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Edit the participant data in the bidseditor (GitHub issue #253)
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@marcelzwiers
marcelzwiers committed Jan 22, 2025
1 parent 1cb1e1c commit c7ec40a
Showing 1 changed file with 130 additions and 67 deletions.
197 changes: 130 additions & 67 deletions bidscoin/bidseditor.py
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Original file line number Diff line number Diff line change
Expand Up @@ -175,7 +175,7 @@ def __init__(self, bidsfolder: Path, input_bidsmap: BidsMap, template_bidsmap: B
tabwidget.setTabPosition(QtWidgets.QTabWidget.TabPosition.North)
tabwidget.setTabShape(QtWidgets.QTabWidget.TabShape.Rounded)

self.subses_table = {}
self.participant_table = {}
self.samples_table = {}
self.options_label = {}
self.options_table = {}
Expand Down Expand Up @@ -250,7 +250,7 @@ def samples_menu(self, pos):
"""Pops up a context-menu for deleting or editing the right-clicked sample in the samples_table"""

# Get the activated row-data
dataformat = self.tabwidget.widget(self.tabwidget.currentIndex()).objectName()
dataformat = self.tabwidget.currentWidget().objectName()
table = self.samples_table[dataformat]
colindex = table.currentColumn()
rowindexes = [index.row() for index in table.selectedIndexes() if index.column() == colindex]
Expand Down Expand Up @@ -303,7 +303,7 @@ def samples_menu(self, pos):
else:
self.ordered_file_index[dataformat][datasource.path] = max(self.ordered_file_index[dataformat][fname] for fname in self.ordered_file_index[dataformat]) + 1
if runitem:
self.update_subses_samples(dataformat)
self.fill_samples_table(dataformat)

elif action == delete:
deleted = False
Expand All @@ -319,7 +319,7 @@ def samples_menu(self, pos):
self.output_bidsmap.delete_run(provenance, datatype, dataformat)
deleted = True
if deleted:
self.update_subses_samples(dataformat)
self.fill_samples_table(dataformat)

elif action == compare:
CompareWindow(runitems, subids, sesids)
Expand Down Expand Up @@ -353,7 +353,7 @@ def samples_menu(self, pos):
self.output_bidsmap.update(datatype, templaterun)
LOGGER.verbose(f"User sets run-item {datatype} -> {templaterun}")

self.update_subses_samples(dataformat)
self.fill_samples_table(dataformat)

def set_menu_statusbar(self):
"""Set up the menu and statusbar"""
Expand Down Expand Up @@ -427,25 +427,25 @@ def set_tab_bidsmap(self, dataformat: str):
"""Set the SOURCE file sample listing tab"""

# Set the Participant table
subses_label = QLabel('Participant data')
subses_label.setToolTip('Subject/session mappings')

subses_table = MyQTable(ncols=2, nrows=2)
subses_table.setToolTip(f"Use e.g. '<<filepath:/sub-(.*?)/>>' to parse the subject and (optional) session label from the pathname. NB: the () parentheses indicate the part that is extracted as the subject/session label\n"
f"Use a dynamic {dataformat} attribute (e.g. '<<PatientName>>') to extract the subject and (optional) session label from the {dataformat} header")
subses_table.setMouseTracking(True)
header = subses_table.horizontalHeader()
participant_label = QLabel('Participant data')
participant_label.setToolTip('Data to parse the subject/session labels, and to populate the participants tsv- and json-files')

self.participant_table[dataformat] = participant_table = MyQTable(ncols=3)
participant_table.setToolTip(f"Use e.g. '<<filepath:/sub-(.*?)/>>' to parse the subject and (optional) session label from the pathname. NB: the () parentheses indicate the part that is extracted as the subject/session label\n"
f"Use a dynamic {dataformat} attribute (e.g. '<<PatientName>>') to extract the subject and (optional) session label from the {dataformat} header")
participant_table.cellChanged.connect(self.participant_table2bidsmap)
header = participant_table.horizontalHeader()
header.setSectionResizeMode(0, QHeaderView.ResizeMode.ResizeToContents)
header.setSectionResizeMode(1, QHeaderView.ResizeMode.Stretch)
subses_table.cellChanged.connect(self.subsescell2bidsmap)
self.subses_table[dataformat] = subses_table

self.fill_participant_table(dataformat)

# Set the bidsmap table
label = QLabel('Data samples')
label.setToolTip('List of unique source-data samples')
label = QLabel('Representative samples')
label.setToolTip('List of unique source-data samples (datatypes)')

self.samples_table[dataformat] = samples_table = MyQTable(minsize=False, ncols=6)
samples_table.setMouseTracking(True)
samples_table.setMouseTracking(True) # Needed for showing filepath in the statusbar
samples_table.setShowGrid(True)
samples_table.setHorizontalHeaderLabels(['', f'{dataformat} input', 'BIDS data type', 'BIDS output', 'Action', 'Provenance'])
samples_table.setSortingEnabled(True)
Expand All @@ -462,8 +462,8 @@ def set_tab_bidsmap(self, dataformat: str):
header.setSectionResizeMode(3, QHeaderView.ResizeMode.Stretch)

layout = QVBoxLayout()
layout.addWidget(subses_label)
layout.addWidget(subses_table)
layout.addWidget(participant_label)
layout.addWidget(participant_table)
layout.addWidget(label)
layout.addWidget(samples_table)
tab = QtWidgets.QWidget()
Expand All @@ -472,7 +472,7 @@ def set_tab_bidsmap(self, dataformat: str):
self.tabwidget.addTab(tab, f"{dataformat} mappings")
self.tabwidget.setCurrentWidget(tab)

self.update_subses_samples(dataformat)
self.fill_samples_table(dataformat)

def set_tab_options(self):
"""Set the options tab"""
Expand Down Expand Up @@ -556,24 +556,86 @@ def set_tab_filebrowser(self):

self.tabwidget.addTab(tab, 'Data browser')

def update_subses_samples(self, dataformat: str):
"""(Re)populates the sample list with bidsnames according to the bidsmap"""
def fill_participant_table(self, dataformat: str):
"""(Re)populate the participant table with the new bidsmap data"""

# Populate the participant table
participant_table = self.participant_table[dataformat]
participant_table.blockSignals(True)
participant_table.hide()
participant_table.setRowCount(len(self.output_bidsmap.dataformat(dataformat).participant) + 1)
participant_table.clearContents()
for n, (key, item) in enumerate(self.output_bidsmap.dataformat(dataformat).participant.items()):
tableitem = MyQTableItem(key, editable=key not in ('participant_id','session_id'))
tableitem.setToolTip(get_columnhelp(key))
participant_table = self.participant_table[dataformat]
participant_table.setItem(n, 0, tableitem)
participant_table.setItem(n, 1, MyQTableItem(item['value']))
edit_button = QPushButton('Metadata')
edit_button.setToolTip('Data for participants json sidecar-file')
edit_button.clicked.connect(self.edit_metadata)
participant_table.setCellWidget(n, 2, edit_button)

participant_table.show()
participant_table.blockSignals(False)

def participant_table2bidsmap(self, rowindex: int, colindex: int):
"""
A value has been changed in the participant table. If it is valid, save it to the bidsmap and update the
participant and samples table
:param rowindex:
:param colindex:
:return:
"""

# Only if cell was actually clicked, update
if self.tabwidget.currentIndex() < 0:
return
dataformat = self.tabwidget.currentWidget().objectName()
if colindex == 1 and dataformat in self.dataformats:
key = self.participant_table[dataformat].item(rowindex, 0).text().strip()
value = self.participant_table[dataformat].item(rowindex, 1).text().strip()
oldvalue = self.output_bidsmap.dataformat(dataformat).participant[key]['value']
if oldvalue is None:
oldvalue = ''

# Only if cell content was changed, update
if key and value != oldvalue:
LOGGER.verbose(f"User sets {dataformat}['{key}'] from '{oldvalue}' to '{value}'")
self.output_bidsmap.dataformat(dataformat).participant[key]['value'] = value
self.fill_participant_table(dataformat)
self.fill_samples_table(dataformat)
self.datachanged = True

def edit_metadata(self):
"""Pop-up a text window to edit the sidecar metadata of participant item"""

dataformat = self.tabwidget.currentWidget().objectName()
participant_table = self.participant_table[dataformat]
clicked = self.focusWidget()
rowindex = participant_table.indexAt(clicked.pos()).row()
key = participant_table.item(rowindex, 0).text().strip()
meta = self.output_bidsmap.dataformat(dataformat).participant[key]['meta']

text, ok = QtWidgets.QInputDialog.getMultiLineText(self, f"Edit sidecar metadata for {key}", 'json data', text=json.dumps(meta, indent=2))
if ok:
try:
meta_ = json.loads(text)
self.output_bidsmap.dataformat(dataformat).participant[key]['meta'] = meta_
if meta_ != meta:
self.datachanged = True
except json.decoder.JSONDecodeError as jsonerror:
QMessageBox.warning(self, f"Sidecar metadata parsing error", f"{text}\n\nPlease provide valid json metadata:\n{jsonerror}")
self.edit_metadata()

def fill_samples_table(self, dataformat: str):
"""(Re)populate the sample table with bidsnames according to the new bidsmap data"""

self.datachanged = True
output_bidsmap = self.output_bidsmap

# Update the subject/session table
subitem = MyQTableItem('subject', editable=False)
subitem.setToolTip(get_entityhelp('sub'))
sesitem = MyQTableItem('session', editable=False)
sesitem.setToolTip(get_entityhelp('ses'))
subses_table = self.subses_table[dataformat]
subses_table.setItem(0, 0, subitem)
subses_table.setItem(1, 0, sesitem)
subses_table.setItem(0, 1, MyQTableItem(output_bidsmap.dataformat(dataformat).subject))
subses_table.setItem(1, 1, MyQTableItem(output_bidsmap.dataformat(dataformat).session))

# Update the run samples table
# Add runs to the samples table
idx = 0
num_files = self.set_ordered_file_index(dataformat)
samples_table = self.samples_table[dataformat]
Expand Down Expand Up @@ -662,28 +724,10 @@ def set_ordered_file_index(self, dataformat: str) -> int:

return len(provenances)

def subsescell2bidsmap(self, rowindex: int, colindex: int):
"""Subject or session value has been changed in subject-session table"""

# Only if cell was actually clicked, update
dataformat = self.tabwidget.widget(self.tabwidget.currentIndex()).objectName()
if colindex == 1 and dataformat in self.dataformats:
key = self.subses_table[dataformat].item(rowindex, 0).text().strip()
value = self.subses_table[dataformat].item(rowindex, 1).text().strip()
oldvalue = getattr(self.output_bidsmap.dataformat(dataformat), key)
if oldvalue is None:
oldvalue = ''

# Only if cell content was changed, update
if key and value != oldvalue:
LOGGER.verbose(f"User sets {dataformat}['{key}'] from '{oldvalue}' to '{value}'")
setattr(self.output_bidsmap.dataformat(dataformat), key, value)
self.update_subses_samples(dataformat)

def open_editwindow(self, provenance: Path=Path(), datatype: str=''):
"""Make sure that index map has been updated"""

dataformat = self.tabwidget.widget(self.tabwidget.currentIndex()).objectName()
dataformat = self.tabwidget.currentWidget().objectName()
if not datatype:
samples_table = self.samples_table[dataformat]
clicked = self.focusWidget()
Expand All @@ -702,7 +746,7 @@ def open_editwindow(self, provenance: Path=Path(), datatype: str=''):
LOGGER.verbose(f'User is editing {provenance}')
self.editwindow = EditWindow(runitem, self.output_bidsmap, self.template_bidsmap)
self.editwindow_opened = str(provenance)
self.editwindow.done_edit.connect(self.update_subses_samples)
self.editwindow.done_edit.connect(self.fill_samples_table)
self.editwindow.finished.connect(self.release_editwindow)
self.editwindow.show()
return
Expand Down Expand Up @@ -777,7 +821,7 @@ def options2bidsmap(self, rowindex: int, colindex: int):
self.ignoredatatypes = newoptions.get('ignoretypes', [])
self.bidsignore = newoptions.get('bidsignore', [])
for dataformat in self.dataformats:
self.update_subses_samples(dataformat)
self.fill_samples_table(dataformat)
else:
self.output_bidsmap.plugins[plugin] = newoptions

Expand Down Expand Up @@ -942,7 +986,7 @@ def save_options(self):
def sample_doubleclicked(self, item):
"""When source file is double-clicked in the samples_table, show the inspect- or edit-window"""

dataformat = self.tabwidget.widget(self.tabwidget.currentIndex()).objectName()
dataformat = self.tabwidget.currentWidget().objectName()
datatype = self.samples_table[dataformat].item(item.row(), 2).text()
sourcefile = self.samples_table[dataformat].item(item.row(), 5).text()
if item.column() == 1:
Expand Down Expand Up @@ -1135,7 +1179,7 @@ def __init__(self, runitem: RunItem, bidsmap: BidsMap, template_bidsmap: BidsMap
layout1_.addWidget(inspect_button, alignment=QtCore.Qt.AlignmentFlag.AlignRight)
layout1_.addWidget(log_table_label)
layout1_.addWidget(log_table)
self.events_inbox = events_inbox = QGroupBox(f"{self.dataformat} input")
self.events_inbox = events_inbox = QGroupBox(f"{self.dataformat} input data")
events_inbox.setSizePolicy(sizepolicy)
events_inbox.setLayout(layout1_)

Expand Down Expand Up @@ -1167,7 +1211,7 @@ def __init__(self, runitem: RunItem, bidsmap: BidsMap, template_bidsmap: BidsMap
layout2_.addWidget(events_time_label)
layout2_.addWidget(events_time)
layout2_.addStretch()
self.events_editbox = events_editbox = QGroupBox(' ')
self.events_editbox = events_editbox = QGroupBox('Mapping')
events_editbox.setSizePolicy(sizepolicy)
events_editbox.setLayout(layout2_)

Expand All @@ -1176,7 +1220,7 @@ def __init__(self, runitem: RunItem, bidsmap: BidsMap, template_bidsmap: BidsMap
layout3.addWidget(done_button, alignment=QtCore.Qt.AlignmentFlag.AlignRight)
layout3.addWidget(events_table_label)
layout3.addWidget(events_table)
self.eventsbox = eventsbox = QGroupBox('BIDS output')
self.eventsbox = eventsbox = QGroupBox('BIDS output data')
eventsbox.setSizePolicy(sizepolicy)
eventsbox.setLayout(layout3)

Expand Down Expand Up @@ -1446,7 +1490,7 @@ def run2data(self) -> tuple:
return properties_data, attributes_data, bids_data, meta_data, events_data

def properties2run(self, rowindex: int, colindex: int):
"""Source attribute value has been changed"""
"""Source attribute value has been changed. If OK, update the target run"""

# Only if cell was actually clicked, update (i.e. not when BIDS datatype changes)
if colindex == 1:
Expand All @@ -1470,7 +1514,7 @@ def properties2run(self, rowindex: int, colindex: int):
self.properties_table.blockSignals(False)

def attributes2run(self, rowindex: int, colindex: int):
"""Source attribute value has been changed"""
"""Source attribute value has been changed. If OK, update the target run"""

# Only if cell was actually clicked, update (i.e. not when BIDS datatype changes)
if colindex == 1:
Expand All @@ -1494,7 +1538,7 @@ def attributes2run(self, rowindex: int, colindex: int):
self.attributes_table.blockSignals(False)

def bids2run(self, rowindex: int, colindex: int):
"""BIDS attribute value has been changed"""
"""BIDS attribute value has been changed. If OK, update the target run"""

# Only if cell was actually clicked, update (i.e. not when BIDS datatype changes) and store the data in the target_run
if colindex == 1:
Expand Down Expand Up @@ -1533,7 +1577,7 @@ def bids2run(self, rowindex: int, colindex: int):
self.refresh_bidsname()

def meta2run(self, rowindex: int, colindex: int):
"""Meta value has been changed"""
"""Meta value has been changed. If OK, update the target run"""

key = self.meta_table.item(rowindex, 0).text().strip()
value = self.meta_table.item(rowindex, 1).text().strip()
Expand Down Expand Up @@ -1566,7 +1610,7 @@ def meta2run(self, rowindex: int, colindex: int):
self.fill_table(self.meta_table, meta_data)

def events_time2run(self, rowindex: int, colindex: int):
"""Events value has been changed. Read the data from the event 'time' table"""
"""Events value has been changed. Read the data from the event 'time' table and, if OK, update the target run"""

# events_data['time'] = [['columns', events.timecols],
# ['units/sec', events.timeunit],
Expand Down Expand Up @@ -1599,7 +1643,7 @@ def events_time2run(self, rowindex: int, colindex: int):
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"""
"""Events value has been changed. Read the data from the event 'rows' table and, if OK, update the target run"""

# row: [[include, {column_in: regex}],
# [cast, {column_out: newvalue}]]
Expand Down Expand Up @@ -1627,7 +1671,7 @@ def events_rows2run(self, rowindex: int, colindex: int):
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"""
"""Events value has been changed. Read the data from the event 'columns' table and, if OK, update the target run"""

# events_data['columns'] = [[{'source1': target1}],
# [{'source2': target2}],
Expand Down Expand Up @@ -2172,6 +2216,25 @@ def get_suffixhelp(suffix: str) -> str:
return f"{suffix}\nAn unknown/private suffix"


def get_columnhelp(column: str) -> str:
"""
Reads the description of a matching entity=entitykey in the bidsschema.objects.columns
:param column: The column name for which the help text is obtained
:return: The obtained help text
"""

if not column:
return "Please provide a column-name"

# Return the description from the entities or a default text
for _, entity in bids.bidsschema.objects.columns.items():
if entity.name == column:
return f"{entity.display_name}\n{entity.description}"

return f"{column}\nAn unknown/private column name"


def get_entityhelp(entitykey: str) -> str:
"""
Reads the description of a matching entity=entitykey in the schema/entities.yaml file
Expand Down

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