dropdown))] + [dropdown.currentIndex()]
-                oldvalue = self.target_run.bids.get(key)
             else:
                 value    = self.bids_table.item(rowindex, 1).text().strip()
-                oldvalue = self.target_run.bids.get(key)
-            if oldvalue is None:
+            if (oldvalue := self.target_run.bids.get(key)) is None:
                 oldvalue = ''
 
             # Only if cell was changed, update
@@ -1602,10 +1611,7 @@ def meta2run(self, rowindex: int, colindex: int):
 
         key      = self.meta_table.item(rowindex, 0).text().strip()
         value    = self.meta_table.item(rowindex, 1).text().strip()
-        oldvalue = self.target_run.meta.get(key)
-        if oldvalue is None:
-            oldvalue = ''
-        if value != oldvalue:
+        if value != (oldvalue := self.target_run.meta.get(key)):
             # Replace the (dynamic) value
             if '<<' not in value or '>>' not in value:
                 value = self.datasource.dynamicvalue(value, cleanup=False)
@@ -1663,6 +1669,34 @@ def events_time2run(self, rowindex: int, colindex: int):
         self.fill_table(self.events_time, events_data['time'])
         self.fill_table(self.events_table, events_data['table'])
 
+    def events_settings2run(self, rowindex: int, colindex: int):
+        """Events settings table has been changed. Read the data from the event 'settings' table and, if OK, update the target run"""
+
+        key = self.events_settings.item(rowindex, 0).text().strip()
+        if hasattr(self.events_settings.cellWidget(rowindex, 1), 'spacedwidget'):
+            dropdown = self.events_settings.cellWidget(rowindex, 1).spacedwidget
+            value    = [dropdown.itemText(n) for n in range(len(dropdown))] + [dropdown.currentIndex()]
+        else:
+            value    = self.events_settings.item(rowindex, 1).text().strip()
+        if (oldvalue := self.target_run.events['settings'].get(key)) is None:
+            oldvalue = ''
+
+        # Only if cell was changed, update
+        if key and value != oldvalue:
+            # Validate user input against BIDS or replace the (dynamic) bids-value if it is a run attribute
+            if isinstance(value, str) and ('<<' not in value or '>>' not in value):
+                value = bids.sanitize(self.datasource.dynamicvalue(value))
+                self.events_settings.blockSignals(True)
+                self.events_settings.item(rowindex, 1).setText(value)
+                self.events_settings.blockSignals(False)
+            LOGGER.verbose(f"User sets events['settings']['{key}'] from '{oldvalue}' to '{value}' for {self.target_run}")
+            self.target_run.events['settings'][key] = value
+
+        # Refresh the log and events tables
+        _,_,_,_,events_data = self.run2data()
+        self.fill_table(self.log_table, events_data['log_table'])
+        self.fill_table(self.events_table, events_data['table'])
+
     def events_rows2run(self, rowindex: int, colindex: int):
         """Events value has been changed. Read the data from the event 'rows' table and, if OK, update the target run"""
 
@@ -1693,7 +1727,7 @@ def events_rows2run(self, rowindex: int, colindex: int):
         # Refresh the events tables, i.e. delete empty rows or add a new row if a key is defined on the last row
         _,_,_,_,events_data = self.run2data()
         self.fill_table(self.events_table, events_data['table'])
-        self.fill_table(self.events_rows,  events_data['rows'])
+        self.fill_table(self.events_rows, events_data['rows'])
 
     def events_columns2run(self, rowindex: int, colindex: int):
         """Events value has been changed. Read the data from the event 'columns' table and, if OK, update the target run"""
@@ -1732,7 +1766,7 @@ def edit_events(self):
         self.sourcebox.hide()
         self.arrow.hide()
         self.bidsbox.hide()
-        self.events_inbox.show()
+        self.events_inputbox.show()
         self.events_editbox.show()
         self.edit_button.hide()
         self.done_button.show()
@@ -1743,7 +1777,7 @@ def done_events(self):
         self.sourcebox.show()
         self.arrow.show()
         self.bidsbox.show()
-        self.events_inbox.hide()
+        self.events_inputbox.hide()
         self.events_editbox.hide()
         self.edit_button.show()
         self.done_button.hide()
@@ -1856,6 +1890,7 @@ def reset(self, refresh: bool=False):
         self.fill_table(self.bids_table, bids_data)
         self.fill_table(self.meta_table, meta_data)
         if events_data:
+            self.fill_table(self.events_settings, events_data['settings'])
             self.fill_table(self.events_time, events_data['time'])
             self.fill_table(self.events_rows, events_data['rows'])
             self.fill_table(self.events_columns, events_data['columns'])
@@ -1940,20 +1975,20 @@ def inspect_sourcefile(self, rowindex: int=None, colindex: int=None):
                 QtGui.QDesktopServices.openUrl(QtCore.QUrl.fromLocalFile(str(Path(self.target_run.provenance).parent)))
 
     @staticmethod
-    def spacedwidget(alignedwidget, align='left'):
+    def spacedwidget(childwidget, align='left'):
         """Place the widget in a QHBoxLayout and add a stretcher next to it. Return the widget as widget.spacedwidget"""
 
         widget = QtWidgets.QWidget()
         layout = QHBoxLayout()
         if align != 'left':
             layout.addStretch()
-            layout.addWidget(alignedwidget)
+            layout.addWidget(childwidget)
         else:
-            layout.addWidget(alignedwidget)
+            layout.addWidget(childwidget)
             layout.addStretch()
         layout.setContentsMargins(0, 0, 0, 0)
         widget.setLayout(layout)
-        widget.spacedwidget = alignedwidget
+        widget.spacedwidget = childwidget
         return widget
 
     def get_help(self):
@@ -2115,7 +2150,7 @@ def __init__(self, filename: Path):
             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 is_parfile(filename) or filename.suffix.lower() in ('.spar', '.txt', '.text', '.log'):
+        elif is_parfile(filename) or filename.suffix.lower() in ('.spar', '.txt', '.text', '.log', '.csv', '.tsv'):
             text = filename.read_text()
         elif filename.suffix.lower() == '.7':
             try: