def get_frame(
self,
value: Union[
Component,
ComponentInfo,
Transformation,
LinkTransformation,
TransformationsList,
FileWriterModule,
],
):
frame = QFrame()
frame.setAutoFillBackground(True)
SizePolicy = QSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
SizePolicy.setHorizontalStretch(0)
SizePolicy.setVerticalStretch(0)
frame.setSizePolicy(SizePolicy)
frame.setLayout(QVBoxLayout())
frame.layout().setContentsMargins(0, 0, 0, 0)
if isinstance(value, Group):
get_group_frame(frame, value)
elif isinstance(value, TransformationsList):
get_transformations_list_frame(frame)
elif isinstance(value, ComponentInfo):
get_group_info_frame(frame, value)
elif isinstance(value, Transformation):
get_transformation_frame(frame, self.model, value)
elif isinstance(value, LinkTransformation):
get_link_transformation_frame(frame, self.model, value)
elif isinstance(value, FileWriterModule):
get_module_frame(frame, self.model, value, self._use_simple_tree_view)
return frame
def get_frame(
self,
value: Union[
Component,
ComponentInfo,
Transformation,
LinkTransformation,
TransformationsList,
],
):
frame = QFrame()
frame.setAutoFillBackground(True)
SizePolicy = QSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed)
SizePolicy.setHorizontalStretch(0)
SizePolicy.setVerticalStretch(0)
frame.setSizePolicy(SizePolicy)
frame.setLayout(QVBoxLayout())
frame.layout().setContentsMargins(0, 0, 0, 0)
if isinstance(value, Component):
get_component_frame(frame, value)
elif isinstance(value, TransformationsList):
get_transformations_list_frame(frame)
elif isinstance(value, ComponentInfo):
get_component_info_frame(frame)
elif isinstance(value, Transformation):
get_transformation_frame(frame, self.instrument, value)
elif isinstance(value, LinkTransformation):
get_link_transformation_frame(frame, self.instrument, value)
return frame
def get_transformation_frame(frame: QFrame, model: Model,
value: Transformation):
if value.transform_type == TransformationType.TRANSLATION:
frame.transformation_frame = EditTranslation(frame, value, model)
elif value.transform_type == TransformationType.ROTATION:
frame.transformation_frame = EditRotation(frame, value, model)
else:
raise (RuntimeError('Transformation type "{}" is unknown.'.format(
value.transform_type)))
frame.layout().addWidget(frame.transformation_frame, Qt.AlignTop)
def get_module_frame(frame: QFrame, model: Model, value: FileWriterModule,
use_simple_tree_view: bool):
if use_simple_tree_view:
module_frame = ModuleView(value, frame)
else:
module_frame = ModuleViewEditable(value, frame, model)
frame.module_frame = module_frame
frame.layout().addWidget(frame.module_frame)
if (isinstance(module_frame, ModuleViewEditable)
and isinstance(value, Dataset)
and value.name in EXCLUDED_PIXEL_GRID):
frame.setEnabled(False)
def __init__(self, parent=None):
super(CloseDialog, self).__init__(parent)
self.setLayout(QVBoxLayout())
self.layout().addWidget(QLabel('Are you sure you want to quit?'))
button_panel = QFrame()
button_panel.setLayout(QHBoxLayout())
yes_button = QPushButton('Yes')
no_button = QPushButton('No')
button_panel.layout().addWidget(yes_button)
button_panel.layout().addWidget(no_button)
self.layout().addWidget(button_panel)
def __init__(self, app):
QFrame.__init__(self)
self.app = app
self.setLayout(QVBoxLayout())
self.layout().setContentsMargins(0, 0, 0, 0)
self.path = QLineEdit("")
self.scan = QLineEdit("")
self.slice = QLabel("")
info = QFrame()
info.setLayout(QFormLayout())
info.layout().addRow("Path:", self.path)
info.layout().addRow("Scan:", self.scan)
info.layout().addRow("Slice:", self.slice)
self.layout().addWidget(info)
self.setSizePolicy(QSizePolicy.Policy.Fixed, QSizePolicy.Policy.Fixed)
self.updateGeometry()
def show_schedule(self):
"""Show the schedule in the table"""
# Limpia el horario
self.schedule_view.clearContents()
# Si no hay módulos, se deshabilita la opción de guardar y termina
if not self.schedule_object.courses:
self.schedule_view.update_size()
self.save_button.setDisabled(True)
return
# Si existen módulos, se muestran en el horario
for i_row, row in enumerate(self.schedule_object.get_table()):
for sub_row in row:
for i_col, element in enumerate(sub_row):
if not element:
continue
module_label = QLabel(self.schedule_view)
module_label.setText(element.code)
module_label.setObjectName(element.type_)
module_label.setAlignment(Qt.AlignCenter)
module_label.setFixedHeight(20)
cell_frame = self.schedule_view.cellWidget(i_row, i_col)
# Se crea un frame para los widgets si no existe
if not cell_frame:
cell_frame = QFrame(self.schedule_view)
cell_layout = QVBoxLayout(cell_frame)
cell_layout.setSpacing(0)
cell_layout.setMargin(0)
self.schedule_view.setCellWidget(
i_row, i_col, cell_frame)
cell_frame.layout().addWidget(module_label)
self.schedule_view.update_size()
self.save_button.setDisabled(False)
class ThumbsWidget(QScrollArea):
"""Widget displaying scan thumbnails in a column."""
def __init__(self, app):
QScrollArea.__init__(self)
self.app = app
self.wrapper = QFrame()
self.wrapper.setLayout(QVBoxLayout())
self.wrapper.layout().setContentsMargins(5, 0, 0, 5)
self.wrapper.layout().addStretch()
self.thumbs = []
self.setSizePolicy(QSizePolicy.Policy.Fixed,
QSizePolicy.Policy.MinimumExpanding)
# Hide horizontal scollbar
self.horizontalScrollBar().setStyleSheet("QScrollBar { height: 0 }")
self.setWidgetResizable(True)
self.setWidget(self.wrapper)
def add_thumb(self, pixmap):
"""Add the thumbnail in *pixmap* to the widget."""
pixmap = pixmap.scaledToWidth(int(settings["ui"]["thumb_size"]))
thumb = QLabel()
thumb.setPixmap(pixmap)
thumb.mousePressEvent = partial(self._thumb_clicked, len(self.thumbs))
thumb.setProperty("role", "scan_thumb")
thumb.setMaximumWidth(int(settings["ui"]["thumb_size"]) + 2)
self.thumbs.append(thumb)
self.wrapper.layout().insertWidget(self.wrapper.layout().count() - 1,
thumb)
self.updateGeometry()
def clear(self):
"""Remove all thumbnails."""
for thumb in self.thumbs:
thumb.deleteLater()
self.thumbs = []
def _thumb_clicked(self, thumb, event): # pylint: disable=W0613
"""Trigger *app.select_scan* when a thumbnail is clicked."""
self.app.select_scan(thumb)
def minimumSizeHint(self): # pylint: disable=C0103
"""Return widget size; width should be *thumb_size + scrollbar_width*
or 0 if there are no thumbnails."""
if self.thumbs:
return QSize(int(settings["ui"]["thumb_size"]) + 25, 0)
return QSize(0, 0)
def _reset_ui(self):
"""Remove all metadata rows and reset the layout."""
table = QFrame()
table.setLayout(QFormLayout())
self.table = table.layout()
self.setWidgetResizable(True)
self.setWidget(table)
self.setSizePolicy(QSizePolicy.Policy.Fixed,
QSizePolicy.Policy.MinimumExpanding)
self.updateGeometry()
def build_adminpanelwidget():
widget = QFrame()
widget.setFrameStyle(QFrame.Panel | QFrame.Raised)
# widget = QWidget()
# widget.setStyleSheet(
# "background-color: rgb(255,0,0); margin:5px; border:1px solid rgb(0, 255, 0); "
# )
# widget.setStyle(QStyle.PE_FrameWindow)
widget.layout = QVBoxLayout()
widget.we_username = QLineEdit("username")
widget.wl_username = QLabel("username")
widget.wl_username.setBuddy(widget.we_username)
widget.we_username.setReadOnly(True)
widget.pas_layout = QHBoxLayout()
widget.we_password = QLineEdit("password")
widget.wl_password = QLabel("password")
widget.wl_password.setBuddy(widget.we_password)
widget.we_password.setReadOnly(True)
widget.we_password.setEchoMode(QLineEdit.Password)
widget.reveal = QPushButton("Reveal")
widget.btn_layout = QHBoxLayout()
widget.update = QPushButton("Update")
widget.delete = QPushButton("Delete")
widget.layout.addWidget(widget.wl_username)
widget.layout.addWidget(widget.we_username)
widget.layout.addWidget(widget.wl_password)
widget.layout.insertLayout(-1, widget.pas_layout)
widget.pas_layout.addWidget(widget.we_password)
widget.pas_layout.addWidget(widget.reveal)
widget.layout.addStretch()
widget.layout.insertLayout(-1, widget.btn_layout)
widget.btn_layout.addWidget(widget.update)
widget.btn_layout.addWidget(widget.delete)
widget.setLayout(widget.layout)
return widget
pass
class SCOUTS(QMainWindow):
"""Main Window Widget for SCOUTS."""
style = {
'title': 'QLabel {font-size: 18pt; font-weight: 600}',
'header': 'QLabel {font-size: 12pt; font-weight: 520}',
'label': 'QLabel {font-size: 10pt}',
'button': 'QPushButton {font-size: 10pt}',
'md button': 'QPushButton {font-size: 12pt}',
'run button': 'QPushButton {font-size: 18pt; font-weight: 600}',
'line edit': 'QLineEdit {font-size: 10pt}',
'checkbox': 'QCheckBox {font-size: 10pt}',
'radio button': 'QRadioButton {font-size: 10pt}'
}
def __init__(self) -> None:
"""SCOUTS Constructor. Defines all aspects of the GUI."""
# ###
# ### Main Window setup
# ###
# Inherits from QMainWindow
super().__init__()
self.rootdir = get_project_root()
self.threadpool = QThreadPool()
# Sets values for QMainWindow
self.setWindowTitle("SCOUTS")
self.setWindowIcon(
QIcon(
os.path.abspath(os.path.join(self.rootdir, 'src',
'scouts.ico'))))
# Creates StackedWidget as QMainWindow's central widget
self.stacked_pages = QStackedWidget(self)
self.setCentralWidget(self.stacked_pages)
# Creates Widgets for individual "pages" and adds them to the StackedWidget
self.main_page = QWidget()
self.samples_page = QWidget()
self.gating_page = QWidget()
self.pages = (self.main_page, self.samples_page, self.gating_page)
for page in self.pages:
self.stacked_pages.addWidget(page)
# ## Sets widget at program startup
self.stacked_pages.setCurrentWidget(self.main_page)
# ###
# ### MAIN PAGE
# ###
# Main page layout
self.main_layout = QVBoxLayout(self.main_page)
# Title section
# Title
self.title = QLabel(self.main_page)
self.title.setText('SCOUTS - Single Cell Outlier Selector')
self.title.setStyleSheet(self.style['title'])
self.title.adjustSize()
self.main_layout.addWidget(self.title)
# ## Input section
# Input header
self.input_header = QLabel(self.main_page)
self.input_header.setText('Input settings')
self.input_header.setStyleSheet(self.style['header'])
self.main_layout.addChildWidget(self.input_header)
self.input_header.adjustSize()
self.main_layout.addWidget(self.input_header)
# Input frame
self.input_frame = QFrame(self.main_page)
self.input_frame.setFrameShape(QFrame.StyledPanel)
self.input_frame.setLayout(QFormLayout())
self.main_layout.addWidget(self.input_frame)
# Input button
self.input_button = QPushButton(self.main_page)
self.input_button.setStyleSheet(self.style['button'])
self.set_icon(self.input_button, 'x-office-spreadsheet')
self.input_button.setObjectName('input')
self.input_button.setText(' Select input file (.xlsx or .csv)')
self.input_button.clicked.connect(self.get_path)
# Input path box
self.input_path = QLineEdit(self.main_page)
self.input_path.setObjectName('input_path')
self.input_path.setStyleSheet(self.style['line edit'])
# Go to sample naming page
self.samples_button = QPushButton(self.main_page)
self.samples_button.setStyleSheet(self.style['button'])
self.set_icon(self.samples_button, 'preferences-other')
self.samples_button.setText(' Name samples...')
self.samples_button.clicked.connect(self.goto_samples_page)
# Go to gating page
self.gates_button = QPushButton(self.main_page)
self.gates_button.setStyleSheet(self.style['button'])
self.set_icon(self.gates_button, 'preferences-other')
self.gates_button.setText(' Gating && outlier options...')
self.gates_button.clicked.connect(self.goto_gates_page)
# Add widgets above to input frame Layout
self.input_frame.layout().addRow(self.input_button, self.input_path)
self.input_frame.layout().addRow(self.samples_button)
self.input_frame.layout().addRow(self.gates_button)
# ## Analysis section
# Analysis header
self.analysis_header = QLabel(self.main_page)
self.analysis_header.setText('Analysis settings')
self.analysis_header.setStyleSheet(self.style['header'])
self.analysis_header.adjustSize()
self.main_layout.addWidget(self.analysis_header)
# Analysis frame
self.analysis_frame = QFrame(self.main_page)
self.analysis_frame.setFrameShape(QFrame.StyledPanel)
self.analysis_frame.setLayout(QVBoxLayout())
self.main_layout.addWidget(self.analysis_frame)
# Cutoff text
self.cutoff_text = QLabel(self.main_page)
self.cutoff_text.setText('Type of outlier to select:')
self.cutoff_text.setToolTip(
'Choose whether to select outliers using the cutoff value from a reference\n'
'sample (OutR) or by using the cutoff value calculated for each sample\n'
'individually (OutS)')
self.cutoff_text.setStyleSheet(self.style['label'])
# Cutoff button group
self.cutoff_group = QButtonGroup(self)
# Cutoff by sample
self.cutoff_sample = QRadioButton(self.main_page)
self.cutoff_sample.setText('OutS')
self.cutoff_sample.setObjectName('sample')
self.cutoff_sample.setStyleSheet(self.style['radio button'])
self.cutoff_sample.setChecked(True)
self.cutoff_group.addButton(self.cutoff_sample)
# Cutoff by reference
self.cutoff_reference = QRadioButton(self.main_page)
self.cutoff_reference.setText('OutR')
self.cutoff_reference.setObjectName('ref')
self.cutoff_reference.setStyleSheet(self.style['radio button'])
self.cutoff_group.addButton(self.cutoff_reference)
# Both cutoffs
self.cutoff_both = QRadioButton(self.main_page)
self.cutoff_both.setText('both')
self.cutoff_both.setObjectName('sample ref')
self.cutoff_both.setStyleSheet(self.style['radio button'])
self.cutoff_group.addButton(self.cutoff_both)
# Markers text
self.markers_text = QLabel(self.main_page)
self.markers_text.setStyleSheet(self.style['label'])
self.markers_text.setText('Show results for:')
self.markers_text.setToolTip(
'Individual markers: for each marker, select outliers\n'
'Any marker: select cells that are outliers for AT LEAST one marker'
)
# Markers button group
self.markers_group = QButtonGroup(self)
# Single marker
self.single_marker = QRadioButton(self.main_page)
self.single_marker.setText('individual markers')
self.single_marker.setObjectName('single')
self.single_marker.setStyleSheet(self.style['radio button'])
self.single_marker.setChecked(True)
self.markers_group.addButton(self.single_marker)
# Any marker
self.any_marker = QRadioButton(self.main_page)
self.any_marker.setText('any marker')
self.any_marker.setObjectName('any')
self.any_marker.setStyleSheet(self.style['radio button'])
self.markers_group.addButton(self.any_marker)
# Both methods
self.both_methods = QRadioButton(self.main_page)
self.both_methods.setText('both')
self.both_methods.setObjectName('single any')
self.both_methods.setStyleSheet(self.style['radio button'])
self.markers_group.addButton(self.both_methods)
# Tukey text
self.tukey_text = QLabel(self.main_page)
self.tukey_text.setStyleSheet(self.style['label'])
# Tukey button group
self.tukey_text.setText('Tukey factor:')
self.tukey_group = QButtonGroup(self)
# Low Tukey value
self.tukey_low = QRadioButton(self.main_page)
self.tukey_low.setText('1.5')
self.tukey_low.setStyleSheet(self.style['radio button'])
self.tukey_low.setChecked(True)
self.tukey_group.addButton(self.tukey_low)
# High Tukey value
self.tukey_high = QRadioButton(self.main_page)
self.tukey_high.setText('3.0')
self.tukey_high.setStyleSheet(self.style['radio button'])
self.tukey_group.addButton(self.tukey_high)
# Add widgets above to analysis frame layout
self.analysis_frame.layout().addWidget(self.cutoff_text)
self.cutoff_buttons = QHBoxLayout()
for button in self.cutoff_group.buttons():
self.cutoff_buttons.addWidget(button)
self.analysis_frame.layout().addLayout(self.cutoff_buttons)
self.analysis_frame.layout().addWidget(self.markers_text)
self.markers_buttons = QHBoxLayout()
for button in self.markers_group.buttons():
self.markers_buttons.addWidget(button)
self.analysis_frame.layout().addLayout(self.markers_buttons)
self.analysis_frame.layout().addWidget(self.tukey_text)
self.tukey_buttons = QHBoxLayout()
for button in self.tukey_group.buttons():
self.tukey_buttons.addWidget(button)
self.tukey_buttons.addWidget(QLabel()) # aligns row with 2 buttons
self.analysis_frame.layout().addLayout(self.tukey_buttons)
# ## Output section
# Output header
self.output_header = QLabel(self.main_page)
self.output_header.setText('Output settings')
self.output_header.setStyleSheet(self.style['header'])
self.output_header.adjustSize()
self.main_layout.addWidget(self.output_header)
# Output frame
self.output_frame = QFrame(self.main_page)
self.output_frame.setFrameShape(QFrame.StyledPanel)
self.output_frame.setLayout(QFormLayout())
self.main_layout.addWidget(self.output_frame)
# Output button
self.output_button = QPushButton(self.main_page)
self.output_button.setStyleSheet(self.style['button'])
self.set_icon(self.output_button, 'folder')
self.output_button.setObjectName('output')
self.output_button.setText(' Select output folder')
self.output_button.clicked.connect(self.get_path)
# Output path box
self.output_path = QLineEdit(self.main_page)
self.output_path.setStyleSheet(self.style['line edit'])
# Generate CSV checkbox
self.output_csv = QCheckBox(self.main_page)
self.output_csv.setText('Export multiple text files (.csv)')
self.output_csv.setStyleSheet(self.style['checkbox'])
self.output_csv.setChecked(True)
# Generate XLSX checkbox
self.output_excel = QCheckBox(self.main_page)
self.output_excel.setText('Export multiple Excel spreadsheets (.xlsx)')
self.output_excel.setStyleSheet(self.style['checkbox'])
self.output_excel.clicked.connect(self.enable_single_excel)
# Generate single, large XLSX checkbox
self.single_excel = QCheckBox(self.main_page)
self.single_excel.setText(
'Also save one multi-sheet Excel spreadsheet')
self.single_excel.setToolTip(
'After generating all Excel spreadsheets, SCOUTS combines them into '
'a single\nExcel spreadsheet where each sheet corresponds to an output'
'file from SCOUTS')
self.single_excel.setStyleSheet(self.style['checkbox'])
self.single_excel.setEnabled(False)
self.single_excel.clicked.connect(self.memory_warning)
# Add widgets above to output frame layout
self.output_frame.layout().addRow(self.output_button, self.output_path)
self.output_frame.layout().addRow(self.output_csv)
self.output_frame.layout().addRow(self.output_excel)
self.output_frame.layout().addRow(self.single_excel)
# ## Run & help-quit section
# Run button (stand-alone)
self.run_button = QPushButton(self.main_page)
self.set_icon(self.run_button, 'system-run')
self.run_button.setText(' Run!')
self.run_button.setStyleSheet(self.style['run button'])
self.main_layout.addWidget(self.run_button)
self.run_button.clicked.connect(self.run)
# Help-quit frame (invisible)
self.helpquit_frame = QFrame(self.main_page)
self.helpquit_frame.setLayout(QHBoxLayout())
self.helpquit_frame.layout().setMargin(0)
self.main_layout.addWidget(self.helpquit_frame)
# Help button
self.help_button = QPushButton(self.main_page)
self.set_icon(self.help_button, 'help-about')
self.help_button.setText(' Help')
self.help_button.setStyleSheet(self.style['md button'])
self.help_button.clicked.connect(self.get_help)
# Quit button
self.quit_button = QPushButton(self.main_page)
self.set_icon(self.quit_button, 'process-stop')
self.quit_button.setText(' Quit')
self.quit_button.setStyleSheet(self.style['md button'])
self.quit_button.clicked.connect(self.close)
# Add widgets above to help-quit layout
self.helpquit_frame.layout().addWidget(self.help_button)
self.helpquit_frame.layout().addWidget(self.quit_button)
# ###
# ### SAMPLES PAGE
# ###
# Samples page layout
self.samples_layout = QVBoxLayout(self.samples_page)
# ## Title section
# Title
self.samples_title = QLabel(self.samples_page)
self.samples_title.setText('Name your samples')
self.samples_title.setStyleSheet(self.style['title'])
self.samples_title.adjustSize()
self.samples_layout.addWidget(self.samples_title)
# Subtitle
self.samples_subtitle = QLabel(self.samples_page)
string = (
'Please name the samples to be analysed by SCOUTS.\n\nSCOUTS searches the first '
'column of your data\nand locates the exact string as part of the sample name.'
)
self.samples_subtitle.setText(string)
self.samples_subtitle.setStyleSheet(self.style['label'])
self.samples_subtitle.adjustSize()
self.samples_layout.addWidget(self.samples_subtitle)
# ## Sample addition section
# Sample addition frame
self.samples_frame = QFrame(self.samples_page)
self.samples_frame.setFrameShape(QFrame.StyledPanel)
self.samples_frame.setLayout(QGridLayout())
self.samples_layout.addWidget(self.samples_frame)
# Sample name box
self.sample_name = QLineEdit(self.samples_page)
self.sample_name.setStyleSheet(self.style['line edit'])
self.sample_name.setPlaceholderText('Sample name ...')
# Reference check
self.is_reference = QCheckBox(self.samples_page)
self.is_reference.setText('Reference?')
self.is_reference.setStyleSheet(self.style['checkbox'])
# Add sample to table
self.add_sample_button = QPushButton(self.samples_page)
QShortcut(QKeySequence("Return"), self.add_sample_button,
self.write_to_sample_table)
self.set_icon(self.add_sample_button, 'list-add')
self.add_sample_button.setText(' Add sample (Enter)')
self.add_sample_button.setStyleSheet(self.style['button'])
self.add_sample_button.clicked.connect(self.write_to_sample_table)
# Remove sample from table
self.remove_sample_button = QPushButton(self.samples_page)
QShortcut(QKeySequence("Delete"), self.remove_sample_button,
self.remove_from_sample_table)
self.set_icon(self.remove_sample_button, 'list-remove')
self.remove_sample_button.setText(' Remove sample (Del)')
self.remove_sample_button.setStyleSheet(self.style['button'])
self.remove_sample_button.clicked.connect(
self.remove_from_sample_table)
# Add widgets above to sample addition layout
self.samples_frame.layout().addWidget(self.sample_name, 0, 0)
self.samples_frame.layout().addWidget(self.is_reference, 1, 0)
self.samples_frame.layout().addWidget(self.add_sample_button, 0, 1)
self.samples_frame.layout().addWidget(self.remove_sample_button, 1, 1)
# ## Sample table
self.sample_table = QTableWidget(self.samples_page)
self.sample_table.setColumnCount(2)
self.sample_table.setHorizontalHeaderItem(0,
QTableWidgetItem('Sample'))
self.sample_table.setHorizontalHeaderItem(
1, QTableWidgetItem('Reference?'))
self.sample_table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.Stretch)
self.sample_table.horizontalHeader().setSectionResizeMode(
1, QHeaderView.ResizeToContents)
self.samples_layout.addWidget(self.sample_table)
# ## Save & clear buttons
# Save & clear frame (invisible)
self.saveclear_frame = QFrame(self.samples_page)
self.saveclear_frame.setLayout(QHBoxLayout())
self.saveclear_frame.layout().setMargin(0)
self.samples_layout.addWidget(self.saveclear_frame)
# Clear samples button
self.clear_samples = QPushButton(self.samples_page)
self.set_icon(self.clear_samples, 'edit-delete')
self.clear_samples.setText(' Clear table')
self.clear_samples.setStyleSheet(self.style['md button'])
self.clear_samples.clicked.connect(self.prompt_clear_data)
# Save samples button
self.save_samples = QPushButton(self.samples_page)
self.set_icon(self.save_samples, 'document-save')
self.save_samples.setText(' Save samples')
self.save_samples.setStyleSheet(self.style['md button'])
self.save_samples.clicked.connect(self.goto_main_page)
# Add widgets above to save & clear layout
self.saveclear_frame.layout().addWidget(self.clear_samples)
self.saveclear_frame.layout().addWidget(self.save_samples)
# ###
# ### GATING PAGE
# ###
# Gating page layout
self.gating_layout = QVBoxLayout(self.gating_page)
# ## Title section
# Title
self.gates_title = QLabel(self.gating_page)
self.gates_title.setText('Gating & outlier options')
self.gates_title.setStyleSheet(self.style['title'])
self.gates_title.adjustSize()
self.gating_layout.addWidget(self.gates_title)
# ## Gating options section
# Gating header
self.gate_header = QLabel(self.gating_page)
self.gate_header.setText('Gating')
self.gate_header.setStyleSheet(self.style['header'])
self.gate_header.adjustSize()
self.gating_layout.addWidget(self.gate_header)
# Gating frame
self.gate_frame = QFrame(self.gating_page)
self.gate_frame.setFrameShape(QFrame.StyledPanel)
self.gate_frame.setLayout(QFormLayout())
self.gating_layout.addWidget(self.gate_frame)
# Gating button group
self.gating_group = QButtonGroup(self)
# Do not gate samples
self.no_gates = QRadioButton(self.gating_page)
self.no_gates.setObjectName('no_gate')
self.no_gates.setText("Don't gate samples")
self.no_gates.setStyleSheet(self.style['radio button'])
self.no_gates.setChecked(True)
self.gating_group.addButton(self.no_gates)
self.no_gates.clicked.connect(self.activate_gate)
# CyToF gating
self.cytof_gates = QRadioButton(self.gating_page)
self.cytof_gates.setObjectName('cytof')
self.cytof_gates.setText('Mass Cytometry gating')
self.cytof_gates.setStyleSheet(self.style['radio button'])
self.cytof_gates.setToolTip(
'Exclude cells for which the average expression of all\n'
'markers is below the selected value')
self.gating_group.addButton(self.cytof_gates)
self.cytof_gates.clicked.connect(self.activate_gate)
# CyToF gating spinbox
self.cytof_gates_value = QDoubleSpinBox(self.gating_page)
self.cytof_gates_value.setMinimum(0)
self.cytof_gates_value.setMaximum(1)
self.cytof_gates_value.setValue(0.1)
self.cytof_gates_value.setSingleStep(0.05)
self.cytof_gates_value.setEnabled(False)
# scRNA-Seq gating
self.rnaseq_gates = QRadioButton(self.gating_page)
self.rnaseq_gates.setText('scRNA-Seq gating')
self.rnaseq_gates.setStyleSheet(self.style['radio button'])
self.rnaseq_gates.setToolTip(
'When calculating cutoff, ignore reads below the selected value')
self.rnaseq_gates.setObjectName('rnaseq')
self.gating_group.addButton(self.rnaseq_gates)
self.rnaseq_gates.clicked.connect(self.activate_gate)
# scRNA-Seq gating spinbox
self.rnaseq_gates_value = QDoubleSpinBox(self.gating_page)
self.rnaseq_gates_value.setMinimum(0)
self.rnaseq_gates_value.setMaximum(10)
self.rnaseq_gates_value.setValue(0)
self.rnaseq_gates_value.setSingleStep(1)
self.rnaseq_gates_value.setEnabled(False)
# export gated population checkbox
self.export_gated = QCheckBox(self.gating_page)
self.export_gated.setText('Export gated cells as an output file')
self.export_gated.setStyleSheet(self.style['checkbox'])
self.export_gated.setEnabled(False)
# Add widgets above to Gate frame layout
self.gate_frame.layout().addRow(self.no_gates, QLabel())
self.gate_frame.layout().addRow(self.cytof_gates,
self.cytof_gates_value)
self.gate_frame.layout().addRow(self.rnaseq_gates,
self.rnaseq_gates_value)
self.gate_frame.layout().addRow(self.export_gated, QLabel())
# ## Outlier options section
# Outlier header
self.outlier_header = QLabel(self.gating_page)
self.outlier_header.setText('Outliers')
self.outlier_header.setStyleSheet(self.style['header'])
self.outlier_header.adjustSize()
self.gating_layout.addWidget(self.outlier_header)
# Outlier frame
self.outlier_frame = QFrame(self.gating_page)
self.outlier_frame.setFrameShape(QFrame.StyledPanel)
self.outlier_frame.setLayout(QVBoxLayout())
self.gating_layout.addWidget(self.outlier_frame)
# Top outliers information
self.top_outliers = QLabel(self.gating_page)
self.top_outliers.setStyleSheet(self.style['label'])
self.top_outliers.setText(
'By default, SCOUTS selects the top outliers from the population')
self.top_outliers.setStyleSheet(self.style['label'])
# Bottom outliers data
self.bottom_outliers = QCheckBox(self.gating_page)
self.bottom_outliers.setText('Include results for low outliers')
self.bottom_outliers.setStyleSheet(self.style['checkbox'])
# Non-outliers data
self.not_outliers = QCheckBox(self.gating_page)
self.not_outliers.setText('Include results for non-outliers')
self.not_outliers.setStyleSheet(self.style['checkbox'])
# Add widgets above to Gate frame layout
self.outlier_frame.layout().addWidget(self.top_outliers)
self.outlier_frame.layout().addWidget(self.bottom_outliers)
self.outlier_frame.layout().addWidget(self.not_outliers)
# ## Save/back button
self.save_gates = QPushButton(self.gating_page)
self.set_icon(self.save_gates, 'go-next')
self.save_gates.setText(' Back to main menu')
self.save_gates.setStyleSheet(self.style['md button'])
self.gating_layout.addWidget(self.save_gates)
self.save_gates.clicked.connect(self.goto_main_page)
# ## Add empty label to take vertical space
self.empty_label = QLabel(self.gating_page)
self.empty_label.setSizePolicy(QSizePolicy.Expanding,
QSizePolicy.Expanding)
self.gating_layout.addWidget(self.empty_label)
# ###
# ### ICON SETTING
# ###
def set_icon(self, widget: QWidget, icon: str) -> None:
"""Associates an icon to a widget."""
i = QIcon()
i.addPixmap(
QPixmap(
os.path.abspath(
os.path.join(self.rootdir, 'src', 'default_icons',
f'{icon}.svg'))))
widget.setIcon(QIcon.fromTheme(icon, i))
# ###
# ### STACKED WIDGET PAGE SWITCHING
# ###
def goto_main_page(self) -> None:
"""Switches stacked widget pages to the main page."""
self.stacked_pages.setCurrentWidget(self.main_page)
def goto_samples_page(self) -> None:
"""Switches stacked widget pages to the samples table page."""
self.stacked_pages.setCurrentWidget(self.samples_page)
def goto_gates_page(self) -> None:
"""Switches stacked widget pages to the gating & other options page."""
self.stacked_pages.setCurrentWidget(self.gating_page)
# ###
# ### MAIN PAGE GUI LOGIC
# ###
def get_path(self) -> None:
"""Opens a dialog box and sets the chosen file/folder path, depending on the caller widget."""
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
sender_name = self.sender().objectName()
if sender_name == 'input':
query, _ = QFileDialog.getOpenFileName(self,
"Select file",
"",
"All Files (*)",
options=options)
elif sender_name == 'output':
query = QFileDialog.getExistingDirectory(self,
"Select Directory",
options=options)
else:
return
if query:
getattr(self, f'{sender_name}_path').setText(query)
def enable_single_excel(self) -> None:
"""Enables checkbox for generating a single Excel output."""
if self.output_excel.isChecked():
self.single_excel.setEnabled(True)
else:
self.single_excel.setEnabled(False)
self.single_excel.setChecked(False)
# ###
# ### SAMPLE NAME/SAMPLE TABLE GUI LOGIC
# ###
def write_to_sample_table(self) -> None:
"""Writes data to sample table."""
table = self.sample_table
ref = 'no'
sample = self.sample_name.text()
if sample:
for cell in range(table.rowCount()):
item = table.item(cell, 0)
if item.text() == sample:
self.same_sample()
return
if self.is_reference.isChecked():
for cell in range(table.rowCount()):
item = table.item(cell, 1)
if item.text() == 'yes':
self.more_than_one_reference()
return
ref = 'yes'
sample = QTableWidgetItem(sample)
is_reference = QTableWidgetItem(ref)
is_reference.setFlags(Qt.ItemIsEnabled)
row_position = table.rowCount()
table.insertRow(row_position)
table.setItem(row_position, 0, sample)
table.setItem(row_position, 1, is_reference)
self.is_reference.setChecked(False)
self.sample_name.setText('')
def remove_from_sample_table(self) -> None:
"""Removes data from sample table."""
table = self.sample_table
rows = set(index.row() for index in table.selectedIndexes())
for index in sorted(rows, reverse=True):
self.sample_table.removeRow(index)
def prompt_clear_data(self) -> None:
"""Prompts option to clear all data in the sample table."""
if self.confirm_clear_data():
table = self.sample_table
while table.rowCount():
self.sample_table.removeRow(0)
# ###
# ### GATING GUI LOGIC
# ###
def activate_gate(self) -> None:
"""Activates/deactivates buttons related to gating."""
if self.sender().objectName() == 'no_gate':
self.cytof_gates_value.setEnabled(False)
self.rnaseq_gates_value.setEnabled(False)
self.export_gated.setEnabled(False)
self.export_gated.setChecked(False)
elif self.sender().objectName() == 'cytof':
self.cytof_gates_value.setEnabled(True)
self.rnaseq_gates_value.setEnabled(False)
self.export_gated.setEnabled(True)
elif self.sender().objectName() == 'rnaseq':
self.cytof_gates_value.setEnabled(False)
self.rnaseq_gates_value.setEnabled(True)
self.export_gated.setEnabled(True)
# ###
# ### CONNECT SCOUTS TO ANALYTICAL MODULES
# ###
def run(self) -> None:
"""Runs SCOUTS as a Worker, based on user input in the GUI."""
try:
data = self.parse_input()
except Exception as error:
trace = traceback.format_exc()
self.propagate_error((error, trace))
else:
data['widget'] = self
worker = Worker(func=start_scouts, **data)
worker.signals.started.connect(self.analysis_has_started)
worker.signals.finished.connect(self.analysis_has_finished)
worker.signals.success.connect(self.success_message)
worker.signals.error.connect(self.propagate_error)
self.threadpool.start(worker)
def parse_input(self) -> Dict:
"""Returns user input on the GUI as a dictionary."""
# Input and output
input_dict = {
'input_file': str(self.input_path.text()),
'output_folder': str(self.output_path.text())
}
if not input_dict['input_file'] or not input_dict['output_folder']:
raise NoIOPathError
# Set cutoff by reference or by sample rule
input_dict['cutoff_rule'] = self.cutoff_group.checkedButton(
).objectName() # 'sample', 'ref', 'sample ref'
# Outliers for each individual marker or any marker in row
input_dict['marker_rule'] = self.markers_group.checkedButton(
).objectName() # 'single', 'any', 'single any'
# Tukey factor used for calculating cutoff
input_dict['tukey_factor'] = float(
self.tukey_group.checkedButton().text()) # '1.5', '3.0'
# Output settings
input_dict['export_csv'] = True if self.output_csv.isChecked(
) else False
input_dict['export_excel'] = True if self.output_excel.isChecked(
) else False
input_dict['single_excel'] = True if self.single_excel.isChecked(
) else False
# Retrieve samples from sample table
input_dict['sample_list'] = []
for tuples in self.yield_samples_from_table():
input_dict['sample_list'].append(tuples)
if not input_dict['sample_list']:
raise NoSampleError
# Set gate cutoff (if any)
input_dict['gating'] = self.gating_group.checkedButton().objectName(
) # 'no_gate', 'cytof', 'rnaseq'
input_dict['gate_cutoff_value'] = None
if input_dict['gating'] != 'no_gate':
input_dict['gate_cutoff_value'] = getattr(
self, f'{input_dict["gating"]}_gates_value').value()
input_dict['export_gated'] = True if self.export_gated.isChecked(
) else False
# Generate results for non-outliers
input_dict['non_outliers'] = False
if self.not_outliers.isChecked():
input_dict['non_outliers'] = True
# Generate results for bottom outliers
input_dict['bottom_outliers'] = False
if self.bottom_outliers.isChecked():
input_dict['bottom_outliers'] = True
# return dictionary with all gathered inputs
return input_dict
def yield_samples_from_table(
self) -> Generator[Tuple[str, str], None, None]:
"""Yields sample names from the sample table."""
table = self.sample_table
for cell in range(table.rowCount()):
sample_name = table.item(cell, 0).text()
sample_type = table.item(cell, 1).text()
yield sample_name, sample_type
# ###
# ### MESSAGE BOXES
# ###
def analysis_has_started(self) -> None:
"""Disables run button while SCOUTS analysis is underway."""
self.run_button.setText(' Working...')
self.run_button.setEnabled(False)
def analysis_has_finished(self) -> None:
"""Enables run button after SCOUTS analysis has finished."""
self.run_button.setEnabled(True)
self.run_button.setText(' Run!')
def success_message(self) -> None:
"""Info message box used when SCOUTS finished without errors."""
title = "Analysis finished!"
mes = "Your analysis has finished. No errors were reported."
if self.stacked_pages.isEnabled() is True:
QMessageBox.information(self, title, mes)
def memory_warning(self) -> None:
"""Warning message box used when user wants to generate a single excel file."""
if self.sender().isChecked():
title = 'Memory warning!'
mes = (
"Depending on your dataset, this option can consume a LOT of memory and take"
" a long time to process. Please make sure that your computer can handle it!"
)
QMessageBox.information(self, title, mes)
def same_sample(self) -> None:
"""Error message box used when the user tries to input the same sample twice in the sample table."""
title = 'Error: sample name already in table'
mes = (
"Sorry, you can't do this because this sample name is already in the table. "
"Please select a different name.")
QMessageBox.critical(self, title, mes)
def more_than_one_reference(self) -> None:
"""Error message box used when the user tries to input two reference samples in the sample table."""
title = "Error: more than one reference selected"
mes = (
"Sorry, you can't do this because there is already a reference column in the table. "
"Please remove it before adding a reference.")
QMessageBox.critical(self, title, mes)
def confirm_clear_data(self) -> bool:
"""Question message box used to confirm user action of clearing sample table."""
title = 'Confirm Action'
mes = "Table will be cleared. Are you sure?"
reply = QMessageBox.question(self, title, mes,
QMessageBox.Yes | QMessageBox.No,
QMessageBox.No)
if reply == QMessageBox.Yes:
return True
return False
# ###
# ### EXCEPTIONS & ERRORS
# ###
def propagate_error(self, error: Tuple[Exception, str]) -> None:
"""Calls the appropriate error message box based on type of Exception raised."""
if isinstance(error[0], NoIOPathError):
self.no_io_path_error_message()
elif isinstance(error[0], NoReferenceError):
self.no_reference_error_message()
elif isinstance(error[0], NoSampleError):
self.no_sample_error_message()
elif isinstance(error[0], PandasInputError):
self.pandas_input_error_message()
elif isinstance(error[0], SampleNamingError):
self.sample_naming_error_message()
else:
self.generic_error_message(error)
def no_io_path_error_message(self) -> None:
"""Message displayed when the user did not include an input file path, or an output folder path."""
title = 'Error: no file/folder'
message = ("Sorry, no input file and/or output folder was provided. "
"Please add the path to the necessary file/folder.")
QMessageBox.critical(self, title, message)
def no_reference_error_message(self) -> None:
"""Message displayed when the user wants to analyse cutoff based on a reference, but did not specify what
sample corresponds to the reference."""
title = "Error: No reference selected"
message = (
"Sorry, no reference sample was found on the sample list, but analysis was set to "
"reference. Please add a reference sample, or change the rule for cutoff calculation."
)
QMessageBox.critical(self, title, message)
def no_sample_error_message(self) -> None:
"""Message displayed when the user did not add any samples to the sample table."""
title = "Error: No samples selected"
message = (
"Sorry, the analysis cannot be performed because no sample names were input. "
"Please add your sample names.")
QMessageBox.critical(self, title, message)
def pandas_input_error_message(self) -> None:
"""Message displayed when the input file cannot be read (likely because it is not a Excel or csv file)."""
title = 'Error: unexpected input file'
message = (
"Sorry, the input file could not be read. Please make sure that "
"the data is save in a valid format (supported formats are: "
".csv, .xlsx).")
QMessageBox.critical(self, title, message)
def sample_naming_error_message(self) -> None:
"""Message displayed when none of the sample names passed by the user are found in the input DataFrame."""
title = 'Error: sample names not in input file'
message = (
"Sorry, your sample names were not found in the input file. Please "
"make sure that the names were typed correctly (case-sensitive).")
QMessageBox.critical(self, title, message)
def generic_error_message(self, error: Tuple[Exception, str]) -> None:
"""Error message box used to display any error message (including traceback) for any uncaught errors."""
title = 'An error occurred!'
name, trace = error
QMessageBox.critical(self, title,
f"{str(name)}\n\nfull traceback:\n{trace}")
def not_implemented_error_message(self) -> None:
"""Error message box used when the user accesses a functionality that hasn't been implemented yet."""
title = "Not yet implemented"
mes = "Sorry, this functionality has not been implemented yet."
QMessageBox.critical(self, title, mes)
# ###
# ### HELP & QUIT
# ###
@staticmethod
def get_help() -> None:
"""Opens SCOUTS documentation on the browser. Called when the user clicks the "help" button"""
webbrowser.open('https://scouts.readthedocs.io/en/master/')
def closeEvent(self, event: QEvent) -> None:
"""Defines the message box for when the user wants to quit SCOUTS."""
title = 'Quit SCOUTS'
mes = "Are you sure you want to quit?"
reply = QMessageBox.question(self, title, mes,
QMessageBox.Yes | QMessageBox.No,
QMessageBox.No)
if reply == QMessageBox.Yes:
self.stacked_pages.setEnabled(False)
message = self.quit_message()
waiter = Waiter(waiter_func=self.threadpool.activeThreadCount)
waiter.signals.started.connect(message.show)
waiter.signals.finished.connect(message.destroy)
waiter.signals.finished.connect(sys.exit)
self.threadpool.start(waiter)
event.ignore()
def quit_message(self) -> QDialog:
"""Displays a window while SCOUTS is exiting"""
message = QDialog(self)
message.setWindowTitle('Exiting SCOUTS')
message.resize(300, 50)
label = QLabel('SCOUTS is exiting, please wait...', message)
label.setStyleSheet(self.style['label'])
label.adjustSize()
label.setAlignment(Qt.AlignCenter)
label.move(int((message.width() - label.width()) / 2),
int((message.height() - label.height()) / 2))
return message
def get_link_transformation_frame(frame: QFrame, model: Model,
value: LinkTransformation):
frame.transformation_frame = EditTransformationLink(frame, value, model)
frame.layout().addWidget(frame.transformation_frame, Qt.AlignTop)
class Card(QWidget):
def __init__(self, parent: QWidget, card_details: Dict[str, Any]):
super().__init__()
if parent is not None:
self.setParent(parent)
self.model = create_card(card_details)
self.setupUi()
def get_card_background_colour(self):
if isinstance(self.model, SpellCard):
return QColor(CardColours[CardType.SPELL])
elif isinstance(self.model, TrapCard):
return QColor(CardColours[CardType.TRAP])
else:
pass
def setupUi(self):
self.main_layout = QVBoxLayout()
self.name_attr_layout = QHBoxLayout()
self.name_label = QLabel(self.model.name)
font = self.name_label.font()
font.setBold(True)
font.setCapitalization(QFont.AllUppercase)
font.setPointSize(12)
self.name_label.setFont(font)
self.name_label.setMargin(5)
pixmap = get_attr_icon(self.model.attribute)
self.attr_icon = QLabel()
self.attr_icon.setPixmap(pixmap)
self.attr_icon.setAlignment(Qt.AlignRight)
self.name_attr_layout.addWidget(self.name_label)
self.name_attr_layout.addWidget(self.attr_icon)
self.main_layout.addLayout(self.name_attr_layout)
self.level_layout = QHBoxLayout()
self.main_layout.addLayout(self.level_layout)
self.picture_frame = QFrame()
self.picture_frame.setFixedSize(250, 250)
self.picture_frame.setFrameStyle(QFrame.Box | QFrame.Plain)
self.picture_frame.setFrameShadow(QFrame.Shadow.Raised)
self.picture_frame.setLineWidth(1)
self.picture_frame.setContentsMargins(0, 0, 0, 0)
self.picture_frame.setLayout(QGridLayout())
self.image_holder = QLabel()
pixmap = self._get_card_image()
self.image_holder.setPixmap(
pixmap.scaled(
self.picture_frame.width(),
self.picture_frame.height(),
Qt.KeepAspectRatio,
))
self.picture_frame.layout().addWidget(self.image_holder)
self.main_layout.addWidget(self.picture_frame)
# Card sets here?
self.desc_group_box = QGroupBox()
self.desc_group_box.setMaximumWidth(250)
self.set_up_group_box()
self.main_layout.addWidget(self.desc_group_box)
self.id_label = QLabel(self.model.id)
self.id_label.setAlignment(Qt.AlignLeft)
self.id_label.setMargin(5)
self.main_layout.addWidget(self.id_label)
self.setLayout(self.main_layout)
pal = QPalette()
pal.setColor(QPalette.Background, self.get_card_background_colour())
self.setAutoFillBackground(True)
self.setPalette(pal)
def _get_card_image(self):
image_name = self.model.img_url.split("/")[-1]
if os.path.exists(self.get_image_path(image_name)):
image = Image.open(self.get_image_path(image_name))
else:
image_data = requests.get(self.model.img_url).content
image = Image.open(BytesIO(image_data))
image.save(self.get_image_path(image_name))
image = image.crop((44, 106, 380, 438)) # this is about correct
data = image.tobytes("raw", "RGB")
qimage = QImage(data, image.size[0], image.size[1],
QImage.Format_RGB888)
pixmap = QPixmap.fromImage(qimage)
return pixmap
def get_image_path(self, image_name):
return os.path.join(os.getcwd(), "images", image_name)
def set_up_group_box(self):
self.desc_group_box.setLayout(QVBoxLayout())
self.desc_label = QLabel(self.model.desc)
self.desc_label.setWordWrap(True)
self.desc_group_box.layout().addWidget(self.desc_label)
if isinstance(self.model, (MonsterCard)):
self.desc_group_box.setTitle(self.get_group_box_title())
line = QFrame()
line.setFrameShape((QFrame.HLine))
line.setFrameShadow(QFrame.Sunken)
self.desc_group_box.layout().addWidget(line)
label = QLabel(
f"ATK/{self.model.attack} DEF/{self.model.defence}")
label.setAlignment(Qt.AlignRight)
self.desc_group_box.layout().addWidget(label)
def get_group_box_title(self):
return "[TEST/TEST]"
class ViolinGUI(QMainWindow):
"""Main Window Widget for ViolinGUI."""
style = {
'title': 'QLabel {font-size: 18pt; font-weight: 600}',
'header': 'QLabel {font-size: 12pt; font-weight: 520}',
'label': 'QLabel {font-size: 10pt}',
'button': 'QPushButton {font-size: 10pt}',
'run button': 'QPushButton {font-size: 18pt; font-weight: 600}',
'line edit': 'QLineEdit {font-size: 10pt}',
'checkbox': 'QCheckBox {font-size: 10pt}',
'drop down': 'QComboBox {font-size: 10pt}'
}
def __init__(self) -> None:
"""ViolinGUI Constructor. Defines all aspects of the GUI."""
# ## Setup section
# Inherits from QMainWindow
super().__init__()
self.rootdir = get_project_root()
# QMainWindow basic properties
self.setWindowTitle("SCOUTS - Violins")
self.setWindowIcon(
QIcon(
os.path.abspath(os.path.join(self.rootdir, 'src',
'scouts.ico'))))
# Creates QWidget as QMainWindow's central widget
self.page = QWidget(self)
self.setCentralWidget(self.page)
# Miscellaneous initialization values
self.threadpool = QThreadPool() # Threadpool for workers
self.population_df = None # DataFrame of whole population (raw data)
self.summary_df = None # DataFrame indicating which SCOUTS output corresponds to which rule
self.summary_path = None # path to all DataFrames generated by SCOUTS
self.main_layout = QVBoxLayout(self.page)
# Title section
# Title
self.title = QLabel(self.page)
self.title.setText('SCOUTS - Violins')
self.title.setStyleSheet(self.style['title'])
self.title.adjustSize()
self.main_layout.addWidget(self.title)
# ## Input section
# Input header
self.input_header = QLabel(self.page)
self.input_header.setText('Load data')
self.input_header.setStyleSheet(self.style['header'])
self.input_header.adjustSize()
self.main_layout.addWidget(self.input_header)
# Input/Output frame
self.input_frame = QFrame(self.page)
self.input_frame.setFrameShape(QFrame.StyledPanel)
self.input_frame.setLayout(QFormLayout())
self.main_layout.addWidget(self.input_frame)
# Raw data button
self.input_button = QPushButton(self.page)
self.input_button.setStyleSheet(self.style['button'])
self.set_icon(self.input_button, 'x-office-spreadsheet')
self.input_button.setObjectName('file')
self.input_button.setText(' Load raw data file')
self.input_button.setToolTip(
'Load raw data file (the file given to SCOUTS as the input file)')
self.input_button.clicked.connect(self.get_path)
# SCOUTS results button
self.output_button = QPushButton(self.page)
self.output_button.setStyleSheet(self.style['button'])
self.set_icon(self.output_button, 'folder')
self.output_button.setObjectName('folder')
self.output_button.setText(' Load SCOUTS results')
self.output_button.setToolTip(
'Load data from SCOUTS analysis '
'(the folder given to SCOUTS as the output folder)')
self.output_button.clicked.connect(self.get_path)
# Add widgets above to input frame Layout
self.input_frame.layout().addRow(self.input_button)
self.input_frame.layout().addRow(self.output_button)
# ## Samples section
# Samples header
self.samples_header = QLabel(self.page)
self.samples_header.setText('Select sample names')
self.samples_header.setStyleSheet(self.style['header'])
self.samples_header.adjustSize()
self.main_layout.addWidget(self.samples_header)
# Samples frame
self.samples_frame = QFrame(self.page)
self.samples_frame.setFrameShape(QFrame.StyledPanel)
self.samples_frame.setLayout(QFormLayout())
self.main_layout.addWidget(self.samples_frame)
# Samples label
self.samples_label = QLabel(self.page)
self.samples_label.setText(
'Write sample names delimited by semicolons below.\nEx: Control;Treat_01;Pac-03'
)
self.samples_label.setStyleSheet(self.style['label'])
# Sample names line edit
self.sample_names = QLineEdit(self.page)
self.sample_names.setStyleSheet(self.style['line edit'])
# Add widgets above to samples frame Layout
self.samples_frame.layout().addRow(self.samples_label)
self.samples_frame.layout().addRow(self.sample_names)
# ## Analysis section
# Analysis header
self.analysis_header = QLabel(self.page)
self.analysis_header.setText('Plot parameters')
self.analysis_header.setStyleSheet(self.style['header'])
self.analysis_header.adjustSize()
self.main_layout.addWidget(self.analysis_header)
# Analysis frame
self.analysis_frame = QFrame(self.page)
self.analysis_frame.setFrameShape(QFrame.StyledPanel)
self.analysis_frame.setLayout(QFormLayout())
self.main_layout.addWidget(self.analysis_frame)
# Analysis labels
self.analysis_label_01 = QLabel(self.page)
self.analysis_label_01.setText('Compare')
self.analysis_label_01.setStyleSheet(self.style['label'])
self.analysis_label_02 = QLabel(self.page)
self.analysis_label_02.setText('with')
self.analysis_label_02.setStyleSheet(self.style['label'])
self.analysis_label_03 = QLabel(self.page)
self.analysis_label_03.setText('for marker')
self.analysis_label_03.setStyleSheet(self.style['label'])
self.analysis_label_04 = QLabel(self.page)
self.analysis_label_04.setText('Outlier type')
self.analysis_label_04.setStyleSheet(self.style['label'])
# Analysis drop-down boxes
self.drop_down_01 = QComboBox(self.page)
self.drop_down_01.addItems([
'whole population', 'non-outliers', 'top outliers',
'bottom outliers', 'none'
])
self.drop_down_01.setStyleSheet(self.style['drop down'])
self.drop_down_01.setCurrentIndex(2)
self.drop_down_02 = QComboBox(self.page)
self.drop_down_02.addItems([
'whole population', 'non-outliers', 'top outliers',
'bottom outliers', 'none'
])
self.drop_down_02.setStyleSheet(self.style['drop down'])
self.drop_down_02.setCurrentIndex(0)
self.drop_down_03 = QComboBox(self.page)
self.drop_down_03.setStyleSheet(self.style['drop down'])
self.drop_down_04 = QComboBox(self.page)
self.drop_down_04.addItems(['OutS', 'OutR'])
self.drop_down_04.setStyleSheet(self.style['drop down'])
# Add widgets above to samples frame Layout
self.analysis_frame.layout().addRow(self.analysis_label_01,
self.drop_down_01)
self.analysis_frame.layout().addRow(self.analysis_label_02,
self.drop_down_02)
self.analysis_frame.layout().addRow(self.analysis_label_03,
self.drop_down_03)
self.analysis_frame.layout().addRow(self.analysis_label_04,
self.drop_down_04)
self.legend_checkbox = QCheckBox(self.page)
self.legend_checkbox.setText('Add legend to the plot')
self.legend_checkbox.setStyleSheet(self.style['checkbox'])
self.main_layout.addWidget(self.legend_checkbox)
# Plot button (stand-alone)
self.plot_button = QPushButton(self.page)
self.set_icon(self.plot_button, 'system-run')
self.plot_button.setText(' Plot')
self.plot_button.setToolTip(
'Plot data after loading the input data and selecting parameters')
self.plot_button.setStyleSheet(self.style['run button'])
self.plot_button.setEnabled(False)
self.plot_button.clicked.connect(self.run_plot)
self.main_layout.addWidget(self.plot_button)
# ## Secondary Window
# This is used to plot the violins only
self.secondary_window = QMainWindow(self)
self.secondary_window.resize(720, 720)
self.dynamic_canvas = DynamicCanvas(self.secondary_window,
width=6,
height=6,
dpi=120)
self.secondary_window.setCentralWidget(self.dynamic_canvas)
self.secondary_window.addToolBar(
NavBar(self.dynamic_canvas, self.secondary_window))
def set_icon(self, widget: QWidget, icon: str) -> None:
"""Associates an icon to a widget."""
i = QIcon()
i.addPixmap(
QPixmap(
os.path.abspath(
os.path.join(self.rootdir, 'src', 'default_icons',
f'{icon}.svg'))))
widget.setIcon(QIcon.fromTheme(icon, i))
def get_path(self) -> None:
"""Opens a dialog box and loads the corresponding data into memory, depending on the caller widget."""
options = QFileDialog.Options()
options |= QFileDialog.DontUseNativeDialog
query = None
func = None
if self.sender().objectName() == 'file':
query, _ = QFileDialog.getOpenFileName(self,
"Select file",
"",
"All Files (*)",
options=options)
func = self.load_scouts_input_data
elif self.sender().objectName() == 'folder':
query = QFileDialog.getExistingDirectory(self,
"Select Directory",
options=options)
func = self.load_scouts_results
if query:
self.load_data(query, func)
def load_data(self, query: str, func: Callable) -> None:
"""Loads input data into memory, while displaying a loading message as a separate worker."""
worker = Worker(func=func, query=query)
message = self.loading_message()
worker.signals.started.connect(message.show)
worker.signals.started.connect(self.page.setDisabled)
worker.signals.error.connect(self.generic_error_message)
worker.signals.error.connect(message.destroy)
worker.signals.failed.connect(self.plot_button.setDisabled)
worker.signals.success.connect(message.destroy)
worker.signals.success.connect(self.enable_plot)
worker.signals.finished.connect(self.page.setEnabled)
self.threadpool.start(worker)
def loading_message(self) -> QDialog:
"""Returns the message box to be displayed while the user waits for the input data to load."""
message = QDialog(self)
message.setWindowTitle('Loading')
message.resize(300, 50)
label = QLabel('loading DataFrame into memory...', message)
label.setStyleSheet(self.style['label'])
label.adjustSize()
label.setAlignment(Qt.AlignCenter)
label.move(int((message.width() - label.width()) / 2),
int((message.height() - label.height()) / 2))
return message
def load_scouts_input_data(self, query: str) -> None:
"""Loads data for whole population prior to SCOUTS into memory (used for plotting the whole population)."""
try:
self.population_df = pd.read_excel(query, index_col=0)
except XLRDError:
self.population_df = pd.read_csv(query, index_col=0)
self.drop_down_03.clear()
self.drop_down_03.addItems(list(self.population_df.columns))
self.drop_down_03.setCurrentIndex(0)
def load_scouts_results(self, query: str) -> None:
"""Loads the SCOUTS summary file into memory, in order to dynamically locate SCOUTS output files later when
the user chooses which data to plot."""
self.summary_df = pd.read_excel(os.path.join(query, 'summary.xlsx'),
index_col=None)
self.summary_path = query
def enable_plot(self) -> None:
"""Enables plot button if all necessary files are placed in memory."""
if isinstance(self.summary_df, pd.DataFrame) and isinstance(
self.population_df, pd.DataFrame):
self.plot_button.setEnabled(True)
def run_plot(self) -> None:
"""Sets and starts the plot worker."""
worker = Worker(func=self.plot)
worker.signals.error.connect(self.generic_error_message)
worker.signals.success.connect(self.secondary_window.show)
self.threadpool.start(worker)
def plot(self) -> None:
"""Logic for plotting data based on user selection of populations, markers, etc."""
# Clear figure currently on plot
self.dynamic_canvas.axes.cla()
# Initialize values and get parameters from GUI
columns = ['sample', 'marker', 'population', 'expression']
samples = self.parse_sample_names()
pop_01 = self.drop_down_01.currentText()
pop_02 = self.drop_down_02.currentText()
pops_to_analyse = [pop_01, pop_02]
marker = self.drop_down_03.currentText()
cutoff_from_reference = True if self.drop_down_04.currentText(
) == 'OutR' else False
violin_df = pd.DataFrame(columns=columns)
# Start fetching data from files
# Whole population
for pop in pops_to_analyse:
if pop == 'whole population':
for partial_df in self.yield_violin_values(
df=self.population_df,
population='whole population',
samples=samples,
marker=marker,
columns=columns):
violin_df = violin_df.append(partial_df)
# Other comparisons
elif pop != 'none':
for file_number in self.yield_selected_file_numbers(
summary_df=self.summary_df,
population=pop,
cutoff_from_reference=cutoff_from_reference,
marker=marker):
df_path = os.path.join(self.summary_path, 'data',
f'{"%04d" % file_number}.')
try:
sample_df = pd.read_excel(df_path + 'xlsx',
index_col=0)
except FileNotFoundError:
sample_df = pd.read_csv(df_path + 'csv', index_col=0)
if not sample_df.empty:
for partial_df in self.yield_violin_values(
df=sample_df,
population=pop,
samples=samples,
marker=marker,
columns=columns):
violin_df = violin_df.append(partial_df)
# Plot data
pops_to_analyse = [p for p in pops_to_analyse if p != 'none']
violin_df = violin_df[violin_df['marker'] == marker]
for pop in pops_to_analyse:
pop_subset = violin_df.loc[violin_df['population'] == pop]
for sample in samples:
sample_subset = pop_subset.loc[pop_subset['sample'] == sample]
sat = 1.0 - samples.index(sample) / (len(samples) + 1)
self.dynamic_canvas.update_figure(
subset_by_sample=sample_subset,
pop=pop,
sat=sat,
samples=samples)
# Draw plotted data on canvas
if self.legend_checkbox.isChecked():
self.dynamic_canvas.add_legend()
self.dynamic_canvas.axes.set_title(
f'{marker} expression - {self.drop_down_04.currentText()}')
self.dynamic_canvas.fig.canvas.draw()
def parse_sample_names(self) -> List[str]:
"""Parse sample names from the QLineEdit Widget."""
return self.sample_names.text().split(';')
def generic_error_message(self, error: Tuple[Exception, str]) -> None:
"""Error message box used to display any error message (including traceback) for any uncaught errors."""
name, trace = error
QMessageBox.critical(
self, 'An error occurred!',
f"Error: {str(name)}\n\nfull traceback:\n{trace}")
def closeEvent(self, event: QEvent) -> None:
"""Defines the message box for when the user wants to quit ViolinGUI."""
title = 'Quit Application'
mes = "Are you sure you want to quit?"
reply = QMessageBox.question(self, title, mes,
QMessageBox.Yes | QMessageBox.No,
QMessageBox.No)
if reply == QMessageBox.Yes:
self.setEnabled(False)
self.threadpool.waitForDone()
event.accept()
else:
event.ignore()
@staticmethod
def yield_violin_values(df: pd.DataFrame, population: str,
samples: List[str], marker: str,
columns: List[str]) -> pd.DataFrame:
"""Returns a DataFrame from expression values, along with information of sample, marker and population. This
DataFrame is appended to the violin plot DataFrame in order to simplify plotting the violins afterwards."""
for sample in samples:
series = df.loc[df.index.str.contains(sample)].loc[:, marker]
yield pd.DataFrame(
{
'sample': sample,
'marker': marker,
'population': population,
'expression': series
},
columns=columns)
@staticmethod
def yield_selected_file_numbers(
summary_df: pd.DataFrame, population: str,
cutoff_from_reference: bool,
marker: str) -> Generator[pd.DataFrame, None, None]:
"""Yields file numbers from DataFrames resulting from SCOUTS analysis. DataFrames are yielded based on
global values, i.e. the comparisons the user wants to perform."""
cutoff = 'sample'
if cutoff_from_reference is True:
cutoff = 'reference'
for index, (file_number, cutoff_from, reference, outliers_for,
category) in summary_df.iterrows():
if cutoff_from == cutoff and outliers_for == marker and category == population:
yield file_number
def __init__(self, app):
QMainWindow.__init__(self)
self.setWindowTitle("PySEUS")
self.app = app
"""Reference to the main application object."""
self.thumbs = ThumbsWidget(app)
"""Reference to the thumbs widget."""
self.view = ViewWidget(app)
"""Reference to the view widget."""
self.info = InfoWidget(app)
"""Reference to the info sidebar widget."""
self.meta = MetaWidget(app)
"""Reference to the meta sidebar widget."""
self.console = ConsoleWidget(app)
"""Reference to the console sidebar widget."""
# Default path for file open dialoge
self._open_path = ""
# Horizontal layout (thumbs, view, sidebar)
wrapper = QFrame(self)
wrapper.setLayout(QHBoxLayout())
wrapper.layout().setContentsMargins(0, 0, 0, 0)
wrapper.layout().addWidget(self.thumbs)
wrapper.layout().addWidget(self.view)
# Sidebar / Vertical layout (info, meta, console)
sidebar = QFrame(self)
sidebar.setLayout(QVBoxLayout())
sidebar.layout().setContentsMargins(0, 0, 5, 0)
sidebar.layout().addWidget(SidebarHeading("File Info", True))
sidebar.layout().addWidget(self.info)
sidebar.layout().addWidget(SidebarHeading("Metadata"))
sidebar.layout().addWidget(self.meta)
sidebar.layout().addWidget(SidebarHeading("Console"))
sidebar.layout().addWidget(self.console)
wrapper.layout().addWidget(sidebar)
self.setup_menu()
self.statusBar().setSizeGripEnabled(False)
self.setCentralWidget(wrapper)
icon = QIcon(
os.path.abspath(
os.path.join(os.path.dirname(__file__), "./icon.png")))
self.setWindowIcon(icon)
# Window dimensions
geometry = self.app.qt_app.desktop().availableGeometry(self)
self.resize(geometry.width() * 0.6, geometry.height() * 0.6)
class CompanionWindow(QMainWindow):
""" The main window the app will be displayed in. """
def __init__(self, min_size, ch):
self.logger = logging.getLogger(__name__)
self.logger.addHandler(ch)
self.logger.debug("Initializing")
super().__init__()
self.setMinimumSize(min_size)
font = QFont()
font.setPointSize(10)
self.setFont(font)
self.setCentralWidget(CentralWidget(self))
self.__graph_and_tab_layout = QHBoxLayout()
self.__graph_frame = QFrame(self)
self.__graph_frame.setLayout(QHBoxLayout())
self.__tab_frame = QFrame(self)
self.__tab_frame.setLayout(QHBoxLayout())
self.__graph_and_tab_layout.addWidget(self.__graph_frame)
self.__graph_and_tab_layout.addWidget(self.__tab_frame)
self.centralWidget().layout().addLayout(self.__graph_and_tab_layout)
self.__icon = QIcon(image_file_path + "rs_icon.png")
self.setWindowIcon(self.__icon)
self.close_callback = None
self.__help_window = None
self.__set_texts()
self.logger.debug("Initialized")
def closeEvent(self, event):
""" Alert controller if desired to the app closing event"""
self.logger.debug("running")
if self.close_callback:
self.close_callback()
self.logger.debug("done")
def add_close_handler(self, func):
self.logger.debug("running")
self.close_callback = func
self.logger.debug("done")
def add_dock_widget(self, widget):
self.logger.debug("running")
self.addDockWidget(Qt.DockWidgetArea(4), widget)
self.logger.debug("done")
def add_menu_bar(self, widget):
self.logger.debug("running")
self.setMenuBar(widget)
self.logger.debug("done")
def add_graph_container(self, widget):
self.logger.debug("running")
self.__graph_frame.layout().addWidget(widget)
self.logger.debug("done")
def add_tab_widget(self, widget):
self.logger.debug("running")
self.__tab_frame.layout().addWidget(widget)
self.logger.debug("done")
def show_help_window(self, title, msg):
""" Show msg in a help window with the title. """
self.logger.debug("running")
self.__help_window = HelpWindow(title, msg)
self.__help_window.setWindowIcon(self.__icon)
self.__help_window.show()
self.logger.debug("done")
def __set_texts(self):
self.logger.debug("running")
self.setWindowTitle("RS Companion App")
self.logger.debug("done")
