def _create_table(self) -> QTableWidget:
"""Create and configure a new table widget."""
table = QTableWidget()
table.verticalHeader().setVisible(False)
table.horizontalHeader().setVisible(False)
table.horizontalHeader().setSectionResizeMode(QHeaderView.Stretch)
table.resizeRowsToContents()
table.setShowGrid(False)
return table
def create_page_rank(self):
widget = QTableWidget()
widget.setEditTriggers(QAbstractItemView.NoEditTriggers)
widget.setSortingEnabled(True)
widget.setRowCount(20)
widget.setColumnCount(len(RANK_LIST))
widget.setHorizontalHeaderLabels(RANK_LIST)
header = widget.horizontalHeader()
for i in range(len(RANK_LIST)):
header.setSectionResizeMode(i, QHeaderView.ResizeToContents)
widget.horizontalHeader().sortIndicatorChanged.connect(
self.update_chart)
return widget
def _make_table_widget(self):
"""
Make a table showing the matplotlib figure number of the
plots, the name with close and edit buttons, and a hidden
column for sorting with the last actuve order
:return: A QTableWidget object which will contain plot widgets
"""
table_widget = QTableWidget(0, 3, self)
table_widget.setHorizontalHeaderLabels(
['No.', 'Plot Name', 'Last Active Order (hidden)'])
table_widget.verticalHeader().setVisible(False)
# Fix the size of 'No.' and let 'Plot Name' fill the space
top_header = table_widget.horizontalHeader()
table_widget.horizontalHeaderItem(Column.Number).setToolTip(
'This is the matplotlib figure number.\n\nFrom a '
'script use plt.figure(N), where N is this figure '
'number, to get a handle to the plot.')
table_widget.horizontalHeaderItem(Column.Name).setToolTip(
'The plot name, also used as the file name when '
'saving multiple plots.')
table_widget.setSelectionBehavior(QAbstractItemView.SelectRows)
table_widget.setSelectionMode(QAbstractItemView.ExtendedSelection)
table_widget.setEditTriggers(QAbstractItemView.NoEditTriggers)
table_widget.sortItems(Column.Number, Qt.AscendingOrder)
table_widget.setSortingEnabled(True)
table_widget.horizontalHeader().sectionClicked.connect(
self.update_sort_menu_selection)
if not DEBUG_MODE:
table_widget.setColumnHidden(Column.LastActive, True)
top_header.resizeSection(Column.Number,
top_header.sectionSizeHint(Column.Number))
top_header.setSectionResizeMode(Column.Name, QHeaderView.Stretch)
return table_widget
def create_page_game(self):
widget = QTableWidget()
widget.setEditTriggers(QAbstractItemView.NoEditTriggers)
widget.setSortingEnabled(True)
widget.setRowCount(1000)
widget.setColumnCount(len(GAME_LIST))
widget.setHorizontalHeaderLabels(GAME_LIST)
header = widget.horizontalHeader()
for i in range(len(GAME_LIST)):
header.setSectionResizeMode(i, QHeaderView.ResizeToContents)
return widget
def _setup_table_widget(self):
"""
Make a table showing
:return: A QTableWidget object which will contain plot widgets
"""
table_widget = QTableWidget(3, 7, self)
table_widget.setVerticalHeaderLabels(['u1', 'u2', 'u3'])
col_headers = [
'a*', 'b*', 'c*'
] if self.frame == SpecialCoordinateSystem.HKL else ['Qx', 'Qy', 'Qz']
col_headers.extend(['start', 'stop', 'nbins', 'step'])
table_widget.setHorizontalHeaderLabels(col_headers)
table_widget.setFixedHeight(
table_widget.verticalHeader().defaultSectionSize() *
(table_widget.rowCount() + 1)) # +1 to include headers
for icol in range(table_widget.columnCount()):
table_widget.setColumnWidth(icol, 50)
table_widget.horizontalHeader().setSectionResizeMode(
QHeaderView.Stretch)
table_widget.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.table = table_widget
self.layout.addWidget(self.table)
def _make_table_widget(self):
"""
Make a table showing the matplotlib figure number of the
plots, the name with close and edit buttons, and a hidden
column for sorting with the last actuve order
:return: A QTableWidget object which will contain plot widgets
"""
table_widget = QTableWidget(0, 3, self)
table_widget.setHorizontalHeaderLabels(['No.', 'Plot Name', 'Last Active Order (hidden)'])
table_widget.verticalHeader().setVisible(False)
# Fix the size of 'No.' and let 'Plot Name' fill the space
top_header = table_widget.horizontalHeader()
table_widget.horizontalHeaderItem(Column.Number).setToolTip('This is the matplotlib figure number.\n\nFrom a '
'script use plt.figure(N), where N is this figure '
'number, to get a handle to the plot.')
table_widget.horizontalHeaderItem(Column.Name).setToolTip('The plot name, also used as the file name when '
'saving multiple plots.')
table_widget.setSelectionBehavior(QAbstractItemView.SelectRows)
table_widget.setSelectionMode(QAbstractItemView.ExtendedSelection)
table_widget.setEditTriggers(QAbstractItemView.NoEditTriggers)
table_widget.sortItems(Column.Number, Qt.AscendingOrder)
table_widget.setSortingEnabled(True)
table_widget.horizontalHeader().sectionClicked.connect(self.update_sort_menu_selection)
if not DEBUG_MODE:
table_widget.setColumnHidden(Column.LastActive, True)
top_header.resizeSection(Column.Number, top_header.sectionSizeHint(Column.Number))
top_header.setSectionResizeMode(Column.Name, QHeaderView.Stretch)
return table_widget
class LevelsPresetDialog(QDialog):
# name of the current preset; whether to set this preset as default; dict of Levels
levels_changed = Signal(str, bool, dict)
def __init__(self, parent, preset_name, levels):
super().__init__(parent)
self.preset_name = preset_name
self.levels = deepcopy(levels)
self.setupUi()
self.update_output()
def setupUi(self):
self.resize(480, 340)
self.vbox = QVBoxLayout(self)
self.presetLabel = QLabel(self)
self.table = QTableWidget(0, 4, self)
self.setAsDefaultCheckbox = QCheckBox("Set as default preset", self)
self.vbox.addWidget(self.presetLabel)
self.vbox.addWidget(self.table)
self.vbox.addWidget(self.setAsDefaultCheckbox)
self.table.setEditTriggers(QTableWidget.NoEditTriggers)
self.table.setSelectionBehavior(QTableWidget.SelectRows)
self.table.setHorizontalHeaderLabels(
["Show", "Level name", "Preview", "Preview (dark)"])
self.table.horizontalHeader().setSectionResizeMode(QHeaderView.Stretch)
self.table.horizontalHeader().setSectionsClickable(False)
self.table.horizontalHeader().setSectionsMovable(False)
self.table.horizontalHeader().setSectionResizeMode(
0, QHeaderView.ResizeToContents)
self.table.verticalHeader().setVisible(False)
self.table.doubleClicked.connect(self.open_level_edit_dialog)
self.table.setContextMenuPolicy(Qt.CustomContextMenu)
self.table.customContextMenuRequested.connect(self.open_menu)
buttons = QDialogButtonBox.Reset | QDialogButtonBox.Save | QDialogButtonBox.Cancel
self.buttonBox = QDialogButtonBox(buttons, self)
self.vbox.addWidget(self.buttonBox)
self.buttonBox.accepted.connect(self.accept)
self.buttonBox.rejected.connect(self.reject)
self.resetButton = self.buttonBox.button(QDialogButtonBox.Reset)
self.resetButton.clicked.connect(self.reset)
def update_output(self):
self.presetLabel.setText("Preset: {}".format(self.preset_name))
self.setAsDefaultCheckbox.setChecked(
CONFIG['default_levels_preset'] == self.preset_name)
self.table.clearContents()
self.table.setRowCount(len(self.levels))
for i, levelname in enumerate(self.levels):
level = self.levels[levelname]
checkbox = self.get_level_show_checkbox(level)
nameItem = QTableWidgetItem(level.levelname)
preview, previewDark = self.get_preview_items(level)
self.table.setCellWidget(i, 0, checkbox)
self.table.setItem(i, 1, nameItem)
self.table.setItem(i, 2, preview)
self.table.setItem(i, 3, previewDark)
def get_level_show_checkbox(self, level):
checkbox_widget = QWidget(self.table)
checkbox_widget.setStyleSheet("QWidget { background-color:none;}")
checkbox = QCheckBox()
checkbox.setStyleSheet(
"QCheckBox::indicator { width: 15px; height: 15px;}")
checkbox.setChecked(level.enabled)
checkbox_layout = QHBoxLayout()
checkbox_layout.setAlignment(Qt.AlignCenter)
checkbox_layout.setContentsMargins(0, 0, 0, 0)
checkbox_layout.addWidget(checkbox)
checkbox_widget.setLayout(checkbox_layout)
return checkbox_widget
def get_preview_items(self, level):
previewItem = QTableWidgetItem("Log message")
previewItem.setBackground(QBrush(level.bg, Qt.SolidPattern))
previewItem.setForeground(QBrush(level.fg, Qt.SolidPattern))
previewItemDark = QTableWidgetItem("Log message")
previewItemDark.setBackground(QBrush(level.bgDark, Qt.SolidPattern))
previewItemDark.setForeground(QBrush(level.fgDark, Qt.SolidPattern))
font = QFont(CONFIG.logger_table_font, CONFIG.logger_table_font_size)
fontDark = QFont(font)
if 'bold' in level.styles:
font.setBold(True)
if 'italic' in level.styles:
font.setItalic(True)
if 'underline' in level.styles:
font.setUnderline(True)
if 'bold' in level.stylesDark:
fontDark.setBold(True)
if 'italic' in level.stylesDark:
fontDark.setItalic(True)
if 'underline' in level.stylesDark:
fontDark.setUnderline(True)
previewItem.setFont(font)
previewItemDark.setFont(fontDark)
return previewItem, previewItemDark
def open_level_edit_dialog(self, index):
levelname = self.table.item(index.row(), 1).data(Qt.DisplayRole)
level = self.levels[levelname]
d = LevelEditDialog(self, level)
d.setWindowModality(Qt.NonModal)
d.setWindowTitle('Level editor')
d.level_changed.connect(self.update_output)
d.open()
def open_menu(self, position):
menu = QMenu(self)
preset_menu = menu.addMenu('Presets')
preset_menu.addAction('New preset', self.new_preset_dialog)
preset_menu.addSeparator()
preset_names = CONFIG.get_levels_presets()
if len(preset_names) == 0:
action = preset_menu.addAction('No presets')
action.setEnabled(False)
else:
delete_menu = menu.addMenu('Delete preset')
for name in preset_names:
preset_menu.addAction(name, partial(self.load_preset, name))
delete_menu.addAction(name, partial(self.delete_preset, name))
menu.addSeparator()
menu.addAction('New level...', self.create_new_level_dialog)
if len(self.table.selectedIndexes()) > 0:
menu.addAction('Delete selected', self.delete_selected)
menu.popup(self.table.viewport().mapToGlobal(position))
def load_preset(self, name):
new_levels = CONFIG.load_levels_preset(name)
if not new_levels:
return
self.levels = new_levels
self.preset_name = name
self.update_output()
def delete_preset(self, name):
CONFIG.delete_levels_preset(name)
if name == self.preset_name:
self.reset()
def delete_selected(self):
selected = self.table.selectionModel().selectedRows()
for index in selected:
item = self.table.item(index.row(), 1)
del self.levels[item.text()]
self.update_output()
def new_preset_dialog(self):
d = QInputDialog(self)
d.setLabelText('Enter the new name for the new preset:')
d.setWindowTitle('Create new preset')
d.textValueSelected.connect(self.create_new_preset)
d.open()
def create_new_preset(self, name):
if name in CONFIG.get_levels_presets():
show_warning_dialog(
self, "Preset creation error",
'Preset named "{}" already exists.'.format(name))
return
if len(name.strip()) == 0:
show_warning_dialog(
self, "Preset creation error",
'This preset name is not allowed.'.format(name))
return
self.preset_name = name
self.update_output()
CONFIG.save_levels_preset(name, self.levels)
def create_new_level_dialog(self):
d = LevelEditDialog(self,
creating_new_level=True,
level_names=self.levels.keys())
d.setWindowModality(Qt.NonModal)
d.setWindowTitle('Level editor')
d.level_changed.connect(self.level_changed)
d.open()
def level_changed(self, level):
if level.levelname in self.levels:
self.levels.copy_from(level)
else:
self.levels[level.levelname] = level
self.update_output()
def accept(self):
for i, _ in enumerate(self.levels):
checkbox = self.table.cellWidget(i, 0).children()[1]
levelname = self.table.item(i, 1).text()
self.levels[levelname].enabled = checkbox.isChecked()
self.levels_changed.emit(self.preset_name,
self.setAsDefaultCheckbox.isChecked(),
self.levels)
self.done(0)
def reject(self):
self.done(0)
def reset(self):
for levelname, level in self.levels.items():
level.copy_from(get_default_level(levelname))
self.update_output()
class EventsDialog(QDialog):
def __init__(self, parent, pos, desc):
super().__init__(parent)
self.setWindowTitle("Edit Events")
self.table = QTableWidget(len(pos), 2)
for row, (p, d) in enumerate(zip(pos, desc)):
self.table.setItem(row, 0, IntTableWidgetItem(p))
self.table.setItem(row, 1, IntTableWidgetItem(d))
self.table.setHorizontalHeaderLabels(["Position", "Type"])
self.table.horizontalHeader().setStretchLastSection(True)
self.table.verticalHeader().setVisible(False)
self.table.setShowGrid(False)
self.table.setSelectionBehavior(QAbstractItemView.SelectRows)
self.table.setSortingEnabled(True)
self.table.sortByColumn(0, Qt.AscendingOrder)
vbox = QVBoxLayout(self)
vbox.addWidget(self.table)
hbox = QHBoxLayout()
self.add_button = QPushButton("+")
self.remove_button = QPushButton("-")
buttonbox = QDialogButtonBox(QDialogButtonBox.Ok | QDialogButtonBox.Cancel)
hbox.addWidget(self.add_button)
hbox.addWidget(self.remove_button)
hbox.addStretch()
hbox.addWidget(buttonbox)
vbox.addLayout(hbox)
buttonbox.accepted.connect(self.accept)
buttonbox.rejected.connect(self.reject)
self.table.itemSelectionChanged.connect(self.toggle_buttons)
self.remove_button.clicked.connect(self.remove_event)
self.add_button.clicked.connect(self.add_event)
self.toggle_buttons()
self.resize(300, 500)
@Slot()
def toggle_buttons(self):
"""Toggle + and - buttons."""
n_items = len(self.table.selectedItems())
if n_items == 2: # one row (2 items) selected
self.add_button.setEnabled(True)
self.remove_button.setEnabled(True)
elif n_items > 2: # more than one row selected
self.add_button.setEnabled(False)
self.remove_button.setEnabled(True)
else: # no rows selected
self.add_button.setEnabled(False)
self.remove_button.setEnabled(False)
def add_event(self):
current_row = self.table.selectedIndexes()[0].row()
pos = int(self.table.item(current_row, 0).data(Qt.DisplayRole))
self.table.setSortingEnabled(False)
self.table.insertRow(current_row)
self.table.setItem(current_row, 0, IntTableWidgetItem(pos))
self.table.setItem(current_row, 1, IntTableWidgetItem(0))
self.table.setSortingEnabled(True)
def remove_event(self):
rows = {index.row() for index in self.table.selectedIndexes()}
self.table.clearSelection()
for row in sorted(rows, reverse=True):
self.table.removeRow(row)
class PackagesDialog(DialogBase):
"""Package dependencies dialog."""
sig_setup_ready = Signal()
def __init__(
self,
parent=None,
packages=None,
pip_packages=None,
remove_only=False,
update_only=False,
):
"""About dialog."""
super(PackagesDialog, self).__init__(parent=parent)
# Variables
self.api = AnacondaAPI()
self.actions = None
self.packages = packages or []
self.pip_packages = pip_packages or []
# Widgets
self.stack = QStackedWidget()
self.table = QTableWidget()
self.text = QTextEdit()
self.label_description = LabelBase()
self.label_status = LabelBase()
self.progress_bar = QProgressBar()
self.button_ok = ButtonPrimary('Apply')
self.button_cancel = ButtonNormal('Cancel')
# Widget setup
self.text.setReadOnly(True)
self.stack.addWidget(self.table)
self.stack.addWidget(self.text)
if remove_only:
text = 'The following packages will be removed:<br>'
else:
text = 'The following packages will be modified:<br>'
self.label_description.setText(text)
self.label_description.setWordWrap(True)
self.label_description.setWordWrap(True)
self.label_status.setWordWrap(True)
self.table.horizontalScrollBar().setVisible(False)
self.table.setSelectionBehavior(QAbstractItemView.SelectRows)
self.table.setAlternatingRowColors(True)
self.table.setSelectionMode(QAbstractItemView.NoSelection)
self.table.setSortingEnabled(True)
self._hheader = self.table.horizontalHeader()
self._vheader = self.table.verticalHeader()
self._hheader.setStretchLastSection(True)
self._hheader.setDefaultAlignment(Qt.AlignLeft)
self._hheader.setSectionResizeMode(self._hheader.Fixed)
self._vheader.setSectionResizeMode(self._vheader.Fixed)
self.button_ok.setMinimumWidth(70)
self.button_ok.setDefault(True)
self.base_minimum_width = 300 if remove_only else 420
if remove_only:
self.setWindowTitle("Remove Packages")
elif update_only:
self.setWindowTitle("Update Packages")
else:
self.setWindowTitle("Install Packages")
self.setMinimumWidth(self.base_minimum_width)
# Layouts
layout_progress = QHBoxLayout()
layout_progress.addWidget(self.label_status)
layout_progress.addWidget(SpacerHorizontal())
layout_progress.addWidget(self.progress_bar)
layout_buttons = QHBoxLayout()
layout_buttons.addStretch()
layout_buttons.addWidget(self.button_cancel)
layout_buttons.addWidget(SpacerHorizontal())
layout_buttons.addWidget(self.button_ok)
layout = QVBoxLayout()
layout.addWidget(self.label_description)
layout.addWidget(SpacerVertical())
layout.addWidget(self.stack)
layout.addWidget(SpacerVertical())
layout.addLayout(layout_progress)
layout.addWidget(SpacerVertical())
layout.addWidget(SpacerVertical())
layout.addLayout(layout_buttons)
self.setLayout(layout)
# Signals
self.button_ok.clicked.connect(self.accept)
self.button_cancel.clicked.connect(self.reject)
self.button_ok.setDisabled(True)
# Setup
self.table.setDisabled(True)
self.update_status('Solving package specifications',
value=0,
max_value=0)
def setup(self, worker, output, error):
"""Setup the widget to include the list of dependencies."""
if not isinstance(output, dict):
output = {}
packages = sorted(pkg.split('==')[0] for pkg in self.packages)
success = output.get('success')
error = output.get('error', '')
exception_name = output.get('exception_name', '')
actions = output.get('actions', [])
prefix = worker.prefix
if exception_name:
message = exception_name
else:
# All requested packages already installed
message = output.get('message', ' ')
navi_deps_error = self.api.check_navigator_dependencies(
actions, prefix)
description = self.label_description.text()
if error:
description = 'No packages will be modified.'
self.stack.setCurrentIndex(1)
self.button_ok.setDisabled(True)
if self.api.is_offline():
error = ("Some of the functionality of Anaconda Navigator "
"will be limited in <b>offline mode</b>. <br><br>"
"Installation and upgrade actions will be subject to "
"the packages currently available on your package "
"cache.")
self.text.setText(error)
elif navi_deps_error:
description = 'No packages will be modified.'
error = ('Downgrading/removing these packages will modify '
'Anaconda Navigator dependencies.')
self.text.setText(error)
self.stack.setCurrentIndex(1)
message = 'NavigatorDependenciesError'
self.button_ok.setDisabled(True)
elif success and actions:
self.stack.setCurrentIndex(0)
# Conda 4.3.x
if isinstance(actions, list):
actions_link = actions[0].get('LINK', [])
actions_unlink = actions[0].get('UNLINK', [])
# Conda 4.4.x
else:
actions_link = actions.get('LINK', [])
actions_unlink = actions.get('UNLINK', [])
deps = set()
deps = deps.union({p['name'] for p in actions_link})
deps = deps.union({p['name'] for p in actions_unlink})
deps = deps - set(packages)
deps = sorted(list(deps))
count_total_packages = len(packages) + len(deps)
plural_total = 's' if count_total_packages != 1 else ''
plural_selected = 's' if len(packages) != 1 else ''
self.table.setRowCount(count_total_packages)
self.table.setColumnCount(4)
if actions_link:
description = '{0} package{1} will be installed'.format(
count_total_packages, plural_total)
self.table.showColumn(2)
self.table.showColumn(3)
elif actions_unlink and not actions_link:
self.table.hideColumn(2)
self.table.hideColumn(3)
self.table.setHorizontalHeaderLabels(
['Name', 'Unlink', 'Link', 'Channel'])
description = '{0} package{1} will be removed'.format(
count_total_packages, plural_total)
for row, pkg in enumerate(packages + deps):
link_item = [p for p in actions_link if p['name'] == pkg]
if not link_item:
link_item = {
'version': '-'.center(len('link')),
'channel': '-'.center(len('channel')),
}
else:
link_item = link_item[0]
unlink_item = [p for p in actions_unlink if p['name'] == pkg]
if not unlink_item:
unlink_item = {
'version': '-'.center(len('link')),
}
else:
unlink_item = unlink_item[0]
unlink_version = str(unlink_item['version'])
link_version = str(link_item['version'])
item_unlink_v = QTableWidgetItem(unlink_version)
item_link_v = QTableWidgetItem(link_version)
item_link_c = QTableWidgetItem(link_item['channel'])
if pkg in packages:
item_name = QTableWidgetItem(pkg)
else:
item_name = QTableWidgetItem('*' + pkg)
items = [item_name, item_unlink_v, item_link_v, item_link_c]
for column, item in enumerate(items):
item.setFlags(Qt.ItemIsEnabled | Qt.ItemIsSelectable)
self.table.setItem(row, column, item)
if deps:
message = (
'<b>*</b> indicates the package is a dependency of a '
'selected package{0}<br>').format(plural_selected)
self.button_ok.setEnabled(True)
self.table.resizeColumnsToContents()
unlink_width = self.table.columnWidth(1)
if unlink_width < 60:
self.table.setColumnWidth(1, 60)
self.table.setHorizontalHeaderLabels(
['Name ', 'Unlink ', 'Link ', 'Channel '])
self.table.setEnabled(True)
self.update_status(message=message)
self.label_description.setText(description)
# Adjust size after data has populated the table
self.table.resizeColumnsToContents()
width = sum(
self.table.columnWidth(i) for i in range(self.table.columnCount()))
delta = (self.width() - self.table.width() +
self.table.verticalHeader().width() + 10)
new_width = width + delta
if new_width < self.base_minimum_width:
new_width = self.base_minimum_width
self.setMinimumWidth(new_width)
self.setMaximumWidth(new_width)
self.sig_setup_ready.emit()
def update_status(self, message='', value=None, max_value=None):
"""Update status of packages dialog."""
self.label_status.setText(message)
if max_value is None and value is None:
self.progress_bar.setVisible(False)
else:
self.progress_bar.setVisible(True)
self.progress_bar.setMaximum(max_value)
self.progress_bar.setValue(value)
class Extension2ReaderTable(QWidget):
"""Table showing extension to reader mappings with removal button.
Widget presented in preferences-plugin dialog."""
valueChanged = Signal(int)
def __init__(self, parent=None, npe2_readers=None, npe1_readers=None):
super().__init__(parent=parent)
npe2, npe1 = get_all_readers()
if npe2_readers is None:
npe2_readers = npe2
if npe1_readers is None:
npe1_readers = npe1
self._npe2_readers = npe2_readers
self._npe1_readers = npe1_readers
self._table = QTableWidget()
self._table.setShowGrid(False)
self._set_up_table()
self._edit_row = self._make_new_preference_row()
self._populate_table()
instructions = QLabel(
trans.
_('Enter a filename pattern to associate with a reader e.g. "*.tif" for all TIFF files.'
) + trans.
_('Available readers will be filtered to those compatible with your pattern. Hover over a reader to see what patterns it accepts.'
) + trans.
_('\n\nPreference saving for folder readers is not supported, so these readers are not shown.'
) + trans.
_('\n\nFor documentation on valid filename patterns, see https://docs.python.org/3/library/fnmatch.html'
))
instructions.setWordWrap(True)
instructions.setOpenExternalLinks(True)
layout = QVBoxLayout()
instructions.setSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.Expanding)
layout.addWidget(instructions)
layout.addWidget(self._edit_row)
layout.addWidget(self._table)
self.setLayout(layout)
def _set_up_table(self):
"""Add table columns and headers, define styling"""
self._fn_pattern_col = 0
self._reader_col = 1
header_strs = [trans._('Filename Pattern'), trans._('Reader Plugin')]
self._table.setColumnCount(2)
self._table.setColumnWidth(self._fn_pattern_col, 200)
self._table.setColumnWidth(self._reader_col, 200)
self._table.verticalHeader().setVisible(False)
self._table.setMinimumHeight(120)
self._table.horizontalHeader().setStyleSheet(
'border-bottom: 2px solid white;')
self._table.setHorizontalHeaderLabels(header_strs)
self._table.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
def _populate_table(self):
"""Add row for each extension to reader mapping in settings"""
fnpattern2reader = get_settings().plugins.extension2reader
if len(fnpattern2reader) > 0:
for fn_pattern, plugin_name in fnpattern2reader.items():
self._add_new_row(fn_pattern, plugin_name)
else:
# Display that there are no filename patterns with reader associations
self._display_no_preferences_found()
def _make_new_preference_row(self):
"""Make row for user to add a new filename pattern assignment"""
edit_row_widget = QWidget()
edit_row_widget.setLayout(QGridLayout())
edit_row_widget.layout().setContentsMargins(0, 0, 0, 0)
self._fn_pattern_edit = QLineEdit()
self._fn_pattern_edit.setPlaceholderText(
"Start typing filename pattern...")
self._fn_pattern_edit.textChanged.connect(
self._filter_compatible_readers)
add_reader_widg = QWidget()
add_reader_widg.setLayout(QHBoxLayout())
add_reader_widg.layout().setContentsMargins(0, 0, 0, 0)
self._new_reader_dropdown = QComboBox()
for i, (plugin_name, display_name) in enumerate(
sorted(dict(self._npe2_readers,
**self._npe1_readers).items())):
self._add_reader_choice(i, plugin_name, display_name)
add_btn = QPushButton('Add')
add_btn.setToolTip(trans._('Save reader preference for pattern'))
add_btn.clicked.connect(self._save_new_preference)
add_reader_widg.layout().addWidget(self._new_reader_dropdown)
add_reader_widg.layout().addWidget(add_btn)
edit_row_widget.layout().addWidget(
self._fn_pattern_edit,
0,
0,
)
edit_row_widget.layout().addWidget(add_reader_widg, 0, 1)
return edit_row_widget
def _display_no_preferences_found(self):
self._table.setRowCount(1)
item = QTableWidgetItem(trans._('No filename preferences found.'))
item.setFlags(Qt.NoItemFlags)
self._table.setItem(self._fn_pattern_col, 0, item)
def _add_reader_choice(self, i, plugin_name, display_name):
"""Add dropdown item for plugin_name with reader pattern tooltip"""
reader_patterns = get_filename_patterns_for_reader(plugin_name)
# TODO: no reader_patterns means directory reader,
# we don't support preference association yet
if not reader_patterns:
return
self._new_reader_dropdown.addItem(display_name, plugin_name)
if '*' in reader_patterns:
tooltip_text = 'Accepts all'
else:
reader_patterns_formatted = ', '.join(sorted(
list(reader_patterns)))
tooltip_text = f'Accepts: {reader_patterns_formatted}'
self._new_reader_dropdown.setItemData(i,
tooltip_text,
role=Qt.ToolTipRole)
def _filter_compatible_readers(self, new_pattern):
"""Filter reader dropwdown items to those that accept `new_extension`"""
self._new_reader_dropdown.clear()
readers = self._npe2_readers.copy()
to_delete = []
compatible_readers = get_potential_readers(new_pattern)
for plugin_name, display_name in readers.items():
if plugin_name not in compatible_readers:
to_delete.append(plugin_name)
for reader in to_delete:
del readers[reader]
readers.update(self._npe1_readers)
if not readers:
self._new_reader_dropdown.addItem("None available")
else:
for i, (plugin_name,
display_name) in enumerate(sorted(readers.items())):
self._add_reader_choice(i, plugin_name, display_name)
def _save_new_preference(self, event):
"""Save current preference to settings and show in table"""
fn_pattern = self._fn_pattern_edit.text()
reader = self._new_reader_dropdown.currentData()
if not fn_pattern or not reader:
return
# if user types pattern that starts with a . it's probably a file extension so prepend the *
if fn_pattern.startswith('.'):
fn_pattern = f'*{fn_pattern}'
if fn_pattern in get_settings().plugins.extension2reader:
self._edit_existing_preference(fn_pattern, reader)
else:
self._add_new_row(fn_pattern, reader)
get_settings().plugins.extension2reader = {
**get_settings().plugins.extension2reader,
fn_pattern: reader,
}
def _edit_existing_preference(self, fn_pattern, reader):
"""Edit existing extension preference"""
current_reader_label = self.findChild(QLabel, fn_pattern)
if reader in self._npe2_readers:
reader = self._npe2_readers[reader]
current_reader_label.setText(reader)
def _add_new_row(self, fn_pattern, reader):
"""Add new reader preference to table"""
last_row = self._table.rowCount()
if (last_row == 1 and 'No filename preferences found'
in self._table.item(0, 0).text()):
self._table.removeRow(0)
last_row = 0
self._table.insertRow(last_row)
item = QTableWidgetItem(fn_pattern)
item.setFlags(Qt.NoItemFlags)
self._table.setItem(last_row, self._fn_pattern_col, item)
plugin_widg = QWidget()
# need object name to easily find row
plugin_widg.setObjectName(f'{fn_pattern}')
plugin_widg.setLayout(QHBoxLayout())
plugin_widg.layout().setContentsMargins(0, 0, 0, 0)
if reader in self._npe2_readers:
reader = self._npe2_readers[reader]
plugin_label = QLabel(reader, objectName=fn_pattern)
# need object name to easily work out which button was clicked
remove_btn = QPushButton('X', objectName=fn_pattern)
remove_btn.setFixedWidth(30)
remove_btn.setStyleSheet('margin: 4px;')
remove_btn.setToolTip(
trans._('Remove this filename pattern to reader association'))
remove_btn.clicked.connect(self.remove_existing_preference)
plugin_widg.layout().addWidget(plugin_label)
plugin_widg.layout().addWidget(remove_btn)
self._table.setCellWidget(last_row, self._reader_col, plugin_widg)
def remove_existing_preference(self, event):
"""Delete extension to reader mapping setting and remove table row"""
pattern_to_remove = self.sender().objectName()
current_settings = get_settings().plugins.extension2reader
# need explicit assignment to new object here for persistence
get_settings().plugins.extension2reader = {
k: v
for k, v in current_settings.items() if k != pattern_to_remove
}
for i in range(self._table.rowCount()):
row_widg_name = self._table.cellWidget(
i, self._reader_col).objectName()
if row_widg_name == pattern_to_remove:
self._table.removeRow(i)
break
if self._table.rowCount() == 0:
self._display_no_preferences_found()
def value(self):
"""Return extension:reader mapping from settings.
Returns
-------
Dict[str, str]
mapping of extension to reader plugin display name
"""
return get_settings().plugins.extension2reader
class WndComputeRoiMaps(SecondaryWindow):
# Signal that is sent (to main window) to update global state of the program
update_global_state = Signal()
computations_complete = Signal(object)
signal_roi_computation_complete = Signal()
signal_activate_tab_xrf_maps = Signal()
def __init__(self, *, gpc, gui_vars):
super().__init__()
# Global processing classes
self.gpc = gpc
# Global GUI variables (used for control of GUI state)
self.gui_vars = gui_vars
# Reference to the main window. The main window will hold
# references to all non-modal windows that could be opened
# from multiple places in the program.
self.ref_main_window = self.gui_vars["ref_main_window"]
self.update_global_state.connect(
self.ref_main_window.update_widget_state)
self.initialize()
def initialize(self):
self.setWindowTitle("PyXRF: Compute XRF Maps Based on ROIs")
self.setMinimumWidth(600)
self.setMinimumHeight(300)
self.resize(600, 600)
header_vbox = self._setup_header()
self._setup_table()
footer_hbox = self._setup_footer()
vbox = QVBoxLayout()
vbox.addLayout(header_vbox)
vbox.addWidget(self.table)
vbox.addLayout(footer_hbox)
self.setLayout(vbox)
self._set_tooltips()
def _setup_header(self):
self.pb_clear = QPushButton("Clear")
self.pb_clear.clicked.connect(self.pb_clear_clicked)
self.pb_use_lines_for_fitting = QPushButton(
"Use Lines Selected For Fitting")
self.pb_use_lines_for_fitting.clicked.connect(
self.pb_use_lines_for_fitting_clicked)
self.le_sel_emission_lines = LineEditExtended()
self.le_sel_emission_lines.textChanged.connect(
self.le_sel_emission_lines_text_changed)
self.le_sel_emission_lines.editingFinished.connect(
self.le_sel_emission_lines_editing_finished)
sample_elements = ""
self.le_sel_emission_lines.setText(sample_elements)
vbox = QVBoxLayout()
hbox = QHBoxLayout()
hbox.addWidget(QLabel("Enter emission lines, e.g. Fe_K, Gd_L "))
hbox.addStretch(1)
hbox.addWidget(self.pb_clear)
hbox.addWidget(self.pb_use_lines_for_fitting)
vbox.addLayout(hbox)
vbox.addWidget(self.le_sel_emission_lines)
return vbox
def _setup_table(self):
# Labels for horizontal header
self.tbl_labels = ["Line", "E, keV", "ROI, keV", "Show", "Reset"]
# The list of columns that stretch with the table
self.tbl_cols_stretch = ("E, keV", "ROI, keV")
# Table item representation if different from default
self.tbl_format = {"E, keV": ".3f"}
# Editable items (highlighted with lighter background)
self.tbl_cols_editable = {"ROI, keV"}
# Columns that contain Range Manager
self.tbl_cols_range_manager = ("ROI, keV", )
self.table = QTableWidget()
self.table.setColumnCount(len(self.tbl_labels))
self.table.setHorizontalHeaderLabels(self.tbl_labels)
self.table.verticalHeader().hide()
self.table.setSelectionMode(QTableWidget.NoSelection)
self.table.setStyleSheet("QTableWidget::item{color: black;}")
header = self.table.horizontalHeader()
for n, lbl in enumerate(self.tbl_labels):
# Set stretching for the columns
if lbl in self.tbl_cols_stretch:
header.setSectionResizeMode(n, QHeaderView.Stretch)
else:
header.setSectionResizeMode(n, QHeaderView.ResizeToContents)
self._table_contents = []
self.cb_list = []
self.range_manager_list = []
self.pb_default_list = []
self.fill_table(self._table_contents)
def fill_table(self, table_contents):
self.table.clearContents()
self._table_contents = table_contents # Save new table contents
for item in self.range_manager_list:
item.selection_changed.disconnect(
self.range_manager_selection_changed)
self.range_manager_list = []
for cb in self.cb_list:
cb.stateChanged.disconnect(self.cb_state_changed)
self.cb_list = []
for pb in self.pb_default_list:
pb.clicked.connect(self.pb_default_clicked)
self.pb_default_list = []
self.table.setRowCount(len(table_contents))
for nr, row in enumerate(table_contents):
eline_name = row["eline"] + "a1"
energy = row["energy_center"]
energy_left = row["energy_left"]
energy_right = row["energy_right"]
range_displayed = row["range_displayed"]
table_row = [eline_name, energy, (energy_left, energy_right)]
for nc, entry in enumerate(table_row):
label = self.tbl_labels[nc]
# Set alternating background colors for the table rows
# Make background for editable items a little brighter
brightness = 240 if label in self.tbl_cols_editable else 220
if nr % 2:
rgb_bckg = (255, brightness, brightness)
else:
rgb_bckg = (brightness, 255, brightness)
if self.tbl_labels[nc] not in self.tbl_cols_range_manager:
if self.tbl_labels[nc] in self.tbl_format:
fmt = self.tbl_format[self.tbl_labels[nc]]
s = ("{:" + fmt + "}").format(entry)
else:
s = f"{entry}"
item = QTableWidgetItem(s)
if nc > 0:
item.setTextAlignment(Qt.AlignCenter)
else:
item.setTextAlignment(Qt.AlignRight | Qt.AlignVCenter)
# Set all columns not editable (unless needed)
item.setFlags(item.flags() & ~Qt.ItemIsEditable)
# Note, that there is no way to set style sheet for QTableWidgetItem
item.setBackground(QBrush(QColor(*rgb_bckg)))
self.table.setItem(nr, nc, item)
else:
spin_name = f"{nr}"
item = RangeManager(name=spin_name,
add_sliders=False,
selection_to_range_min=0.0001)
item.set_range(
0.0,
100.0) # The range is greater than needed (in keV)
item.set_selection(value_low=entry[0], value_high=entry[1])
item.setTextColor((0, 0, 0)) # In case of dark theme
item.setAlignment(Qt.AlignHCenter | Qt.AlignVCenter)
self.range_manager_list.append(item)
item.selection_changed.connect(
self.range_manager_selection_changed)
color = (rgb_bckg[0], rgb_bckg[1], rgb_bckg[2])
item.setBackground(color)
self.table.setCellWidget(nr, nc, item)
brightness = 220
if nr % 2:
rgb_bckg = (255, brightness, brightness)
else:
rgb_bckg = (brightness, 255, brightness)
item = QWidget()
cb = CheckBoxNamed(name=f"{nr}")
cb.setChecked(Qt.Checked if range_displayed else Qt.Unchecked)
self.cb_list.append(cb)
cb.stateChanged.connect(self.cb_state_changed)
item_hbox = QHBoxLayout(item)
item_hbox.addWidget(cb)
item_hbox.setAlignment(Qt.AlignCenter)
item_hbox.setContentsMargins(0, 0, 0, 0)
color_css = f"rgb({rgb_bckg[0]}, {rgb_bckg[1]}, {rgb_bckg[2]})"
item.setStyleSheet(
f"QWidget {{ background-color: {color_css}; }} "
f"QCheckBox {{ color: black; background-color: white }}")
self.table.setCellWidget(nr, nc + 1, item)
item = PushButtonNamed("Reset", name=f"{nr}")
item.clicked.connect(self.pb_default_clicked)
self.pb_default_list.append(item)
rgb_bckg = [_ - 35 if (_ < 255) else _ for _ in rgb_bckg]
color_css = f"rgb({rgb_bckg[0]}, {rgb_bckg[1]}, {rgb_bckg[2]})"
item.setStyleSheet(
f"QPushButton {{ color: black; background-color: {color_css}; }}"
)
self.table.setCellWidget(nr, nc + 2, item)
def _setup_footer(self):
self.cb_subtract_baseline = QCheckBox("Subtract baseline")
self.cb_subtract_baseline.setChecked(
Qt.Checked if self.gpc.get_roi_subtract_background(
) else Qt.Unchecked)
self.cb_subtract_baseline.toggled.connect(
self.cb_subtract_baseline_toggled)
self.pb_compute_roi = QPushButton("Compute ROIs")
self.pb_compute_roi.clicked.connect(self.pb_compute_roi_clicked)
hbox = QHBoxLayout()
hbox.addWidget(self.cb_subtract_baseline)
hbox.addStretch(1)
hbox.addWidget(self.pb_compute_roi)
return hbox
def _set_tooltips(self):
set_tooltip(self.pb_clear, "<b>Clear</b> the list")
set_tooltip(
self.pb_use_lines_for_fitting,
"Copy the contents of <b>the list of emission lines selected for fitting</b> to the list of ROIs",
)
set_tooltip(
self.le_sel_emission_lines,
"The list of <b>emission lines</b> selected for ROI computation.")
set_tooltip(self.table, "The list of ROIs")
set_tooltip(
self.cb_subtract_baseline,
"<b>Subtract baseline</b> from the pixel spectra before computing ROIs. "
"Subtracting baseline slows down computations and usually have no benefit. "
"In most cases it should remain <b>unchecked</b>.",
)
set_tooltip(
self.pb_compute_roi,
"<b>Run</b> computations of the ROIs. The resulting <b>ROI</b> dataset "
"may be viewed in <b>XRF Maps</b> tab.",
)
def update_widget_state(self, condition=None):
# Update the state of the menu bar
state = not self.gui_vars["gui_state"]["running_computations"]
self.setEnabled(state)
# Hide the window if required by the program state
state_file_loaded = self.gui_vars["gui_state"]["state_file_loaded"]
state_model_exist = self.gui_vars["gui_state"]["state_model_exists"]
if not state_file_loaded or not state_model_exist:
self.hide()
if condition == "tooltips":
self._set_tooltips()
def pb_clear_clicked(self):
self.gpc.clear_roi_element_list()
self._update_displayed_element_list()
self._validate_element_list()
def pb_use_lines_for_fitting_clicked(self):
self.gpc.load_roi_element_list_from_selected()
self._update_displayed_element_list()
self._validate_element_list()
def le_sel_emission_lines_text_changed(self, text):
self._validate_element_list(text)
def le_sel_emission_lines_editing_finished(self):
text = self.le_sel_emission_lines.text()
if self._validate_element_list(text):
self.gpc.set_roi_selected_element_list(text)
self._update_table()
else:
element_list = self.gpc.get_roi_selected_element_list()
self.le_sel_emission_lines.setText(element_list)
def cb_subtract_baseline_toggled(self, state):
self.gpc.set_roi_subtract_background(bool(state))
def cb_state_changed(self, name, state):
try:
nr = int(name) # Row number
checked = state == Qt.Checked
eline = self._table_contents[nr]["eline"]
self._table_contents[nr]["range_displayed"] = checked
self.gpc.show_roi(eline, checked)
except Exception as ex:
logger.error(
f"Failed to process selection change. Exception occurred: {ex}."
)
def _find_spin_box(self, name):
for item in self.spin_list:
if item.getName() == name:
return item
return None
def spin_value_changed(self, name, value):
try:
nr, side = name.split(",")
nr = int(nr)
keys = {"left": "energy_left", "right": "energy_right"}
side = keys[side]
eline = self._table_contents[nr]["eline"]
if self._table_contents[nr][side] == value:
return
if side == "energy_left": # Left boundary
if value < self._table_contents[nr]["energy_right"]:
self._table_contents[nr][side] = value
else: # Right boundary
if value > self._table_contents[nr]["energy_left"]:
self._table_contents[nr][side] = value
# Update plot
left, right = self._table_contents[nr][
"energy_left"], self._table_contents[nr]["energy_right"]
self.gpc.change_roi(eline, left, right)
except Exception as ex:
logger.error(
f"Failed to change the ROI. Exception occurred: {ex}.")
def range_manager_selection_changed(self, left, right, name):
try:
nr = int(name)
eline = self._table_contents[nr]["eline"]
self.gpc.change_roi(eline, left, right)
except Exception as ex:
logger.error(
f"Failed to change the ROI. Exception occurred: {ex}.")
def pb_default_clicked(self, name):
try:
nr = int(name)
eline = self._table_contents[nr]["eline"]
left = self._table_contents[nr]["energy_left_default"]
right = self._table_contents[nr]["energy_right_default"]
self.range_manager_list[nr].set_selection(value_low=left,
value_high=right)
self.gpc.change_roi(eline, left, right)
except Exception as ex:
logger.error(
f"Failed to change the ROI. Exception occurred: {ex}.")
def pb_compute_roi_clicked(self):
def cb():
try:
self.gpc.compute_rois()
success, msg = True, ""
except Exception as ex:
success, msg = False, str(ex)
return {"success": success, "msg": msg}
self._compute_in_background(cb, self.slot_compute_roi_clicked)
@Slot(object)
def slot_compute_roi_clicked(self, result):
self._recover_after_compute(self.slot_compute_roi_clicked)
success = result["success"]
if success:
self.gui_vars["gui_state"]["state_xrf_map_exists"] = True
else:
msg = result["msg"]
msgbox = QMessageBox(QMessageBox.Critical,
"Failed to Compute ROIs",
msg,
QMessageBox.Ok,
parent=self)
msgbox.exec()
self.signal_roi_computation_complete.emit()
self.update_global_state.emit()
if success:
self.signal_activate_tab_xrf_maps.emit()
def _update_displayed_element_list(self):
element_list = self.gpc.get_roi_selected_element_list()
self.le_sel_emission_lines.setText(element_list)
self._validate_element_list()
self._update_table()
def _update_table(self):
table_contents = self.gpc.get_roi_settings()
self.fill_table(table_contents)
def _validate_element_list(self, text=None):
if text is None:
text = self.le_sel_emission_lines.text()
el_list = text.split(",")
el_list = [_.strip() for _ in el_list]
if el_list == [""]:
el_list = []
valid = bool(len(el_list))
for eline in el_list:
if self.gpc.get_eline_name_category(eline) != "eline":
valid = False
self.le_sel_emission_lines.setValid(valid)
self.pb_compute_roi.setEnabled(valid)
return valid
def _compute_in_background(self, func, slot, *args, **kwargs):
"""
Run function `func` in a background thread. Send the signal
`self.computations_complete` once computation is finished.
Parameters
----------
func: function
Reference to a function that is supposed to be executed at the background.
The function return value is passed as a signal parameter once computation is
complete.
slot: qtpy.QtCore.Slot or None
Reference to a slot. If not None, then the signal `self.computation_complete`
is connected to this slot.
args, kwargs
arguments of the function `func`.
"""
signal_complete = self.computations_complete
def func_to_run(func, *args, **kwargs):
class LoadFile(QRunnable):
def run(self):
result_dict = func(*args, **kwargs)
signal_complete.emit(result_dict)
return LoadFile()
if slot is not None:
self.computations_complete.connect(slot)
self.gui_vars["gui_state"]["running_computations"] = True
self.update_global_state.emit()
QThreadPool.globalInstance().start(func_to_run(func, *args, **kwargs))
def _recover_after_compute(self, slot):
"""
The function should be called after the signal `self.computations_complete` is
received. The slot should be the same as the one used when calling
`self.compute_in_background`.
"""
if slot is not None:
self.computations_complete.disconnect(slot)
self.gui_vars["gui_state"]["running_computations"] = False
self.update_global_state.emit()
class Devices(QFrame):
def __init__(self, *args, **kwargs):
super(Devices, self).__init__(*args, **kwargs)
self.setFrameStyle(QFrame.Panel | QFrame.Raised)
self.contentLayout = QGridLayout()
self.devices = []
# Current Action Status
self.status = {}
self.devicePrefixFilterLabel = QLabel(
"Device filter (Ion Pump not the channel!)")
self.devicePrefixFilterInp = QLineEdit()
self.devicePrefixFilterInp.setMaximumWidth(100)
self.updateDeviceListButton = QPushButton("Apply Filter")
self.updateDeviceListButton.clicked.connect(self.updateDeviceList)
self.updateDeviceListButton.setToolTip(
"Filter the device prefix list.")
self.contentLayout.addWidget(self.devicePrefixFilterLabel, 0, 0, 1, 2)
self.contentLayout.addWidget(self.devicePrefixFilterInp, 1, 0, 1, 1)
self.contentLayout.addWidget(self.updateDeviceListButton, 1, 1, 1, 1)
self.deviceList = QListWidget()
self.contentLayout.addWidget(self.deviceList, 2, 0, 2, 2)
self.deviceStatus = QTableWidget()
self.deviceStatus.setColumnCount(2)
self.deviceStatus.horizontalHeader().setSectionResizeMode(
QHeaderView.Stretch)
self.deviceStatus.setHorizontalHeaderLabels(["Device", "Status"])
self.deviceStatusLabel = QLabel("Status")
self.contentLayout.addWidget(self.deviceStatusLabel, 0, 2, 1, 2)
self.contentLayout.addWidget(self.deviceStatus, 1, 2, 4, 2)
self.contentLayout.setRowStretch(2, 2)
self.setLayout(self.contentLayout)
self.deviceList.itemChanged.connect(self.highlightChecked)
self.reloadData()
def updateStatus(self, param):
self.status[param["dev"]] = "{}".format(param["status"])
idx = 0
self.deviceStatus.setRowCount(len(self.status))
for k, v in self.status.items():
self.deviceStatus.setItem(idx, 0, QTableWidgetItem(k))
self.deviceStatus.setItem(idx, 1, QTableWidgetItem(v))
idx += 1
def getSelectedDevices(self):
checked_devices = []
count = 0
while count < self.deviceList.count():
item = self.deviceList.item(count)
if item.checkState() == Qt.Checked:
checked_devices.append(item.text())
count += 1
_devices = []
for prefix in checked_devices:
for device in self.devices:
if device["prefix"] == prefix:
_devices.append(device)
break
return _devices
def highlightChecked(self, item):
if item.checkState() == Qt.Checked:
item.setBackground(QColor("#ffffb2"))
else:
item.setBackground(QColor("#ffffff"))
def updateDeviceList(self):
self.deviceList.clear()
_filter = self.devicePrefixFilterInp.text()
devs = []
for d in self.devices:
if _filter == "" or _filter in d["prefix"]:
devs.append(d["prefix"])
self.deviceList.addItems(devs)
count = 0
while count < self.deviceList.count():
item = self.deviceList.item(count)
item.setFlags(item.flags() | Qt.ItemIsUserCheckable)
item.setCheckState(Qt.Unchecked)
count += 1
def reloadData(self):
data = getAgilent()
self.devices = [d for d in getDevices(data)]
self.updateDeviceList()
class D0(QGroupBox):
def __init__(self, parent=None):
self._parent = parent
super().__init__(parent)
self.setTitle("Define d₀")
layout = QVBoxLayout()
self.d0_grid_switch = QComboBox()
self.d0_grid_switch.addItems(["Constant", "Field"])
self.d0_grid_switch.currentTextChanged.connect(self.set_case)
layout.addWidget(self.d0_grid_switch)
self.d0_box = QWidget()
d0_box_layout = QHBoxLayout()
d0_box_layout.addWidget(QLabel("d₀"))
validator = QDoubleValidator()
validator.setBottom(0)
self.d0 = QLineEdit()
self.d0.setValidator(validator)
self.d0.editingFinished.connect(self.update_d0)
d0_box_layout.addWidget(self.d0)
d0_box_layout.addWidget(QLabel("Δd₀"))
self.d0e = QLineEdit()
self.d0e.setValidator(validator)
self.d0e.editingFinished.connect(self.update_d0)
d0_box_layout.addWidget(self.d0e)
self.d0_box.setLayout(d0_box_layout)
layout.addWidget(self.d0_box)
load_save = QWidget()
load_save_layout = QHBoxLayout()
self.load_grid = QPushButton("Load d₀ Grid")
self.load_grid.clicked.connect(self.load_d0_field)
load_save_layout.addWidget(self.load_grid)
self.save_grid = QPushButton("Save d₀ Grid")
self.save_grid.clicked.connect(self.save_d0_field)
load_save_layout.addWidget(self.save_grid)
load_save.setLayout(load_save_layout)
layout.addWidget(load_save)
self.d0_grid = QTableWidget()
self.d0_grid.setColumnCount(5)
self.d0_grid.setColumnWidth(0, 60)
self.d0_grid.setColumnWidth(1, 60)
self.d0_grid.setColumnWidth(2, 60)
self.d0_grid.setColumnWidth(3, 60)
self.d0_grid.verticalHeader().setVisible(False)
self.d0_grid.horizontalHeader().setStretchLastSection(True)
self.d0_grid.setHorizontalHeaderLabels(['vx', 'vy', 'vz', "d₀", "Δd₀"])
spinBoxDelegate = SpinBoxDelegate()
self.d0_grid.setItemDelegateForColumn(3, spinBoxDelegate)
self.d0_grid.setItemDelegateForColumn(4, spinBoxDelegate)
layout.addWidget(self.d0_grid)
self.setLayout(layout)
self.set_case('Constant')
def set_case(self, case):
if case == "Constant":
self.d0_box.setEnabled(True)
self.load_grid.setEnabled(False)
self.save_grid.setEnabled(False)
self.d0_grid.setEnabled(False)
else:
self.d0_box.setEnabled(False)
self.load_grid.setEnabled(True)
self.save_grid.setEnabled(True)
self.d0_grid.setEnabled(True)
def update_d0(self):
self._parent.update_plot()
def set_d0(self, d0, d0e):
if d0 is None:
self.d0.clear()
self.d0e.clear()
else:
self.d0.setText(str(d0))
self.d0e.setText(str(d0e))
def set_d0_field(self, x, y, z, d0, d0e):
if x is None:
self.d0_grid.clearContents()
else:
self.d0_grid.setRowCount(len(x))
for n in range(len(x)):
x_item = QTableWidgetItem(f'{x[n]: 7.2f}')
x_item.setFlags(x_item.flags() ^ Qt.ItemIsEditable)
y_item = QTableWidgetItem(f'{y[n]: 7.2f}')
y_item.setFlags(y_item.flags() ^ Qt.ItemIsEditable)
z_item = QTableWidgetItem(f'{z[n]: 7.2f}')
z_item.setFlags(z_item.flags() ^ Qt.ItemIsEditable)
d0_item = QTableWidgetItem()
d0_item.setData(Qt.EditRole, float(d0[n]))
d0e_item = QTableWidgetItem()
d0e_item.setData(Qt.EditRole, float(d0e[n]))
self.d0_grid.setItem(n, 0, QTableWidgetItem(x_item))
self.d0_grid.setItem(n, 1, QTableWidgetItem(y_item))
self.d0_grid.setItem(n, 2, QTableWidgetItem(z_item))
self.d0_grid.setItem(n, 3, QTableWidgetItem(d0_item))
self.d0_grid.setItem(n, 4, QTableWidgetItem(d0e_item))
def get_d0_field(self):
if self.d0_grid.rowCount() == 0:
return None
else:
x = [
float(self.d0_grid.item(row, 0).text())
for row in range(self.d0_grid.rowCount())
]
y = [
float(self.d0_grid.item(row, 1).text())
for row in range(self.d0_grid.rowCount())
]
z = [
float(self.d0_grid.item(row, 2).text())
for row in range(self.d0_grid.rowCount())
]
d0 = [
float(self.d0_grid.item(row, 3).text())
for row in range(self.d0_grid.rowCount())
]
d0e = [
float(self.d0_grid.item(row, 4).text())
for row in range(self.d0_grid.rowCount())
]
return (d0, d0e, x, y, z)
def save_d0_field(self):
filename, _ = QFileDialog.getSaveFileName(
self, "Save d0 Grid", "", "CSV (*.csv);;All Files (*)")
if filename:
d0, d0e, x, y, z = self.get_d0_field()
np.savetxt(filename,
np.array([x, y, z, d0, d0e]).T,
fmt=['%.4g', '%.4g', '%.4g', '%.9g', '%.9g'],
header="vx, vy, vz, d0, d0_error",
delimiter=',')
def load_d0_field(self):
filename, _ = QFileDialog.getOpenFileName(
self, "Load d0 Grid", "", "CSV (*.csv);;All Files (*)")
if filename:
x, y, z, d0, d0e = np.loadtxt(filename, delimiter=',', unpack=True)
self.set_d0_field(x, y, z, d0, d0e)
def get_d0(self):
if self.d0_grid_switch.currentText() == "Constant":
try:
return (float(self.d0.text()), float(self.d0e.text()))
except ValueError:
return None
else:
return self.get_d0_field()
class WndManageEmissionLines(SecondaryWindow):
signal_selected_element_changed = Signal(str)
signal_update_element_selection_list = Signal()
signal_update_add_remove_btn_state = Signal(bool, bool)
signal_marker_state_changed = Signal(bool)
signal_parameters_changed = Signal()
def __init__(self, *, gpc, gui_vars):
super().__init__()
# Global processing classes
self.gpc = gpc
# Global GUI variables (used for control of GUI state)
self.gui_vars = gui_vars
# Threshold used for peak removal (displayed in lineedit)
self._remove_peak_threshold = self.gpc.get_peak_threshold()
self._enable_events = False
self._eline_list = [
] # List of emission lines (used in the line selection combo)
self._table_contents = [
] # Keep a copy of table contents (list of dict)
self._selected_eline = ""
self.initialize()
self._enable_events = True
# Marker state is reported by Matplotlib plot in 'line_plot' model
def cb(marker_state):
self.signal_marker_state_changed.emit(marker_state)
self.gpc.set_marker_reporter(cb)
self.signal_marker_state_changed.connect(
self.slot_marker_state_changed)
# Update button states
self._update_add_remove_btn_state()
self._update_add_edit_userpeak_btn_state()
self._update_add_edit_pileup_peak_btn_state()
def initialize(self):
self.setWindowTitle("PyXRF: Add/Remove Emission Lines")
self.resize(600, 600)
top_buttons = self._setup_select_elines()
self._setup_elines_table()
bottom_buttons = self._setup_action_buttons()
vbox = QVBoxLayout()
# Group of buttons above the table
vbox.addLayout(top_buttons)
# Tables
hbox = QHBoxLayout()
hbox.addWidget(self.tbl_elines)
vbox.addLayout(hbox)
vbox.addLayout(bottom_buttons)
self.setLayout(vbox)
self._set_tooltips()
def _setup_select_elines(self):
self.cb_select_all = QCheckBox("All")
self.cb_select_all.setChecked(True)
self.cb_select_all.toggled.connect(self.cb_select_all_toggled)
self.element_selection = ElementSelection()
# The following field should switched to 'editable' state from when needed
self.le_peak_intensity = LineEditReadOnly()
self.pb_add_eline = QPushButton("Add")
self.pb_add_eline.clicked.connect(self.pb_add_eline_clicked)
self.pb_remove_eline = QPushButton("Remove")
self.pb_remove_eline.clicked.connect(self.pb_remove_eline_clicked)
self.pb_user_peaks = QPushButton("New User Peak ...")
self.pb_user_peaks.clicked.connect(self.pb_user_peaks_clicked)
self.pb_pileup_peaks = QPushButton("New Pileup Peak ...")
self.pb_pileup_peaks.clicked.connect(self.pb_pileup_peaks_clicked)
self.element_selection.signal_current_item_changed.connect(
self.element_selection_item_changed)
vbox = QVBoxLayout()
hbox = QHBoxLayout()
hbox.addWidget(self.element_selection)
hbox.addWidget(self.le_peak_intensity)
hbox.addWidget(self.pb_add_eline)
hbox.addWidget(self.pb_remove_eline)
vbox.addLayout(hbox)
hbox = QHBoxLayout()
hbox.addWidget(self.cb_select_all)
hbox.addStretch(1)
hbox.addWidget(self.pb_user_peaks)
hbox.addWidget(self.pb_pileup_peaks)
vbox.addLayout(hbox)
# Wrap vbox into hbox, because it will be inserted into vbox
hbox = QHBoxLayout()
hbox.addLayout(vbox)
hbox.addStretch(1)
return hbox
def _setup_elines_table(self):
"""The table has only functionality necessary to demonstrate how it is going
to look. A lot more code is needed to actually make it run."""
self._validator_peak_height = QDoubleValidator()
self._validator_peak_height.setBottom(0.01)
self.tbl_elines = QTableWidget()
self.tbl_elines.setStyleSheet(
"QTableWidget::item{color: black;}"
"QTableWidget::item:selected{background-color: red;}"
"QTableWidget::item:selected{color: white;}")
self.tbl_labels = [
"", "Z", "Line", "E, keV", "Peak Int.", "Rel. Int.(%)", "CS"
]
self.tbl_cols_editable = ["Peak Int."]
self.tbl_value_min = {"Rel. Int.(%)": 0.1}
tbl_cols_resize_to_content = ["", "Z", "Line"]
self.tbl_elines.setColumnCount(len(self.tbl_labels))
self.tbl_elines.verticalHeader().hide()
self.tbl_elines.setHorizontalHeaderLabels(self.tbl_labels)
self.tbl_elines.setSelectionBehavior(QTableWidget.SelectRows)
self.tbl_elines.setSelectionMode(QTableWidget.SingleSelection)
self.tbl_elines.itemSelectionChanged.connect(
self.tbl_elines_item_selection_changed)
self.tbl_elines.itemChanged.connect(self.tbl_elines_item_changed)
header = self.tbl_elines.horizontalHeader()
for n, lbl in enumerate(self.tbl_labels):
# Set stretching for the columns
if lbl in tbl_cols_resize_to_content:
header.setSectionResizeMode(n, QHeaderView.ResizeToContents)
else:
header.setSectionResizeMode(n, QHeaderView.Stretch)
# Set alignment for the columns headers (HEADERS only)
if n == 0:
header.setDefaultAlignment(Qt.AlignCenter)
else:
header.setDefaultAlignment(Qt.AlignRight)
self.cb_sel_list = [] # List of checkboxes
def _setup_action_buttons(self):
self.pb_remove_rel = QPushButton("Remove Rel.Int.(%) <")
self.pb_remove_rel.clicked.connect(self.pb_remove_rel_clicked)
self.le_remove_rel = LineEditExtended("")
self._validator_le_remove_rel = QDoubleValidator()
self._validator_le_remove_rel.setBottom(0.01) # Some small number
self._validator_le_remove_rel.setTop(100.0)
self.le_remove_rel.setText(
self._format_threshold(self._remove_peak_threshold))
self._update_le_remove_rel_state()
self.le_remove_rel.textChanged.connect(self.le_remove_rel_text_changed)
self.le_remove_rel.editingFinished.connect(
self.le_remove_rel_editing_finished)
self.pb_remove_unchecked = QPushButton("Remove Unchecked Lines")
self.pb_remove_unchecked.clicked.connect(
self.pb_remove_unchecked_clicked)
hbox = QHBoxLayout()
hbox.addWidget(self.pb_remove_rel)
hbox.addWidget(self.le_remove_rel)
hbox.addStretch(1)
hbox.addWidget(self.pb_remove_unchecked)
return hbox
def _set_tooltips(self):
set_tooltip(self.cb_select_all,
"<b>Select/Deselect All</b> emission lines in the list")
set_tooltip(self.element_selection, "<b>Set active</b> emission line")
set_tooltip(self.le_peak_intensity,
"Set or modify <b>intensity</b> of the active peak.")
set_tooltip(self.pb_add_eline, "<b>Add</b> emission line to the list.")
set_tooltip(self.pb_remove_eline,
"<b>Remove</b> emission line from the list.")
set_tooltip(
self.pb_user_peaks,
"Open dialog box to add or modify parameters of the <b>user-defined peak</b>"
)
set_tooltip(
self.pb_pileup_peaks,
"Open dialog box to add or modify parameters of the <b>pileup peak</b>"
)
set_tooltip(self.tbl_elines,
"The list of the selected <b>emission lines</b>")
# set_tooltip(self.pb_update,
# "Update the internally stored list of selected emission lines "
# "and their parameters. This button is <b>deprecated</b>, but still may be "
# "needed in some situations. In future releases it will be <b>removed</b> or replaced "
# "with 'Accept' button. Substantial changes to the computational code is needed before "
# "it happens.")
# set_tooltip(self.pb_undo,
# "<b>Undo</b> changes to the table of selected emission lines. Doesn't always work.")
set_tooltip(
self.pb_remove_rel,
"<b>Remove emission lines</b> from the list if their relative intensity is less "
"then specified threshold.",
)
set_tooltip(
self.le_remove_rel,
"<b>Threshold</b> that controls which emission lines are removed "
"when <b>Remove Rel.Int.(%)</b> button is pressed.",
)
set_tooltip(self.pb_remove_unchecked,
"Remove <b>unchecked</b> emission lines from the list.")
def update_widget_state(self, condition=None):
# Update the state of the menu bar
state = not self.gui_vars["gui_state"]["running_computations"]
self.setEnabled(state)
# Hide the window if required by the program state
state_file_loaded = self.gui_vars["gui_state"]["state_file_loaded"]
state_model_exist = self.gui_vars["gui_state"]["state_model_exists"]
if not state_file_loaded or not state_model_exist:
self.hide()
if condition == "tooltips":
self._set_tooltips()
def fill_eline_table(self, table_contents):
self._table_contents = copy.deepcopy(table_contents)
self._enable_events = False
self.tbl_elines.clearContents()
# Clear the list of checkboxes
for cb in self.cb_sel_list:
cb.stateChanged.connect(self.cb_eline_state_changed)
self.cb_sel_list = []
self.tbl_elines.setRowCount(len(table_contents))
for nr, row in enumerate(table_contents):
sel_status = row["sel_status"]
row_data = [
None, row["z"], row["eline"], row["energy"], row["peak_int"],
row["rel_int"], row["cs"]
]
for nc, entry in enumerate(row_data):
label = self.tbl_labels[nc]
# Set alternating background colors for the table rows
# Make background for editable items a little brighter
brightness = 240 if label in self.tbl_cols_editable else 220
if nr % 2:
rgb_bckg = (255, brightness, brightness) # Light-red
else:
rgb_bckg = (brightness, 255, brightness) # Light-green
if nc == 0:
item = QWidget()
cb = CheckBoxNamed(name=f"{nr}")
item_hbox = QHBoxLayout(item)
item_hbox.addWidget(cb)
item_hbox.setAlignment(Qt.AlignCenter)
item_hbox.setContentsMargins(0, 0, 0, 0)
css1 = get_background_css(rgb_bckg,
widget="QCheckbox",
editable=False)
css2 = get_background_css(rgb_bckg,
widget="QWidget",
editable=False)
item.setStyleSheet(css2 + css1)
cb.setChecked(Qt.Checked if sel_status else Qt.Unchecked)
cb.stateChanged.connect(self.cb_eline_state_changed)
cb.setStyleSheet("QCheckBox {color: black;}")
self.cb_sel_list.append(cb)
self.tbl_elines.setCellWidget(nr, nc, item)
else:
s = None
# The case when the value (Rel. Int.) is limited from the bottom
# We don't want to print very small numbers here
if label in self.tbl_value_min:
v = self.tbl_value_min[label]
if isinstance(entry,
(float, np.float64)) and (entry < v):
s = f"<{v:.2f}"
if s is None:
if isinstance(entry, (float, np.float64)):
s = f"{entry:.2f}" if entry else "-"
else:
s = f"{entry}" if entry else "-"
item = QTableWidgetItem(s)
item.setTextAlignment(Qt.AlignRight | Qt.AlignVCenter)
# Set all columns not editable (unless needed)
if label not in self.tbl_cols_editable:
item.setFlags(item.flags() & ~Qt.ItemIsEditable)
brush = QBrush(QColor(*rgb_bckg))
item.setBackground(brush)
self.tbl_elines.setItem(nr, nc, item)
self._enable_events = True
# Update the rest of the widgets
self._update_widgets_based_on_table_state()
@Slot()
def update_widget_data(self):
# This is typically a new set of emission lines. Clear the selection both
# in the table and in the element selection tool.
self.element_selection.set_current_item("")
self.tbl_elines.clearSelection()
self._set_selected_eline("")
# Now update the tables
self._update_eline_selection_list()
self.update_eline_table()
self._update_add_remove_btn_state()
def pb_pileup_peaks_clicked(self):
data = {}
eline = self._selected_eline
if self.gpc.get_eline_name_category(eline) == "pileup":
logger.error(
f"Attempt to add pileup peak '{eline}' while another pileup peak is selected."
)
return
energy, marker_visible = self.gpc.get_suggested_manual_peak_energy()
best_guess = self.gpc.get_guessed_pileup_peak_components(energy=energy,
tolerance=0.1)
if best_guess is not None:
el1, el2, energy = best_guess
else:
# No peaks were found, enter peaks manually
el1, el2, energy = "", "", 0
data["element1"] = el1
data["element2"] = el2
data["energy"] = energy
data["range_low"], data[
"range_high"] = self.gpc.get_selected_energy_range()
if not marker_visible:
# We shouldn't end up here, but this will protect from crashing in case
# the button was not disabled (a bug).
msg = "Select location of the new peak center (energy)\nby clicking on the plot in 'Fit Model' tab"
msgbox = QMessageBox(QMessageBox.Information,
"User Input Required",
msg,
QMessageBox.Ok,
parent=self)
msgbox.exec()
else:
dlg = DialogPileupPeakParameters()
def func():
def f(e1, e2):
try:
name = self.gpc.generate_pileup_peak_name(e1, e2)
e = self.gpc.get_pileup_peak_energy(name)
except Exception:
e = 0
return e
return f
dlg.set_compute_energy_function(func())
dlg.set_parameters(data)
if dlg.exec():
print("Pileup peak is added")
try:
data = dlg.get_parameters()
eline1, eline2 = data["element1"], data["element2"]
eline = self.gpc.generate_pileup_peak_name(eline1, eline2)
self.gpc.add_peak_manual(eline)
self.update_eline_table() # Update the table
self.tbl_elines_set_selection(
eline) # Select new emission line
self._set_selected_eline(eline)
self._set_fit_status(False)
logger.info(f"New pileup peak {eline} was added")
except RuntimeError as ex:
msg = str(ex)
msgbox = QMessageBox(QMessageBox.Critical,
"Error",
msg,
QMessageBox.Ok,
parent=self)
msgbox.exec()
# Reload the table anyway (nothing is going to be selected)
self.update_eline_table()
def pb_user_peaks_clicked(self):
eline = self._selected_eline
# If current peak is user_defined peak
is_userpeak = self.gpc.get_eline_name_category(eline) == "userpeak"
if is_userpeak:
data = {}
data["enabled"] = True
data["name"] = eline
data["maxv"] = self.gpc.get_eline_intensity(eline)
data["energy"], data[
"fwhm"] = self.gpc.get_current_userpeak_energy_fwhm()
dlg = DialogEditUserPeakParameters()
dlg.set_parameters(data=data)
if dlg.exec():
print("Editing of user defined peak is completed")
try:
eline = data["name"]
data = dlg.get_parameters()
self.gpc.update_userpeak(data["name"], data["energy"],
data["maxv"], data["fwhm"])
self._set_fit_status(False)
logger.info(f"User defined peak {eline} was updated.")
except Exception as ex:
msg = str(ex)
msgbox = QMessageBox(QMessageBox.Critical,
"Error",
msg,
QMessageBox.Ok,
parent=self)
msgbox.exec()
# Reload the table anyway (nothing is going to be selected)
self.update_eline_table()
else:
data = {}
data["name"] = self.gpc.get_unused_userpeak_name()
data[
"energy"], marker_visible = self.gpc.get_suggested_manual_peak_energy(
)
if marker_visible:
dlg = DialogNewUserPeak()
dlg.set_parameters(data=data)
if dlg.exec():
try:
eline = data["name"]
self.gpc.add_peak_manual(eline)
self.update_eline_table() # Update the table
self.tbl_elines_set_selection(
eline) # Select new emission line
self._set_selected_eline(eline)
self._set_fit_status(False)
logger.info(f"New user defined peak {eline} is added")
except RuntimeError as ex:
msg = str(ex)
msgbox = QMessageBox(QMessageBox.Critical,
"Error",
msg,
QMessageBox.Ok,
parent=self)
msgbox.exec()
# Reload the table anyway (nothing is going to be selected)
self.update_eline_table()
else:
msg = ("Select location of the new peak center (energy)\n"
"by clicking on the plot in 'Fit Model' tab")
msgbox = QMessageBox(QMessageBox.Information,
"User Input Required",
msg,
QMessageBox.Ok,
parent=self)
msgbox.exec()
@Slot()
def pb_add_eline_clicked(self):
logger.debug("'Add line' clicked")
# It is assumed that this button is active only if an element is selected from the list
# of available emission lines. It can't be used to add user-defined peaks or pileup peaks.
eline = self._selected_eline
if eline:
try:
self.gpc.add_peak_manual(eline)
self.update_eline_table() # Update the table
self.tbl_elines_set_selection(
eline) # Select new emission line
self._set_fit_status(False)
except RuntimeError as ex:
msg = str(ex)
msgbox = QMessageBox(QMessageBox.Critical,
"Error",
msg,
QMessageBox.Ok,
parent=self)
msgbox.exec()
# Reload the table anyway (nothing is going to be selected)
self.update_eline_table()
@Slot()
def pb_remove_eline_clicked(self):
logger.debug("'Remove line' clicked")
eline = self._selected_eline
if eline:
# If currently selected line is the emission line (like Ca_K), we want
# it to remain selected after it is deleted. This means that nothing is selected
# in the table. For other lines, nothing should remain selected.
self.tbl_elines.clearSelection()
self.gpc.remove_peak_manual(eline)
self.update_eline_table() # Update the table
if self.gpc.get_eline_name_category(eline) != "eline":
eline = ""
# This will update widgets
self._set_selected_eline(eline)
self._set_fit_status(False)
def cb_select_all_toggled(self, state):
self._enable_events = False
eline_list, state_list = [], []
for n_row in range(self.tbl_elines.rowCount()):
eline = self._table_contents[n_row]["eline"]
# Do not deselect lines in category 'other'. They probably never to be deleted.
# They also could be deselected manually.
if self.gpc.get_eline_name_category(
eline) == "other" and not state:
to_check = True
else:
to_check = state
self.cb_sel_list[n_row].setChecked(
Qt.Checked if to_check else Qt.Unchecked)
eline_list.append(eline)
state_list.append(to_check)
self.gpc.set_checked_emission_lines(eline_list, state_list)
self._set_fit_status(False)
self._enable_events = True
def cb_eline_state_changed(self, name, state):
if self._enable_events:
n_row = int(name)
state = state == Qt.Checked
eline = self._table_contents[n_row]["eline"]
self.gpc.set_checked_emission_lines([eline], [state])
self._set_fit_status(False)
def tbl_elines_item_changed(self, item):
if self._enable_events:
n_row, n_col = self.tbl_elines.row(item), self.tbl_elines.column(
item)
# Value was changed
if n_col == 4:
text = item.text()
eline = self._table_contents[n_row]["eline"]
if self._validator_peak_height.validate(
text, 0)[0] != QDoubleValidator.Acceptable:
val = self._table_contents[n_row]["peak_int"]
self._enable_events = False
item.setText(f"{val:.2f}")
self._enable_events = True
self._set_fit_status(False)
else:
self.gpc.update_eline_peak_height(eline, float(text))
self.update_eline_table()
def tbl_elines_item_selection_changed(self):
sel_ranges = self.tbl_elines.selectedRanges()
# The table is configured to have one or no selected ranges
# 'Open' button should be enabled only if a range (row) is selected
if sel_ranges:
index = sel_ranges[0].topRow()
eline = self._table_contents[index]["eline"]
if self._enable_events:
self._enable_events = False
self._set_selected_eline(eline)
self.element_selection.set_current_item(eline)
self._enable_events = True
def tbl_elines_set_selection(self, eline):
"""
Select the row with emission line `eline` in the table. Deselect everything if
the emission line does not exist.
"""
index = self._get_eline_index_in_table(eline)
self.tbl_elines.clearSelection()
if index >= 0:
self.tbl_elines.selectRow(index)
def element_selection_item_changed(self, index, eline):
self.signal_selected_element_changed.emit(eline)
if self._enable_events:
self._enable_events = False
self._set_selected_eline(eline)
self.tbl_elines_set_selection(eline)
self._enable_events = True
def pb_remove_rel_clicked(self):
try:
self.gpc.remove_peaks_below_threshold(self._remove_peak_threshold)
except Exception as ex:
msg = str(ex)
msgbox = QMessageBox(QMessageBox.Critical,
"Error",
msg,
QMessageBox.Ok,
parent=self)
msgbox.exec()
self.update_eline_table()
# Update the displayed estimated peak amplitude value 'le_peak_intensity'
self._set_selected_eline(self._selected_eline)
self._set_fit_status(False)
def le_remove_rel_text_changed(self, text):
self._update_le_remove_rel_state(text)
def le_remove_rel_editing_finished(self):
text = self.le_remove_rel.text()
if self._validator_le_remove_rel.validate(
text, 0)[0] == QDoubleValidator.Acceptable:
self._remove_peak_threshold = float(text)
else:
self.le_remove_rel.setText(
self._format_threshold(self._remove_peak_threshold))
def pb_remove_unchecked_clicked(self):
try:
self.gpc.remove_unchecked_peaks()
except Exception as ex:
msg = str(ex)
msgbox = QMessageBox(QMessageBox.Critical,
"Error",
msg,
QMessageBox.Ok,
parent=self)
msgbox.exec()
# Reload the table
self.update_eline_table()
# Update the displayed estimated peak amplitude value 'le_peak_intensity'
self._set_selected_eline(self._selected_eline)
self._set_fit_status(False)
def _display_peak_intensity(self, eline):
v = self.gpc.get_eline_intensity(eline)
s = f"{v:.10g}" if v is not None else ""
self.le_peak_intensity.setText(s)
def _update_le_remove_rel_state(self, text=None):
if text is None:
text = self.le_remove_rel.text()
state = self._validator_le_remove_rel.validate(
text, 0)[0] == QDoubleValidator.Acceptable
self.le_remove_rel.setValid(state)
self.pb_remove_rel.setEnabled(state)
@Slot(str)
def slot_selection_item_changed(self, eline):
self.element_selection.set_current_item(eline)
@Slot(bool)
def slot_marker_state_changed(self, state):
# If userpeak is selected and plot is clicked (marker is set), then user
# should be allowed to add userpeak at a new location. So deselect the userpeak
# from the table (if it is selected)
logger.debug(
f"Vertical marker on the fit plot changed state to {state}.")
if state:
self._deselect_special_peak_in_table()
# Now update state of all buttons
self._update_add_remove_btn_state()
self._update_add_edit_userpeak_btn_state()
self._update_add_edit_pileup_peak_btn_state()
def _format_threshold(self, value):
return f"{value:.2f}"
def _deselect_special_peak_in_table(self):
"""Deselect userpeak if a userpeak is selected"""
if self.gpc.get_eline_name_category(
self._selected_eline) in ("userpeak", "pileup"):
# Clear all selections
self.tbl_elines_set_selection("")
self._set_selected_eline("")
# We also want to show marker at the new position
self.gpc.show_marker_at_current_position()
def _update_widgets_based_on_table_state(self):
index, eline = self._get_current_index_in_table()
if index >= 0:
# Selection exists. Update the state of element selection widget.
self.element_selection.set_current_item(eline)
else:
# No selection, update the state based on element selection widget.
eline = self._selected_eline
self.tbl_elines_set_selection(eline)
self._update_add_remove_btn_state(eline)
self._update_add_edit_userpeak_btn_state()
self._update_add_edit_pileup_peak_btn_state()
def _update_eline_selection_list(self):
self._eline_list = self.gpc.get_full_eline_list()
self.element_selection.set_item_list(self._eline_list)
self.signal_update_element_selection_list.emit()
@Slot()
def update_eline_table(self):
"""Update table of emission lines without changing anything else"""
eline_table = self.gpc.get_selected_eline_table()
self.fill_eline_table(eline_table)
def _get_eline_index_in_table(self, eline):
try:
index = [_["eline"] for _ in self._table_contents].index(eline)
except ValueError:
index = -1
return index
def _get_eline_index_in_list(self, eline):
try:
index = self._eline_list.index(eline)
except ValueError:
index = -1
return index
def _get_current_index_in_table(self):
sel_ranges = self.tbl_elines.selectedRanges()
# The table is configured to have one or no selected ranges
# 'Open' button should be enabled only if a range (row) is selected
if sel_ranges:
index = sel_ranges[0].topRow()
eline = self._table_contents[index]["eline"]
else:
index, eline = -1, ""
return index, eline
def _get_current_index_in_list(self):
index, eline = self.element_selection.get_current_item()
return index, eline
def _update_add_remove_btn_state(self, eline=None):
if eline is None:
index_in_table, eline = self._get_current_index_in_table()
index_in_list, eline = self._get_current_index_in_list()
else:
index_in_table = self._get_eline_index_in_table(eline)
index_in_list = self._get_eline_index_in_list(eline)
add_enabled, remove_enabled = True, True
if index_in_list < 0 and index_in_table < 0:
add_enabled, remove_enabled = False, False
else:
if index_in_table >= 0:
if self.gpc.get_eline_name_category(eline) != "other":
add_enabled = False
else:
add_enabled, remove_enabled = False, False
else:
remove_enabled = False
self.pb_add_eline.setEnabled(add_enabled)
self.pb_remove_eline.setEnabled(remove_enabled)
self.signal_update_add_remove_btn_state.emit(add_enabled,
remove_enabled)
def _update_add_edit_userpeak_btn_state(self):
enabled = True
add_peak = True
if self.gpc.get_eline_name_category(
self._selected_eline) == "userpeak":
add_peak = False
# Finally check if marker is set (you need it for adding peaks)
_, marker_set = self.gpc.get_suggested_manual_peak_energy()
if not marker_set and add_peak:
enabled = False
if add_peak:
btn_text = "New User Peak ..."
else:
btn_text = "Edit User Peak ..."
self.pb_user_peaks.setText(btn_text)
self.pb_user_peaks.setEnabled(enabled)
def _update_add_edit_pileup_peak_btn_state(self):
enabled = True
if self.gpc.get_eline_name_category(self._selected_eline) == "pileup":
enabled = False
# Finally check if marker is set (you need it for adding peaks)
_, marker_set = self.gpc.get_suggested_manual_peak_energy()
# Ignore set marker for userpeaks (marker is used to display location of userpeaks)
if self.gpc.get_eline_name_category(
self._selected_eline) == "userpeak":
marker_set = False
if not marker_set:
enabled = False
self.pb_pileup_peaks.setEnabled(enabled)
def _set_selected_eline(self, eline):
self._update_add_remove_btn_state(eline)
if eline != self._selected_eline:
self._selected_eline = eline
self.gpc.set_selected_eline(eline)
self._display_peak_intensity(eline)
else:
# Peak intensity may change in some circumstances, so renew the displayed value.
self._display_peak_intensity(eline)
# Update button states after 'self._selected_eline' is set
self._update_add_edit_userpeak_btn_state()
self._update_add_edit_pileup_peak_btn_state()
def _set_fit_status(self, status):
self.gui_vars["gui_state"]["state_model_fit_exists"] = status
self.signal_parameters_changed.emit()
class Extension2ReaderTable(QWidget):
"""Table showing extension to reader mappings with removal button.
Widget presented in preferences-plugin dialog."""
valueChanged = Signal(int)
def __init__(self, parent=None):
super().__init__(parent=parent)
self._table = QTableWidget()
self._table.setShowGrid(False)
self._populate_table()
layout = QVBoxLayout()
layout.addWidget(self._table)
self.setLayout(layout)
def _populate_table(self):
"""Add row for each extension to reader mapping in settings"""
self._extension_col = 0
self._reader_col = 1
header_strs = [trans._('Extension'), trans._('Reader Plugin')]
self._table.setColumnCount(2)
self._table.setColumnWidth(self._extension_col, 100)
self._table.setColumnWidth(self._reader_col, 150)
self._table.verticalHeader().setVisible(False)
self._table.setMinimumHeight(120)
extension2reader = get_settings().plugins.extension2reader
if len(extension2reader) > 0:
self._table.setRowCount(len(extension2reader))
self._table.horizontalHeader().setStretchLastSection(True)
self._table.horizontalHeader().setStyleSheet(
'border-bottom: 2px solid white;')
self._table.setHorizontalHeaderLabels(header_strs)
for row, (extension,
plugin_name) in enumerate(extension2reader.items()):
item = QTableWidgetItem(extension)
item.setFlags(Qt.NoItemFlags)
self._table.setItem(row, self._extension_col, item)
plugin_widg = QWidget()
# need object name to easily find row
plugin_widg.setObjectName(f'{extension}')
plugin_widg.setLayout(QHBoxLayout())
plugin_widg.layout().setContentsMargins(0, 0, 0, 0)
plugin_label = QLabel(plugin_name)
# need object name to easily work out which button was clicked
remove_btn = QPushButton('x', objectName=f'{extension}')
remove_btn.setFixedWidth(30)
remove_btn.setStyleSheet('margin: 4px;')
remove_btn.setToolTip(
trans._('Remove this extension to reader association'))
remove_btn.clicked.connect(self._remove_extension_assignment)
plugin_widg.layout().addWidget(plugin_label)
plugin_widg.layout().addWidget(remove_btn)
self._table.setCellWidget(row, self._reader_col, plugin_widg)
else:
# Display that there are no extensions with reader associations
self._table.setRowCount(1)
self._table.setHorizontalHeaderLabels(header_strs)
self._table.setColumnHidden(self._reader_col, True)
self._table.setColumnWidth(self._extension_col, 200)
item = QTableWidgetItem(trans._('No extensions found.'))
item.setFlags(Qt.NoItemFlags)
self._table.setItem(0, 0, item)
def _remove_extension_assignment(self, event):
"""Delete extension to reader mapping setting and remove table row"""
extension_to_remove = self.sender().objectName()
current_settings = get_settings().plugins.extension2reader
# need explicit assignment to new object here for persistence
get_settings().plugins.extension2reader = {
k: v
for k, v in current_settings.items() if k != extension_to_remove
}
for i in range(self._table.rowCount()):
row_widg_name = self._table.cellWidget(
i, self._reader_col).objectName()
if row_widg_name == extension_to_remove:
self._table.removeRow(i)
return
class WndLoadQuantitativeCalibration(SecondaryWindow):
signal_quantitative_calibration_changed = Signal()
def __init__(self, *, gpc, gui_vars):
super().__init__()
# Global processing classes
self.gpc = gpc
# Global GUI variables (used for control of GUI state)
self.gui_vars = gui_vars
self.initialize()
def initialize(self):
self.table_header_display_names = False
self.setWindowTitle("PyXRF: Load Quantitative Calibration")
self.setMinimumWidth(750)
self.setMinimumHeight(400)
self.resize(750, 600)
self.pb_load_calib = QPushButton("Load Calibration ...")
self.pb_load_calib.clicked.connect(self.pb_load_calib_clicked)
self._changes_exist = False
self._auto_update = True
self.cb_auto_update = QCheckBox("Auto")
self.cb_auto_update.setCheckState(
Qt.Checked if self._auto_update else Qt.Unchecked)
self.cb_auto_update.stateChanged.connect(
self.cb_auto_update_state_changed)
self.pb_update_plots = QPushButton("Update Plots")
self.pb_update_plots.clicked.connect(self.pb_update_plots_clicked)
self.grp_current_scan = QGroupBox(
"Parameters of Currently Processed Scan")
self._distance_to_sample = 0.0
self.le_distance_to_sample = LineEditExtended()
le_dist_validator = QDoubleValidator()
le_dist_validator.setBottom(0)
self.le_distance_to_sample.setValidator(le_dist_validator)
self._set_distance_to_sample()
self.le_distance_to_sample.editingFinished.connect(
self.le_distance_to_sample_editing_finished)
self.le_distance_to_sample.focusOut.connect(
self.le_distance_to_sample_focus_out)
hbox = QHBoxLayout()
hbox.addWidget(QLabel("Distance-to-sample:"))
hbox.addWidget(self.le_distance_to_sample)
hbox.addStretch(1)
self.grp_current_scan.setLayout(hbox)
self.eline_rb_exclusive = [
] # Holds the list of groups of exclusive radio buttons
self._setup_tab_widget()
vbox = QVBoxLayout()
hbox = QHBoxLayout()
hbox.addWidget(self.pb_load_calib)
hbox.addStretch(1)
hbox.addWidget(self.cb_auto_update)
hbox.addWidget(self.pb_update_plots)
vbox.addLayout(hbox)
vbox.addWidget(self.tab_widget)
vbox.addWidget(self.grp_current_scan)
self.setLayout(vbox)
# Display data
self.update_all_data()
self._set_tooltips()
def _setup_tab_widget(self):
self.tab_widget = QTabWidget()
self.loaded_standards = QWidget()
# self.display_loaded_standards()
self.scroll = QScrollArea()
self.scroll.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.scroll.setWidget(self.loaded_standards)
self.tab_widget.addTab(self.scroll, "Loaded Standards")
self.combo_set_table_header = QComboBox()
self.combo_set_table_header.addItems(
["Standard Serial #", "Standard Name"])
self.combo_set_table_header.currentIndexChanged.connect(
self.combo_set_table_header_index_changed)
vbox = QVBoxLayout()
vbox.addSpacing(5)
hbox = QHBoxLayout()
hbox.addWidget(QLabel("Display in table header:"))
hbox.addWidget(self.combo_set_table_header)
hbox.addStretch(1)
vbox.addLayout(hbox)
self.table = QTableWidget()
self.table.verticalHeader().hide()
self.table.setSelectionMode(QTableWidget.NoSelection)
self.table.horizontalHeader().setSectionResizeMode(
QHeaderView.ResizeToContents)
self.table.horizontalHeader().setMinimumSectionSize(150)
vbox.addWidget(self.table)
self.table.setStyleSheet("QTableWidget::item{color: black;}")
frame = QFrame()
vbox.setContentsMargins(0, 0, 0, 0)
frame.setLayout(vbox)
self.tab_widget.addTab(frame, "Selected Emission Lines")
def display_loaded_standards(self):
calib_data = self.gpc.get_quant_calibration_data()
calib_settings = self.gpc.get_quant_calibration_settings()
# Create the new widget (this deletes the old widget)
self.loaded_standards = QWidget()
self.loaded_standards.setMinimumWidth(700)
# Also delete references to all components
self.frames_calib_data = []
self.pbs_view = []
self.pbs_remove = []
# All 'View' buttons are added to the group in order to be connected to the same slot
self.group_view = QButtonGroup()
self.group_view.setExclusive(False)
self.group_view.buttonClicked.connect(self.pb_view_clicked)
# The same for the 'Remove' buttons
self.group_remove = QButtonGroup()
self.group_remove.setExclusive(False)
self.group_remove.buttonClicked.connect(self.pb_remove_clicked)
vbox = QVBoxLayout()
class _LabelBlack(QLabel):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.setStyleSheet("color: black")
for cdata, csettings in zip(calib_data, calib_settings):
frame = QFrame()
frame.setFrameStyle(QFrame.StyledPanel)
frame.setStyleSheet(
get_background_css((200, 255, 200), widget="QFrame"))
_vbox = QVBoxLayout()
name = cdata["name"] # Standard name (can be arbitrary string
# If name is long, then print it in a separate line
_name_is_long = len(name) > 30
pb_view = QPushButton("View ...")
self.group_view.addButton(pb_view)
pb_remove = QPushButton("Remove")
self.group_remove.addButton(pb_remove)
# Row 1: serial, name
serial = cdata["serial"]
_hbox = QHBoxLayout()
_hbox.addWidget(_LabelBlack(f"<b>Standard</b> #{serial}"))
if not _name_is_long:
_hbox.addWidget(_LabelBlack(f"'{name}'"))
_hbox.addStretch(1)
_hbox.addWidget(pb_view)
_hbox.addWidget(pb_remove)
_vbox.addLayout(_hbox)
# Optional row
if _name_is_long:
# Wrap name if it is extemely long
name = textwrap.fill(name, width=80)
_hbox = QHBoxLayout()
_hbox.addWidget(_LabelBlack("<b>Name:</b> "), 0, Qt.AlignTop)
_hbox.addWidget(_LabelBlack(name), 0, Qt.AlignTop)
_hbox.addStretch(1)
_vbox.addLayout(_hbox)
# Row 2: description
description = textwrap.fill(cdata["description"], width=80)
_hbox = QHBoxLayout()
_hbox.addWidget(_LabelBlack("<b>Description:</b>"), 0, Qt.AlignTop)
_hbox.addWidget(_LabelBlack(f"{description}"), 0, Qt.AlignTop)
_hbox.addStretch(1)
_vbox.addLayout(_hbox)
# Row 3:
incident_energy = cdata["incident_energy"]
scaler = cdata["scaler_name"]
detector_channel = cdata["detector_channel"]
distance_to_sample = cdata["distance_to_sample"]
_hbox = QHBoxLayout()
_hbox.addWidget(
_LabelBlack(f"<b>Incident energy, keV:</b> {incident_energy}"))
_hbox.addWidget(_LabelBlack(f" <b>Scaler:</b> {scaler}"))
_hbox.addWidget(
_LabelBlack(f" <b>Detector channel:</b> {detector_channel}"))
_hbox.addWidget(
_LabelBlack(
f" <b>Distance-to-sample:</b> {distance_to_sample}"))
_hbox.addStretch(1)
_vbox.addLayout(_hbox)
# Row 4: file name
fln = textwrap.fill(csettings["file_path"], width=80)
_hbox = QHBoxLayout()
_hbox.addWidget(_LabelBlack("<b>Source file:</b>"), 0, Qt.AlignTop)
_hbox.addWidget(_LabelBlack(fln), 0, Qt.AlignTop)
_hbox.addStretch(1)
_vbox.addLayout(_hbox)
frame.setLayout(_vbox)
# Now the group box is added to the upper level layout
vbox.addWidget(frame)
vbox.addSpacing(5)
self.frames_calib_data.append(frame)
self.pbs_view.append(pb_view)
self.pbs_remove.append(pb_remove)
# Add the layout to the widget
self.loaded_standards.setLayout(vbox)
# ... and put the widget inside the scroll area. This will update the
# contents of the scroll area.
self.scroll.setWidget(self.loaded_standards)
def display_table_header(self):
calib_data = self.gpc.get_quant_calibration_data()
header_by_name = self.table_header_display_names
tbl_labels = ["Lines"]
for n, cdata in enumerate(calib_data):
if header_by_name:
txt = cdata["name"]
else:
txt = cdata["serial"]
txt = textwrap.fill(txt, width=20)
tbl_labels.append(txt)
self.table.setHorizontalHeaderLabels(tbl_labels)
def display_standard_selection_table(self):
calib_data = self.gpc.get_quant_calibration_data()
self._quant_file_paths = self.gpc.get_quant_calibration_file_path_list(
)
brightness = 220
table_colors = [(255, brightness, brightness),
(brightness, 255, brightness)]
# Disconnect all radio button signals before clearing the table
for bgroup in self.eline_rb_exclusive:
bgroup.buttonToggled.disconnect(self.rb_selection_toggled)
# This list will hold radio button groups for horizontal rows
# Those are exclusive groups. They are not going to be
# used directly, but they must be kept alive in order
# for the radiobuttons to work properly. Most of the groups
# will contain only 1 radiobutton, which will always remain checked.
self.eline_rb_exclusive = []
# The following list will contain the list of radio buttons for each
# row. If there is no radiobutton in a position, then the element is
# set to None.
# N rows: the number of emission lines, N cols: the number of standards
self.eline_rb_lists = []
self.table.clear()
if not calib_data:
self.table.setRowCount(0)
self.table.setColumnCount(0)
else:
# Create the sorted list of available element lines
line_set = set()
for cdata in calib_data:
ks = list(cdata["element_lines"].keys())
line_set.update(list(ks))
self.eline_list = list(line_set)
self.eline_list.sort()
for n in range(len(self.eline_list)):
self.eline_rb_exclusive.append(QButtonGroup())
self.eline_rb_lists.append([None] * len(calib_data))
self.table.setColumnCount(len(calib_data) + 1)
self.table.setRowCount(len(self.eline_list))
self.display_table_header()
for n, eline in enumerate(self.eline_list):
rgb = table_colors[n % 2]
item = QTableWidgetItem(eline)
item.setTextAlignment(Qt.AlignCenter)
item.setFlags(item.flags() & ~Qt.ItemIsEditable)
item.setBackground(QBrush(QColor(*rgb)))
self.table.setItem(n, 0, item)
for ns, cdata in enumerate(calib_data):
q_file_path = self._quant_file_paths[
ns] # Used to identify standard
if eline in cdata["element_lines"]:
rb = QRadioButton()
if self.gpc.get_quant_calibration_is_eline_selected(
eline, q_file_path):
rb.setChecked(True)
rb.setStyleSheet("color: black")
self.eline_rb_lists[n][ns] = rb
# self.eline_rb_by_standard[ns].addButton(rb)
self.eline_rb_exclusive[n].addButton(rb)
item = QWidget()
item_hbox = QHBoxLayout(item)
item_hbox.addWidget(rb)
item_hbox.setAlignment(Qt.AlignCenter)
item_hbox.setContentsMargins(0, 0, 0, 0)
item.setStyleSheet(get_background_css(rgb))
# Generate tooltip
density = cdata["element_lines"][eline]["density"]
fluorescence = cdata["element_lines"][eline][
"fluorescence"]
ttip = f"Fluorescence (F): {fluorescence:12g}\nDensity (D): {density:12g}\n"
# Avoid very small values of density (probably zero)
if abs(density) > 1e-30:
ttip += f"F/D: {fluorescence/density:12g}"
item.setToolTip(ttip)
self.table.setCellWidget(n, ns + 1, item)
else:
# There is no radio button, but we still need to fill the cell
item = QTableWidgetItem("")
item.setFlags(item.flags() & ~Qt.ItemIsEditable)
item.setBackground(QBrush(QColor(*rgb)))
self.table.setItem(n, ns + 1, item)
# Now the table is set (specifically radio buttons).
# So we can connect the button groups with the event processing function
for bgroup in self.eline_rb_exclusive:
bgroup.buttonToggled.connect(self.rb_selection_toggled)
@Slot()
def update_all_data(self):
self.display_loaded_standards()
self.display_standard_selection_table()
self._set_distance_to_sample()
def _set_distance_to_sample(self):
"""Set 'le_distance_to_sample` without updating maps"""
distance_to_sample = self.gpc.get_quant_calibration_distance_to_sample(
)
if distance_to_sample is None:
distance_to_sample = 0.0
self._distance_to_sample = distance_to_sample
self._set_le_distance_to_sample(distance_to_sample)
def _set_tooltips(self):
set_tooltip(self.pb_load_calib,
"Load <b>calibration data</b> from JSON file.")
set_tooltip(
self.cb_auto_update,
"Automatically <b>update the plots</b> when changes are made. "
"If unchecked, then button <b>Update Plots</b> must be pressed "
"to update the plots. Automatic update is often undesirable "
"when large maps are displayed and multiple changes to parameters "
"are made.",
)
set_tooltip(
self.pb_update_plots,
"<b>Update plots</b> based on currently selected parameters.")
set_tooltip(
self.le_distance_to_sample,
"Distance between <b>the sample and the detector</b>. The ratio between of the distances "
"during calibration and measurement is used to scale computed concentrations. "
"If distance-to-sample is 0 for calibration or measurement, then no scaling is performed.",
)
set_tooltip(
self.combo_set_table_header,
"Use <b>Serial Number</b> or <b>Name</b> of the calibration standard in the header of the table",
)
set_tooltip(
self.table,
"Use Radio Buttons to select the <b>source of calibration data</b> for each emission line. "
"This feature is needed if multiple loaded calibration files have data on the same "
"emission line.",
)
def update_widget_state(self, condition=None):
# Update the state of the menu bar
state = not self.gui_vars["gui_state"]["running_computations"]
self.setEnabled(state)
# Hide the window if required by the program state
state_xrf_map_exists = self.gui_vars["gui_state"][
"state_xrf_map_exists"]
if not state_xrf_map_exists:
self.hide()
if condition == "tooltips":
self._set_tooltips()
def cb_auto_update_state_changed(self, state):
self._auto_update = state
self.pb_update_plots.setEnabled(not state)
# If changes were made, apply the changes while switching to 'auto' mode
if state and self._changes_exist:
self._update_maps_auto()
def pb_update_plots_clicked(self):
self._update_maps()
def pb_load_calib_clicked(self):
current_dir = self.gpc.get_current_working_directory()
file_name = QFileDialog.getOpenFileName(
self, "Select File with Quantitative Calibration Data",
current_dir, "JSON (*.json);; All (*)")
file_name = file_name[0]
if file_name:
try:
logger.debug(
f"Loading quantitative calibration from file: '{file_name}'"
)
self.gpc.load_quantitative_calibration_data(file_name)
self.update_all_data()
self._update_maps_auto()
except Exception:
msg = "The selected JSON file has incorrect format. Select a different file."
msgbox = QMessageBox(QMessageBox.Critical,
"Data Loading Error",
msg,
QMessageBox.Ok,
parent=self)
msgbox.exec()
def pb_view_clicked(self, button):
try:
n_standard = self.pbs_view.index(button)
calib_settings = self.gpc.get_quant_calibration_settings()
file_path = calib_settings[n_standard]["file_path"]
calib_preview = self.gpc.get_quant_calibration_text_preview(
file_path)
dlg = DialogViewCalibStandard(None,
file_path=file_path,
calib_preview=calib_preview)
dlg.exec()
except ValueError:
logger.error(
"'View' button was pressed, but not found in the list of buttons"
)
def pb_remove_clicked(self, button):
try:
n_standard = self.pbs_remove.index(button)
calib_settings = self.gpc.get_quant_calibration_settings()
file_path = calib_settings[n_standard]["file_path"]
self.gpc.quant_calibration_remove_entry(file_path)
self.update_all_data()
self._update_maps_auto()
except ValueError:
logger.error(
"'Remove' button was pressed, but not found in the list of buttons"
)
def rb_selection_toggled(self, button, checked):
if checked:
# Find the button in 2D list 'self.eline_rb_lists'
button_found = False
for nr, rb_list in enumerate(self.eline_rb_lists):
try:
nc = rb_list.index(button)
button_found = True
break
except ValueError:
pass
if button_found:
eline = self.eline_list[nr]
n_standard = nc
file_path = self._quant_file_paths[n_standard]
self.gpc.set_quant_calibration_select_eline(eline, file_path)
self._update_maps_auto()
else:
# This should never happen
logger.error(
"Selection radio button was pressed, but not found in the list"
)
def combo_set_table_header_index_changed(self, index):
self.table_header_display_names = bool(index)
self.display_table_header()
def le_distance_to_sample_editing_finished(self):
distance_to_sample = float(self.le_distance_to_sample.text())
if distance_to_sample != self._distance_to_sample:
self._distance_to_sample = distance_to_sample
self.gpc.set_quant_calibration_distance_to_sample(
distance_to_sample)
self._update_maps_auto()
def le_distance_to_sample_focus_out(self):
try:
float(self.le_distance_to_sample.text())
except ValueError:
# If the text can not be interpreted to float, then replace the text with the old value
self._set_le_distance_to_sample(self._distance_to_sample)
def _set_le_distance_to_sample(self, distance_to_sample):
self.le_distance_to_sample.setText(f"{distance_to_sample:.12g}")
def _update_maps_auto(self):
"""Update maps only if 'auto' update is ON. Used as a 'filter'
to prevent extra plot updates."""
self._changes_exist = True
if self._auto_update:
self._update_maps()
def _update_maps(self):
"""Upload the selections (limit table) and update plot"""
self._changes_exist = False
self._redraw_maps()
# Emit signal only after the maps are redrawn. This should change
# ranges in the respective controls for the plots
self.signal_quantitative_calibration_changed.emit()
def _redraw_maps(self):
# We don't emit any signals here, but we don't really need to.
logger.debug("Redrawing RGB XRF Maps")
self.gpc.compute_map_ranges()
self.gpc.redraw_maps()
self.gpc.compute_rgb_map_ranges()
self.gpc.redraw_rgb_maps()
class OpticsAdjustSettings(SiriusDialog):
"""Auxiliar window to optics adjust settings."""
updateSettings = Signal(str, str)
def __init__(self, tuneconfig_currname, chromconfig_currname, parent=None):
"""Initialize object."""
super().__init__(parent)
self.setWindowTitle('Optics Adjust Settings')
self.setObjectName('BOApp')
self.tuneconfig_currname = tuneconfig_currname
self.chromconfig_currname = chromconfig_currname
self.conn_tuneparams = _ConfigDBClient(
config_type='bo_tunecorr_params')
self.conn_chromparams = _ConfigDBClient(
config_type='bo_chromcorr_params')
self._setupUi()
def _setupUi(self):
self.tune_settings = QWidget(self)
self.tune_settings.setLayout(self._setupTuneSettings())
self.le_tuneconfig.setText(self.tuneconfig_currname)
self.chrom_settings = QWidget(self)
self.chrom_settings.setLayout(self._setupChromSettings())
self.le_chromconfig.setText(self.chromconfig_currname)
self.bt_apply = QPushButton('Apply Settings', self)
self.bt_apply.setStyleSheet("""min-width:8em; max-width:8em;""")
self.bt_apply.clicked.connect(self._emitSettings)
self.bt_apply.setAutoDefault(False)
self.bt_apply.setDefault(False)
hlay_apply = QHBoxLayout()
hlay_apply.addItem(
QSpacerItem(20, 60, QSzPlcy.Expanding, QSzPlcy.Ignored))
hlay_apply.addWidget(self.bt_apply)
tabs = QTabWidget(self)
tabs.addTab(self.tune_settings, 'Tune')
tabs.addTab(self.chrom_settings, 'Chromaticity')
lay = QVBoxLayout()
lay.addWidget(tabs)
lay.addLayout(hlay_apply)
self.setLayout(lay)
def _setupTuneSettings(self):
l_tuneconfig = QLabel('<h3>Tune Variation Config</h3>', self)
l_tuneconfig.setAlignment(Qt.AlignCenter)
self.le_tuneconfig = _ConfigLineEdit(parent=self,
config_type='bo_tunecorr_params')
self.le_tuneconfig.textChanged.connect(self._showTuneConfigData)
label_tunemat = QLabel('<h4>Matrix</h4>', self)
label_tunemat.setAlignment(Qt.AlignCenter)
self.table_tunemat = QTableWidget(self)
self.table_tunemat.setObjectName('tunemat')
self.table_tunemat.setStyleSheet("""
#tunemat{
background-color: #efebe7;
min-width: 22.14em;
min-height: 6em; max-height: 6em;}""")
self.table_tunemat.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.table_tunemat.setEditTriggers(QAbstractItemView.NoEditTriggers)
self.table_tunemat.setRowCount(2)
self.table_tunemat.setColumnCount(2)
self.table_tunemat.setVerticalHeaderLabels([' X', ' Y'])
self.table_tunemat.setHorizontalHeaderLabels(['QF', 'QD'])
self.table_tunemat.horizontalHeader().setStyleSheet("""
min-height:1.55em; max-height:1.55em;""")
self.table_tunemat.verticalHeader().setStyleSheet("""
min-width:1.55em; max-width:1.55em;""")
self.table_tunemat.horizontalHeader().setSectionResizeMode(
QHeaderView.Stretch)
self.table_tunemat.verticalHeader().setSectionResizeMode(
QHeaderView.Stretch)
self.table_tunemat.setSizePolicy(QSzPlcy.MinimumExpanding,
QSzPlcy.Preferred)
label_nomKL = QLabel('<h4>Nominal KL</h4>')
label_nomKL.setAlignment(Qt.AlignCenter)
self.table_nomKL = QTableWidget(self)
self.table_nomKL.setObjectName('nomKL')
self.table_nomKL.setStyleSheet("""
#nomKL{
background-color: #efebe7;
min-width: 22.14em;
min-height: 4em; max-height: 4em;}""")
self.table_nomKL.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.table_nomKL.setEditTriggers(QAbstractItemView.NoEditTriggers)
self.table_nomKL.setRowCount(1)
self.table_nomKL.setColumnCount(2)
self.table_nomKL.setVerticalHeaderLabels(['KL'])
self.table_nomKL.setHorizontalHeaderLabels(['QF', 'QD'])
self.table_nomKL.horizontalHeader().setStyleSheet("""
min-height:1.55em; max-height:1.55em;""")
self.table_nomKL.verticalHeader().setStyleSheet("""
min-width:1.55em; max-width:1.55em;""")
self.table_nomKL.horizontalHeader().setSectionResizeMode(
QHeaderView.Stretch)
self.table_nomKL.verticalHeader().setSectionResizeMode(
QHeaderView.Stretch)
self.table_nomKL.setSizePolicy(QSzPlcy.MinimumExpanding,
QSzPlcy.Preferred)
lay = QVBoxLayout()
lay.addWidget(l_tuneconfig)
lay.addWidget(self.le_tuneconfig)
lay.addItem(QSpacerItem(20, 10, QSzPlcy.Ignored, QSzPlcy.Expanding))
lay.addWidget(label_tunemat)
lay.addWidget(self.table_tunemat)
lay.addItem(QSpacerItem(20, 10, QSzPlcy.Ignored, QSzPlcy.Expanding))
lay.addWidget(label_nomKL)
lay.addWidget(self.table_nomKL)
lay.addItem(QSpacerItem(20, 10, QSzPlcy.Ignored, QSzPlcy.Expanding))
return lay
def _setupChromSettings(self):
l_chromconfig = QLabel('<h3>Chromaticity Variation Config</h3>', self)
l_chromconfig.setAlignment(Qt.AlignCenter)
self.le_chromconfig = _ConfigLineEdit(
parent=self, config_type='bo_chromcorr_params')
self.le_chromconfig.textChanged.connect(self._showChromConfigData)
l_chrommat = QLabel('<h4>Matrix</h4>', self)
l_chrommat.setAlignment(Qt.AlignCenter)
self.table_chrommat = QTableWidget(self)
self.table_chrommat.setObjectName('chrommat')
self.table_chrommat.setStyleSheet("""
#chrommat{
background-color: #efebe7;
min-width: 22.14em;
min-height: 6em; max-height: 6em;}""")
self.table_chrommat.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.table_chrommat.setEditTriggers(QAbstractItemView.NoEditTriggers)
self.table_chrommat.setRowCount(2)
self.table_chrommat.setColumnCount(2)
self.table_chrommat.setVerticalHeaderLabels([' X', ' Y'])
self.table_chrommat.setHorizontalHeaderLabels(['SF', 'SD'])
self.table_chrommat.horizontalHeader().setStyleSheet("""
min-height:1.55em; max-height:1.55em;""")
self.table_chrommat.verticalHeader().setStyleSheet("""
min-width:1.55em; max-width:1.55em;""")
self.table_chrommat.horizontalHeader().setSectionResizeMode(
QHeaderView.Stretch)
self.table_chrommat.verticalHeader().setSectionResizeMode(
QHeaderView.Stretch)
self.table_chrommat.setSizePolicy(QSzPlcy.MinimumExpanding,
QSzPlcy.Preferred)
l_nomSL = QLabel('<h4>Nominal SL</h4>')
l_nomSL.setAlignment(Qt.AlignCenter)
self.table_nomSL = QTableWidget(self)
self.table_nomSL.setObjectName('nomSL')
self.table_nomSL.setStyleSheet("""
#nomSL{
background-color: #efebe7;
min-width: 22.14em;
min-height: 4em; max-height: 4em;}""")
self.table_nomSL.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.table_nomSL.setEditTriggers(QAbstractItemView.NoEditTriggers)
self.table_nomSL.setRowCount(1)
self.table_nomSL.setColumnCount(2)
self.table_nomSL.setVerticalHeaderLabels(['SL'])
self.table_nomSL.setHorizontalHeaderLabels(['SF', 'SD'])
self.table_nomSL.horizontalHeader().setStyleSheet("""
min-height:1.55em; max-height:1.55em;""")
self.table_nomSL.verticalHeader().setStyleSheet("""
min-width:1.55em; max-width:1.55em;""")
self.table_nomSL.horizontalHeader().setSectionResizeMode(
QHeaderView.Stretch)
self.table_nomSL.verticalHeader().setSectionResizeMode(
QHeaderView.Stretch)
self.table_nomSL.setSizePolicy(QSzPlcy.MinimumExpanding,
QSzPlcy.Preferred)
l_nomchrom = QLabel('<h4>Nominal Chrom</h4>')
l_nomchrom.setAlignment(Qt.AlignCenter)
self.label_nomchrom = QLabel()
self.label_nomchrom.setAlignment(Qt.AlignCenter)
lay = QVBoxLayout()
lay.addWidget(l_chromconfig)
lay.addWidget(self.le_chromconfig)
lay.addItem(QSpacerItem(20, 10, QSzPlcy.Expanding, QSzPlcy.Expanding))
lay.addWidget(l_chrommat)
lay.addWidget(self.table_chrommat)
lay.addItem(QSpacerItem(20, 10, QSzPlcy.Expanding, QSzPlcy.Expanding))
lay.addWidget(l_nomSL)
lay.addWidget(self.table_nomSL)
lay.addItem(QSpacerItem(20, 10, QSzPlcy.Expanding, QSzPlcy.Expanding))
lay.addWidget(l_nomchrom)
lay.addWidget(self.label_nomchrom)
return lay
def _showTuneConfigData(self):
try:
name = self.le_tuneconfig.text()
config = self.conn_tuneparams.get_config_value(name=name)
mat = config['matrix']
nomKL = config['nominal KLs']
except _ConfigDBException as err:
QMessageBox.critical(self, 'Error', str(err), QMessageBox.Ok)
else:
self.tuneconfig_currname = name
self.table_tunemat.setItem(0, 0, QTableWidgetItem(str(mat[0][0])))
self.table_tunemat.setItem(0, 1, QTableWidgetItem(str(mat[0][1])))
self.table_tunemat.setItem(1, 0, QTableWidgetItem(str(mat[1][0])))
self.table_tunemat.setItem(1, 1, QTableWidgetItem(str(mat[1][1])))
self.table_tunemat.item(0, 0).setFlags(Qt.ItemIsEnabled)
self.table_tunemat.item(0, 1).setFlags(Qt.ItemIsEnabled)
self.table_tunemat.item(1, 0).setFlags(Qt.ItemIsEnabled)
self.table_tunemat.item(1, 1).setFlags(Qt.ItemIsEnabled)
self.table_nomKL.setItem(0, 0, QTableWidgetItem(str(nomKL[0])))
self.table_nomKL.setItem(0, 1, QTableWidgetItem(str(nomKL[1])))
self.table_nomKL.item(0, 0).setFlags(Qt.ItemIsEnabled)
self.table_nomKL.item(0, 1).setFlags(Qt.ItemIsEnabled)
def _showChromConfigData(self):
try:
name = self.le_chromconfig.text()
config = self.conn_chromparams.get_config_value(name=name)
mat = config['matrix']
nomSL = config['nominal SLs']
nomChrom = config['nominal chrom']
except _ConfigDBException as err:
QMessageBox.critical(self, 'Error', str(err), QMessageBox.Ok)
else:
self.chromconfig_currname = name
self.table_chrommat.setItem(0, 0, QTableWidgetItem(str(mat[0][0])))
self.table_chrommat.setItem(0, 1, QTableWidgetItem(str(mat[0][1])))
self.table_chrommat.setItem(1, 0, QTableWidgetItem(str(mat[1][0])))
self.table_chrommat.setItem(1, 1, QTableWidgetItem(str(mat[1][1])))
self.table_chrommat.item(0, 0).setFlags(Qt.ItemIsEnabled)
self.table_chrommat.item(0, 1).setFlags(Qt.ItemIsEnabled)
self.table_chrommat.item(1, 0).setFlags(Qt.ItemIsEnabled)
self.table_chrommat.item(1, 1).setFlags(Qt.ItemIsEnabled)
self.table_nomSL.setItem(0, 0, QTableWidgetItem(str(nomSL[0])))
self.table_nomSL.setItem(0, 1, QTableWidgetItem(str(nomSL[1])))
self.table_nomSL.item(0, 0).setFlags(Qt.ItemIsEnabled)
self.table_nomSL.item(0, 1).setFlags(Qt.ItemIsEnabled)
self.label_nomchrom.setText(str(nomChrom))
def _emitSettings(self):
tuneconfig_name = self.le_tuneconfig.text()
chromconfig_name = self.le_chromconfig.text()
self.updateSettings.emit(tuneconfig_name, chromconfig_name)
self.close()
class PMGRuleCtrl(BaseExtendedWidget):
"""
rules:
{'name':'regex',
'text':'匹配正则表达式',
'init':False
}
"""
def __init__(self,
layout_dir='v',
title='',
rules: List[Dict[str, Union[bool, int, float, str]]] = None):
super().__init__(layout_dir)
self.table_h_headers = []
self.table_keys = []
self.initial_values = []
for rule in rules:
self.table_h_headers.append(rule['text'])
self.table_keys.append(rule['name'])
self.initial_values.append(rule['init'])
self.regulations_table = QTableWidget(0, len(self.table_h_headers))
self.regulations_table.horizontalHeader().setSectionResizeMode(
QHeaderView.Stretch)
self.regulations_table.setHorizontalHeaderLabels(self.table_h_headers)
self.layout().addWidget(self.regulations_table)
self.set_layout = QHBoxLayout()
self.layout().addLayout(self.set_layout)
self.button_add = QPushButton('Add')
self.button_remove = QPushButton('Remove')
self.set_layout.addWidget(self.button_add)
self.set_layout.addWidget(self.button_remove)
self.button_add.clicked.connect(self.add_regulation)
self.button_remove.clicked.connect(self.remove_regulation)
def load_regulations(self, regulations: List[Dict[str,
Union[int, str, float,
bool]]]):
row_count = len(regulations)
self.regulations_table.setRowCount(row_count)
for i, regulation in enumerate(regulations):
l = [regulation[k] for k in self.table_keys]
for j, obj in enumerate(l):
item = QTableWidgetItem()
item.setData(0, obj)
self.regulations_table.setItem(i, j, item)
def add_regulation(self):
rc = self.regulations_table.rowCount()
self.regulations_table.setRowCount(rc + 1)
for i, obj in enumerate(self.initial_values):
item = QTableWidgetItem()
item.setData(0, obj)
self.regulations_table.setItem(rc, i, item)
def remove_regulation(self):
self.regulations_table.removeRow(self.regulations_table.currentRow())
def get_value(self) -> List[Dict]:
l = []
for i in range(self.regulations_table.rowCount()):
dic = {}
for j in range(self.regulations_table.columnCount()):
item = self.regulations_table.item(i, j)
dic[self.table_keys[j]] = item.data(0)
l.append(dic)
return l
def set_value(self, value):
self.load_regulations(value)
class WndDetailedFittingParams(SecondaryWindow):
# Signal that is sent (to main window) to update global state of the program
update_global_state = Signal()
computations_complete = Signal(object)
def __init__(self, *, window_title, gpc, gui_vars):
super().__init__()
# Global processing classes
self.gpc = gpc
# Global GUI variables (used for control of GUI state)
self.gui_vars = gui_vars
# Reference to the main window. The main window will hold
# references to all non-modal windows that could be opened
# from multiple places in the program.
self.ref_main_window = self.gui_vars["ref_main_window"]
self.update_global_state.connect(
self.ref_main_window.update_widget_state)
self._enable_events = False
self._dialog_data = {}
self._load_dialog_data()
self._selected_index = 0
self._selected_eline = "-"
self.setWindowTitle(window_title)
self.setMinimumWidth(1100)
self.setMinimumHeight(500)
self.resize(1100, 500)
hbox_el_select = self._setup_element_selection()
self._setup_table()
vbox = QVBoxLayout()
vbox.addLayout(hbox_el_select)
vbox.addWidget(self.table)
self.setLayout(vbox)
self.update_form_data()
self._enable_events = True
self._data_changed = False
def _setup_element_selection(self):
self.combo_element_sel = QComboBox()
self.combo_element_sel.setMinimumWidth(200)
self.combo_element_sel.currentIndexChanged.connect(
self.combo_element_sel_current_index_changed)
self.pb_apply = QPushButton("Apply")
self.pb_apply.setEnabled(False)
self.pb_apply.clicked.connect(self.pb_apply_clicked)
self.pb_cancel = QPushButton("Cancel")
self.pb_cancel.setEnabled(False)
self.pb_cancel.clicked.connect(self.pb_cancel_clicked)
hbox = QHBoxLayout()
hbox.addWidget(QLabel("Select element:"))
hbox.addWidget(self.combo_element_sel)
hbox.addStretch(1)
hbox.addWidget(self.pb_apply)
hbox.addWidget(self.pb_cancel)
return hbox
def _setup_table(self):
self._value_keys = ("value", "min", "max")
# Labels for horizontal header
labels_presets = [
fitting_preset_names[_] for _ in self._fit_strategy_list
]
labels_values = [value_names[_] for _ in self._value_keys]
self.tbl_labels = ["Name", "E, keV"] + labels_values + labels_presets
# Labels for editable columns
self.tbl_cols_editable = ("Value", "Min", "Max")
# Labels for the columns that contain combo boxes
self.tbl_cols_combobox = labels_presets
# The list of columns with fixed size
self.tbl_cols_stretch = ("Value", "Min", "Max")
# Table item representation if different from default
self.tbl_format = {
"E, keV": ".4f",
"Value": ".8g",
"Min": ".8g",
"Max": ".8g"
}
# Combobox items. All comboboxes in the table contain identical list of items.
self.combo_items = self._bound_options
self._combo_list = []
self.table = QTableWidget()
self.table.setColumnCount(len(self.tbl_labels))
self.table.verticalHeader().hide()
self.table.setHorizontalHeaderLabels(self.tbl_labels)
self.table.setStyleSheet("QTableWidget::item{color: black;}")
header = self.table.horizontalHeader()
for n, lbl in enumerate(self.tbl_labels):
# Set stretching for the columns
if lbl in self.tbl_cols_stretch:
header.setSectionResizeMode(n, QHeaderView.Stretch)
else:
header.setSectionResizeMode(n, QHeaderView.ResizeToContents)
self.table.itemChanged.connect(self.tbl_elines_item_changed)
def _fill_table(self, table_contents):
self._enable_events = False
# Clear the list of combo boxes
for item in self._combo_list:
item.currentIndexChanged.disconnect(
self.combo_strategy_current_index_changed)
self._combo_list = []
self.table.clearContents()
self.table.setRowCount(len(table_contents))
for nr, row in enumerate(table_contents):
n_fit_strategy = 0
row_name = row[0]
for nc, entry in enumerate(row):
label = self.tbl_labels[nc]
# Set alternating background colors for the table rows
# Make background for editable items a little brighter
brightness = 240 if label in self.tbl_cols_editable else 220
if nr % 2:
rgb_bckg = (255, brightness, brightness)
else:
rgb_bckg = (brightness, 255, brightness)
if label not in self.tbl_cols_combobox:
if label in self.tbl_format and not isinstance(entry, str):
fmt = self.tbl_format[self.tbl_labels[nc]]
s = ("{:" + fmt + "}").format(entry)
else:
s = f"{entry}"
item = QTableWidgetItem(s)
if nc > 0:
item.setTextAlignment(Qt.AlignRight | Qt.AlignVCenter)
# Set all columns not editable (unless needed)
if label not in self.tbl_cols_editable:
item.setFlags(item.flags() & ~Qt.ItemIsEditable)
# Make all items not selectable (we are not using selections)
item.setFlags(item.flags() & ~Qt.ItemIsSelectable)
# Note, that there is no way to set style sheet for QTableWidgetItem
item.setBackground(QBrush(QColor(*rgb_bckg)))
self.table.setItem(nr, nc, item)
else:
if n_fit_strategy < len(self._fit_strategy_list):
combo_name = f"{row_name},{self._fit_strategy_list[n_fit_strategy]}"
else:
combo_name = ""
n_fit_strategy += 1
item = ComboBoxNamedNoWheel(name=combo_name)
# Set text color for QComboBox widget (necessary if the program is used with Dark theme)
pal = item.palette()
pal.setColor(QPalette.ButtonText, Qt.black)
item.setPalette(pal)
# Set text color for drop-down view (necessary if the program is used with Dark theme)
pal = item.view().palette()
pal.setColor(QPalette.Text, Qt.black)
item.view().setPalette(pal)
css1 = get_background_css(rgb_bckg,
widget="QComboBox",
editable=False)
css2 = get_background_css(rgb_bckg,
widget="QWidget",
editable=False)
item.setStyleSheet(css2 + css1)
item.addItems(self.combo_items)
if item.findText(entry) < 0:
logger.warning(
f"Text '{entry}' is not found. The ComboBox is not set properly."
)
item.setCurrentText(entry) # Try selecting the item anyway
self.table.setCellWidget(nr, nc, item)
item.currentIndexChanged.connect(
self.combo_strategy_current_index_changed)
self._combo_list.append(item)
self._enable_events = True
def _set_tooltips(self):
set_tooltip(self.pb_apply, "Save changes and <b>update plots</b>.")
set_tooltip(self.pb_cancel, "<b>Discard</b> all changes.")
set_tooltip(
self.combo_element_sel,
"Select K, L or M <b>emission line</b> to edit the optimization parameters "
"used for the line during total spectrum fitting.",
)
set_tooltip(
self.table,
"Edit optimization parameters for the selected emission line. "
"Processing presets may be configured by specifying optimization strategy "
"for each parameter may be selected. A preset for each fitting step "
"of the total spectrum fitting may be selected in <b>Model</b> tab.",
)
def combo_element_sel_current_index_changed(self, index):
self._selected_index = index
try:
self._selected_eline = self._eline_list[index]
except Exception:
self._selected_eline = "-"
self._update_table()
def combo_strategy_current_index_changed(self, name, index):
if self._enable_events:
try:
name_row, name_strategy = name.split(",")
option = self._bound_options[index]
self._param_dict[name_row][name_strategy] = option
except Exception as ex:
logger.error(
f"Error occurred while changing strategy options: {ex}")
self._data_changed = True
self._validate_all()
def tbl_elines_item_changed(self, item):
if self._enable_events:
try:
n_row, n_col = self.table.row(item), self.table.column(item)
n_key = n_col - 2
if n_key < 0 or n_key >= len(self._value_keys):
raise RuntimeError(f"Incorrect column {n_col}")
value_key = self._value_keys[n_key]
eline_key = self._table_contents[n_row][0]
try:
value = float(item.text())
self._param_dict[eline_key][value_key] = value
except Exception:
value = self._param_dict[eline_key][value_key]
item.setText(f"{value:.8g}")
self._data_changed = True
self._validate_all()
except Exception as ex:
logger.error(
f"Error occurred while setting edited value: {ex}")
def pb_apply_clicked(self):
"""Save dialog data and update plots"""
self.save_form_data()
def pb_cancel_clicked(self):
"""Reload data (discard all changes)"""
self.update_form_data()
def _set_combo_element_sel_items(self):
element_list = self._eline_list
self.combo_element_sel.clear()
self.combo_element_sel.addItems(element_list)
# Deselect all (this should clear the table)
self.select_eline(self._selected_eline)
def _set_dialog_data(self, dialog_data):
self._param_dict = dialog_data["param_dict"]
self._eline_list = dialog_data["eline_list"]
self._eline_key_dict = dialog_data["eline_key_dict"]
self._eline_energy_dict = dialog_data["eline_energy_dict"]
self._other_param_list = dialog_data["other_param_list"]
self._fit_strategy_list = dialog_data["fit_strategy_list"]
self._bound_options = dialog_data["bound_options"]
def _show_all(self):
selected_eline = self._selected_eline
self._set_combo_element_sel_items()
self.select_eline(selected_eline)
self._update_table()
def _update_table(self):
self._enable_events = False
eline_list = []
if "shared" in self._selected_eline.lower(): # Shared parameters
eline_list = self._other_param_list
energy_list = [""] * len(eline_list)
elif self._selected_eline == self._eline_list[
self._selected_index]: # Emission lines
eline = self._selected_eline
eline_list = self._eline_key_dict[eline]
energy_list = self._eline_energy_dict[eline]
self._table_contents = []
for n, key in enumerate(eline_list):
data = [
key,
energy_list[n],
self._param_dict[key]["value"],
self._param_dict[key]["min"],
self._param_dict[key]["max"],
]
for strategy in self._fit_strategy_list:
data.append(self._param_dict[key][strategy])
self._table_contents.append(data)
self._fill_table(self._table_contents)
self._enable_events = True
def select_eline(self, eline):
if eline in self._eline_list:
index = self._eline_list.index(eline)
elif self._eline_list:
index = 0
eline = self._eline_list[0]
else:
index = -1
eline = "-"
self._selected_eline = eline
self._selected_index = index
self.combo_element_sel.setCurrentIndex(index)
self._update_table()
def update_widget_state(self, condition=None):
# Update the state of the menu bar
state = not self.gui_vars["gui_state"]["running_computations"]
self.setEnabled(state)
if condition == "tooltips":
self._set_tooltips()
def _validate_all(self):
self.pb_apply.setEnabled(self._data_changed)
self.pb_cancel.setEnabled(self._data_changed)
def _load_dialog_data(self):
...
def _save_dialog_data_function(self):
...
def update_form_data(self):
self._load_dialog_data()
self._show_all()
self._data_changed = False
self._validate_all()
def save_form_data(self):
if self._data_changed:
f_save_data = self._save_dialog_data_function()
def cb(dialog_data):
try:
f_save_data(dialog_data)
success, msg = True, ""
except Exception as ex:
success, msg = False, str(ex)
return {"success": success, "msg": msg}
self._compute_in_background(cb,
self.slot_save_form_data,
dialog_data=self._dialog_data)
@Slot(object)
def slot_save_form_data(self, result):
self._recover_after_compute(self.slot_save_form_data)
if not result["success"]:
msg = result["msg"]
msgbox = QMessageBox(QMessageBox.Critical,
"Failed to Apply Fit Parameters",
msg,
QMessageBox.Ok,
parent=self)
msgbox.exec()
else:
self._data_changed = False
self._validate_all()
self.gui_vars["gui_state"]["state_model_fit_exists"] = False
self.update_global_state.emit()
def _compute_in_background(self, func, slot, *args, **kwargs):
"""
Run function `func` in a background thread. Send the signal
`self.computations_complete` once computation is finished.
Parameters
----------
func: function
Reference to a function that is supposed to be executed at the background.
The function return value is passed as a signal parameter once computation is
complete.
slot: qtpy.QtCore.Slot or None
Reference to a slot. If not None, then the signal `self.computation_complete`
is connected to this slot.
args, kwargs
arguments of the function `func`.
"""
signal_complete = self.computations_complete
def func_to_run(func, *args, **kwargs):
class RunTask(QRunnable):
def run(self):
result_dict = func(*args, **kwargs)
signal_complete.emit(result_dict)
return RunTask()
if slot is not None:
self.computations_complete.connect(slot)
self.gui_vars["gui_state"]["running_computations"] = True
self.update_global_state.emit()
QThreadPool.globalInstance().start(func_to_run(func, *args, **kwargs))
def _recover_after_compute(self, slot):
"""
The function should be called after the signal `self.computations_complete` is
received. The slot should be the same as the one used when calling
`self.compute_in_background`.
"""
if slot is not None:
self.computations_complete.disconnect(slot)
self.gui_vars["gui_state"]["running_computations"] = False
self.update_global_state.emit()
class MetabolitesMask(QWidget):
"""The input mask for a metabolites"""
def __init__(self, appdata):
QWidget.__init__(self)
self.appdata = appdata
self.metabolite = None
self.is_valid = True
self.changed = False
self.setAcceptDrops(False)
layout = QVBoxLayout()
l = QHBoxLayout()
label = QLabel("Id:")
self.id = QLineEdit()
l.addWidget(label)
l.addWidget(self.id)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Name:")
self.name = QLineEdit()
l.addWidget(label)
l.addWidget(self.name)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Formula:")
self.formula = QLineEdit()
l.addWidget(label)
l.addWidget(self.formula)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Charge:")
self.charge = QLineEdit()
l.addWidget(label)
l.addWidget(self.charge)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Compartment:")
self.compartment = QLineEdit()
l.addWidget(label)
l.addWidget(self.compartment)
layout.addItem(l)
l = QVBoxLayout()
label = QLabel("Annotations:")
l.addWidget(label)
l2 = QHBoxLayout()
self.annotation = QTableWidget(0, 2)
self.annotation.setHorizontalHeaderLabels(
["key", "value"])
self.annotation.horizontalHeader().setSectionResizeMode(QHeaderView.Stretch)
l2.addWidget(self.annotation)
self.add_anno = QPushButton("+")
self.add_anno.clicked.connect(self.add_anno_row)
l2.addWidget(self.add_anno)
l.addItem(l2)
layout.addItem(l)
l = QVBoxLayout()
label = QLabel("Reactions using this metabolite:")
l.addWidget(label)
l2 = QHBoxLayout()
self.reactions = QTreeWidget()
self.reactions.setHeaderLabels(["Id"])
self.reactions.setSortingEnabled(True)
l2.addWidget(self.reactions)
l.addItem(l2)
self.reactions.itemDoubleClicked.connect(self.emit_jump_to_reaction)
layout.addItem(l)
self.setLayout(layout)
self.throttler = SignalThrottler(500)
self.throttler.triggered.connect(self.metabolites_data_changed)
self.id.textEdited.connect(self.throttler.throttle)
self.name.textEdited.connect(self.throttler.throttle)
self.formula.textEdited.connect(self.throttler.throttle)
self.charge.textEdited.connect(self.throttler.throttle)
self.compartment.textEdited.connect(self.throttler.throttle)
self.annotation.itemChanged.connect(self.throttler.throttle)
self.validate_mask()
def add_anno_row(self):
i = self.annotation.rowCount()
self.annotation.insertRow(i)
self.changed = True
def apply(self):
try:
self.metabolite.id = self.id.text()
except ValueError:
turn_red(self.id)
QMessageBox.information(
self, 'Invalid id', 'Could not apply changes identifier ' +
self.id.text()+' already used.')
else:
self.metabolite.name = self.name.text()
self.metabolite.formula = self.formula.text()
if self.charge.text() == "":
self.metabolite.charge = None
else:
self.metabolite.charge = int(self.charge.text())
self.metabolite.compartment = self.compartment.text()
self.metabolite.annotation = {}
rows = self.annotation.rowCount()
for i in range(0, rows):
key = self.annotation.item(i, 0).text()
if self.annotation.item(i, 1) is None:
value = ""
else:
value = self.annotation.item(i, 1).text()
self.metabolite.annotation[key] = value
self.changed = False
self.metaboliteChanged.emit(self.metabolite)
def validate_id(self):
with self.appdata.project.cobra_py_model as model:
text = self.id.text()
if text == "":
turn_red(self.id)
return False
if ' ' in text:
turn_red(self.id)
return False
try:
m = cobra.Metabolite(id=self.id.text())
model.add_metabolites([m])
except ValueError:
turn_red(self.id)
return False
else:
turn_white(self.id)
return True
def validate_name(self):
with self.appdata.project.cobra_py_model as model:
try:
m = cobra.Metabolite(id="test_id", name=self.name.text())
model.add_metabolites([m])
except ValueError:
turn_red(self.name)
return False
else:
turn_white(self.name)
return True
def validate_formula(self):
return True
def validate_charge(self):
try:
if self.charge.text() != "":
_x = int(self.charge.text())
except ValueError:
turn_red(self.charge)
return False
else:
turn_white(self.charge)
return True
def validate_compartment(self):
try:
if ' ' in self.compartment.text():
turn_red(self.compartment)
return False
if '-' in self.compartment.text():
turn_red(self.compartment)
return False
_m = cobra.Metabolite(id="test_id", name=self.compartment.text())
except ValueError:
turn_red(self.compartment)
return False
else:
turn_white(self.compartment)
return True
def validate_mask(self):
valid_id = self.validate_id()
valid_name = self.validate_name()
valid_formula = self.validate_formula()
valid_charge = self.validate_charge()
valid_compartment = self.validate_compartment()
if valid_id & valid_name & valid_formula & valid_charge & valid_compartment:
self.is_valid = True
else:
self.is_valid = False
def metabolites_data_changed(self):
self.changed = True
self.validate_mask()
if self.is_valid:
self.apply()
self.update_state()
def update_state(self):
self.reactions.clear()
if self.appdata.project.cobra_py_model.metabolites.has_id(self.id.text()):
metabolite = self.appdata.project.cobra_py_model.metabolites.get_by_id(
self.id.text())
for r in metabolite.reactions:
item = QTreeWidgetItem(self.reactions)
item.setText(0, r.id)
item.setText(1, r.name)
item.setData(2, 0, r)
text = "Id: " + r.id + "\nName: " + r.name
item.setToolTip(1, text)
def emit_jump_to_reaction(self, reaction):
self.jumpToReaction.emit(reaction.data(2, 0).id)
jumpToReaction = Signal(str)
metaboliteChanged = Signal(cobra.Metabolite)
class RgbSelectionWidget(QWidget):
signal_update_map_selections = Signal()
def __init__(self):
super().__init__()
self._range_table = []
self._limit_table = []
self._rgb_keys = ["red", "green", "blue"]
self._rgb_dict = {_: None for _ in self._rgb_keys}
widget_layout = self._setup_rgb_widget()
self.setLayout(widget_layout)
sp = QSizePolicy()
sp.setControlType(QSizePolicy.PushButton)
sp.setHorizontalPolicy(QSizePolicy.Expanding)
sp.setVerticalPolicy(QSizePolicy.Fixed)
self.setSizePolicy(sp)
def _setup_rgb_element(self, n_row, *, rb_check=0):
"""
Parameters
----------
rb_check: int
The number of QRadioButton to check. Typically this would be the row number.
"""
combo_elements = ComboBoxNamed(name=f"{n_row}")
# combo_elements.setSizeAdjustPolicy(QComboBox.AdjustToContents)
# Set text color for QComboBox widget (necessary if the program is used with Dark theme)
pal = combo_elements.palette()
pal.setColor(QPalette.ButtonText, Qt.black)
combo_elements.setPalette(pal)
# Set text color for drop-down view (necessary if the program is used with Dark theme)
pal = combo_elements.view().palette()
pal.setColor(QPalette.Text, Qt.black)
combo_elements.view().setPalette(pal)
btns = [QRadioButton(), QRadioButton(), QRadioButton()]
if 0 <= rb_check < len(btns):
btns[rb_check].setChecked(True)
# Color is set for operation with Dark theme
for btn in btns:
pal = btn.palette()
pal.setColor(QPalette.Text, Qt.black)
btn.setPalette(pal)
btn_group = QButtonGroup()
for btn in btns:
btn_group.addButton(btn)
rng = RangeManager(name=f"{n_row}", add_sliders=True)
rng.setTextColor([0, 0, 0]) # Set text color to 'black'
# Set some text in edit boxes (just to demonstrate how the controls will look like)
rng.le_min_value.setText("0.0")
rng.le_max_value.setText("1.0")
rng.setAlignment(Qt.AlignCenter)
return combo_elements, btns, rng, btn_group
def _enable_selection_events(self, enable):
if enable:
if not self.elements_btn_groups_events_enabled:
for btn_group in self.elements_btn_groups:
btn_group.buttonToggled.connect(self.rb_toggled)
for el_combo in self.elements_combo:
el_combo.currentIndexChanged.connect(
self.combo_element_current_index_changed)
for el_range in self.elements_range:
el_range.selection_changed.connect(
self.range_selection_changed)
self.elements_btn_groups_events_enabled = True
else:
if self.elements_btn_groups_events_enabled:
for btn_group in self.elements_btn_groups:
btn_group.buttonToggled.disconnect(self.rb_toggled)
for el_combo in self.elements_combo:
el_combo.currentIndexChanged.disconnect(
self.combo_element_current_index_changed)
# Disconnecting the Range Manager signals is not necessary, but let's do it for consistency
for el_range in self.elements_range:
el_range.selection_changed.disconnect(
self.range_selection_changed)
self.elements_btn_groups_events_enabled = False
def _setup_rgb_widget(self):
self.elements_combo = []
self.elements_rb_color = []
self.elements_range = []
self.elements_btn_groups = []
self.elements_btn_groups_events_enabled = False
self.row_colors = []
self.table = QTableWidget()
# Horizontal header entries
tbl_labels = ["Element", "Red", "Green", "Blue", "Range"]
# The list of columns that stretch with the table
self.tbl_cols_stretch = ("Range", )
self.table.setColumnCount(len(tbl_labels))
self.table.setRowCount(3)
self.table.setHorizontalHeaderLabels(tbl_labels)
self.table.verticalHeader().hide()
self.table.setSelectionMode(QTableWidget.NoSelection)
header = self.table.horizontalHeader()
for n, lbl in enumerate(tbl_labels):
# Set stretching for the columns
if lbl in self.tbl_cols_stretch:
header.setSectionResizeMode(n, QHeaderView.Stretch)
else:
header.setSectionResizeMode(n, QHeaderView.ResizeToContents)
vheader = self.table.verticalHeader()
vheader.setSectionResizeMode(QHeaderView.Stretch) # ResizeToContents)
for n_row in range(3):
combo_elements, btns, rng, btn_group = self._setup_rgb_element(
n_row, rb_check=n_row)
combo_elements.setMinimumWidth(180)
self.table.setCellWidget(n_row, 0, combo_elements)
for i, btn in enumerate(btns):
item = QWidget()
item_hbox = QHBoxLayout(item)
item_hbox.addWidget(btn)
item_hbox.setAlignment(Qt.AlignCenter)
item_hbox.setContentsMargins(0, 0, 0, 0)
item.setMinimumWidth(70)
self.table.setCellWidget(n_row, i + 1, item)
rng.setMinimumWidth(200)
rng.setMaximumWidth(400)
self.table.setCellWidget(n_row, 4, rng)
self.elements_combo.append(combo_elements)
self.elements_rb_color.append(btns)
self.elements_range.append(rng)
self.elements_btn_groups.append(btn_group)
self.row_colors.append(self._rgb_keys[n_row])
# Colors that are used to paint rows of the table in RGB colors
br = 150
self._rgb_row_colors = {
"red": (255, br, br),
"green": (br, 255, br),
"blue": (br, br, 255)
}
self._rgb_color_keys = ["red", "green", "blue"]
# Set initial colors
for n_row in range(self.table.rowCount()):
self._set_row_color(n_row)
self._enable_selection_events(True)
self.table.resizeRowsToContents()
# Table height is computed based on content. It doesn't seem
# to account for the height of custom widgets, but the table
# looks good enough
table_height = 0
for n_row in range(self.table.rowCount()):
table_height += self.table.rowHeight(n_row)
self.table.setMaximumHeight(table_height)
table_width = 650
self.table.setMinimumWidth(table_width)
self.table.setMaximumWidth(800)
hbox = QHBoxLayout()
hbox.addWidget(self.table)
return hbox
def combo_element_current_index_changed(self, name, index):
if index < 0 or index >= len(self._range_table):
return
n_row = int(name)
sel_eline = self._range_table[index][0]
row_color = self.row_colors[n_row]
self._rgb_dict[row_color] = sel_eline
self.elements_range[n_row].set_range(self._range_table[index][1],
self._range_table[index][2])
self.elements_range[n_row].set_selection(
value_low=self._limit_table[index][1],
value_high=self._limit_table[index][2])
self._update_map_selections()
def range_selection_changed(self, v_low, v_high, name):
n_row = int(name)
row_color = self.row_colors[n_row]
sel_eline = self._rgb_dict[row_color]
ind = None
try:
ind = [_[0] for _ in self._limit_table].index(sel_eline)
except ValueError:
pass
if ind is not None:
self._limit_table[ind][1] = v_low
self._limit_table[ind][2] = v_high
self._update_map_selections()
# We are not preventing users to select the same emission line in to rows.
# Update the selected limits in other rows where the same element is selected.
for nr, el_range in enumerate(self.elements_range):
if (nr != n_row) and (self._rgb_dict[self.row_colors[nr]]
== sel_eline):
el_range.set_selection(value_low=v_low, value_high=v_high)
def _get_selected_row_color(self, n_row):
color_key = None
btns = self.elements_rb_color[n_row]
for n, btn in enumerate(btns):
if btn.isChecked():
color_key = self._rgb_color_keys[n]
break
return color_key
def _set_row_color(self, n_row, *, color_key=None):
"""
Parameters
----------
n_row: int
The row number that needs background color change (0..2 if table has 3 rows)
color_key: int
Color key: "red", "green" or "blue"
"""
if color_key is None:
color_key = self._get_selected_row_color(n_row)
if color_key is None:
return
self.row_colors[n_row] = color_key
rgb = self._rgb_row_colors[color_key]
# The following code is based on the arrangement of the widgets in the table
# Modify the code if widgets are arranged differently or the table structure
# is changed
for n_col in range(self.table.columnCount()):
wd = self.table.cellWidget(n_row, n_col)
if n_col == 0:
# Combo box: update both QComboBox and QWidget backgrounds
# QWidget - background of the drop-down selection list
css1 = get_background_css(rgb,
widget="QComboBox",
editable=False)
css2 = get_background_css(rgb, widget="QWidget", editable=True)
wd.setStyleSheet(css2 + css1)
elif n_col <= 3:
# 3 QRadioButton's. The buttons are inserted into QWidget objects,
# and we need to change backgrounds of QWidgets, not only buttons.
wd.setStyleSheet(
get_background_css(rgb, widget="QWidget", editable=False))
elif n_col == 4:
# Custom RangeManager widget, color is updated using custom method
wd.setBackground(rgb)
n_col = self._rgb_color_keys.index(color_key)
for n, n_btn in enumerate(self.elements_rb_color[n_row]):
check_status = True if n == n_col else False
n_btn.setChecked(check_status)
def _fill_table(self):
self._enable_selection_events(False)
eline_list = [_[0] for _ in self._range_table]
for n_row in range(self.table.rowCount()):
self.elements_combo[n_row].clear()
self.elements_combo[n_row].addItems(eline_list)
for n_row, color in enumerate(self._rgb_color_keys):
# Initially set colors in order
self._set_row_color(n_row, color_key=color)
eline_key = self._rgb_dict[color]
if eline_key is not None:
try:
ind = eline_list.index(eline_key)
self.elements_combo[n_row].setCurrentIndex(ind)
range_low, range_high = self._range_table[ind][1:]
self.elements_range[n_row].set_range(range_low, range_high)
sel_low, sel_high = self._limit_table[ind][1:]
self.elements_range[n_row].set_selection(
value_low=sel_low, value_high=sel_high)
except ValueError:
pass
else:
self.elements_combo[n_row].setCurrentIndex(-1) # Deselect all
self.elements_range[n_row].set_range(0, 1)
self.elements_range[n_row].set_selection(value_low=0,
value_high=1)
self._enable_selection_events(True)
def _find_rbutton(self, button):
for nr, btns in enumerate(self.elements_rb_color):
for nc, btn in enumerate(btns):
if btn == button:
# Return tuple (nr, nc)
return nr, nc
# Return None if the button is not found (this shouldn't happen)
return None
def rb_toggled(self, button, state):
if state: # Ignore signals from unchecked buttons
nr, nc = self._find_rbutton(button)
color_current = self.row_colors[nr]
color_to_set = self._rgb_color_keys[nc]
nr_switch = self.row_colors.index(color_to_set)
self._enable_selection_events(False)
self._set_row_color(nr, color_key=color_to_set)
self._set_row_color(nr_switch, color_key=color_current)
# Swap selected maps
tmp = self._rgb_dict[color_to_set]
self._rgb_dict[color_to_set] = self._rgb_dict[color_current]
self._rgb_dict[color_current] = tmp
self._enable_selection_events(True)
self._update_map_selections()
def set_ranges_and_limits(self,
*,
range_table=None,
limit_table=None,
rgb_dict=None):
if range_table is not None:
self._range_table = copy.deepcopy(range_table)
if limit_table is not None:
self._limit_table = copy.deepcopy(limit_table)
if rgb_dict is not None:
self._rgb_dict = rgb_dict.copy()
self._fill_table()
def _update_map_selections(self):
"""Upload the selections (limit table) and update plot"""
self.signal_update_map_selections.emit()
class ReactionMask(QWidget):
"""The input mask for a reaction"""
def __init__(self, parent: ReactionList):
QWidget.__init__(self)
self.parent = parent
self.reaction = None
self.is_valid = True
self.changed = False
self.setAcceptDrops(False)
layout = QVBoxLayout()
l = QHBoxLayout()
self.delete_button = QPushButton("Delete reaction")
self.delete_button.setIcon(QIcon.fromTheme("edit-delete"))
policy = QSizePolicy()
policy.ShrinkFlag = True
self.delete_button.setSizePolicy(policy)
l.addWidget(self.delete_button)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Id:")
self.id = QLineEdit()
l.addWidget(label)
l.addWidget(self.id)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Name:")
self.name = QLineEdit()
l.addWidget(label)
l.addWidget(self.name)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Equation:")
self.equation = QLineEdit()
l.addWidget(label)
l.addWidget(self.equation)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Rate min:")
self.lower_bound = QLineEdit()
l.addWidget(label)
l.addWidget(self.lower_bound)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Rate max:")
self.upper_bound = QLineEdit()
l.addWidget(label)
l.addWidget(self.upper_bound)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Coefficient in obj. function:")
self.coefficent = QLineEdit()
l.addWidget(label)
l.addWidget(self.coefficent)
layout.addItem(l)
l = QHBoxLayout()
label = QLabel("Gene reaction rule:")
self.gene_reaction_rule = QLineEdit()
l.addWidget(label)
l.addWidget(self.gene_reaction_rule)
layout.addItem(l)
l = QVBoxLayout()
label = QLabel("Annotations:")
l.addWidget(label)
l2 = QHBoxLayout()
self.annotation = QTableWidget(0, 2)
self.annotation.setHorizontalHeaderLabels(
["key", "value"])
self.annotation.horizontalHeader().setSectionResizeMode(QHeaderView.Stretch)
l2.addWidget(self.annotation)
self.add_anno = QPushButton("+")
self.add_anno.clicked.connect(self.add_anno_row)
l2.addWidget(self.add_anno)
l.addItem(l2)
layout.addItem(l)
l = QVBoxLayout()
label = QLabel("Metabolites involved in this reaction:")
l.addWidget(label)
l2 = QHBoxLayout()
self.metabolites = QTreeWidget()
self.metabolites.setHeaderLabels(["Id"])
self.metabolites.setSortingEnabled(True)
l2.addWidget(self.metabolites)
l.addItem(l2)
self.metabolites.itemDoubleClicked.connect(
self.emit_jump_to_metabolite)
layout.addItem(l)
self.jump_list = JumpList(self)
layout.addWidget(self.jump_list)
self.setLayout(layout)
self.delete_button.clicked.connect(self.delete_reaction)
self.throttler = SignalThrottler(500)
self.throttler.triggered.connect(self.reaction_data_changed)
self.id.textEdited.connect(self.throttler.throttle)
self.name.textEdited.connect(self.throttler.throttle)
self.equation.textEdited.connect(self.throttler.throttle)
self.lower_bound.textEdited.connect(self.throttler.throttle)
self.upper_bound.textEdited.connect(self.throttler.throttle)
self.coefficent.textEdited.connect(self.throttler.throttle)
self.gene_reaction_rule.textEdited.connect(self.throttler.throttle)
self.annotation.itemChanged.connect(self.throttler.throttle)
self.validate_mask()
def add_anno_row(self):
i = self.annotation.rowCount()
self.annotation.insertRow(i)
self.changed = True
def apply(self):
try:
self.reaction.id = self.id.text()
except ValueError:
turn_red(self.id)
QMessageBox.information(
self, 'Invalid id', 'Could not apply changes identifier ' +
self.id.text() + ' already used.')
else:
self.reaction.name = self.name.text()
self.reaction.build_reaction_from_string(self.equation.text())
self.reaction.lower_bound = float(self.lower_bound.text())
self.reaction.upper_bound = float(self.upper_bound.text())
self.reaction.objective_coefficient = float(self.coefficent.text())
self.reaction.gene_reaction_rule = self.gene_reaction_rule.text()
self.reaction.annotation = {}
rows = self.annotation.rowCount()
for i in range(0, rows):
key = self.annotation.item(i, 0).text()
if self.annotation.item(i, 1) is None:
value = ""
else:
value = self.annotation.item(i, 1).text()
self.reaction.annotation[key] = value
self.changed = False
self.reactionChanged.emit(self.reaction)
def delete_reaction(self):
self.hide()
self.reactionDeleted.emit(self.reaction)
def validate_id(self):
with self.parent.appdata.project.cobra_py_model as model:
try:
r = cobra.Reaction(id=self.id.text())
model.add_reaction(r)
except ValueError:
turn_red(self.id)
return False
else:
turn_white(self.id)
return True
def validate_name(self):
with self.parent.appdata.project.cobra_py_model as model:
try:
r = cobra.Reaction(id="testid", name=self.name.text())
model.add_reaction(r)
except ValueError:
turn_red(self.name)
return False
else:
turn_white(self.name)
return True
def validate_equation(self):
ok = False
test_reaction = cobra.Reaction(
"xxxx_cnapy_test_reaction", name="cnapy test reaction")
with self.parent.appdata.project.cobra_py_model as model:
model.add_reaction(test_reaction)
try:
eqtxt = self.equation.text().rstrip()
if len(eqtxt) > 0 and eqtxt[-1] == '+':
turn_red(self.equation)
else:
test_reaction.build_reaction_from_string(eqtxt)
turn_white(self.equation)
ok = True
except ValueError:
turn_red(self.equation)
try:
test_reaction = self.parent.appdata.project.cobra_py_model.reactions.get_by_id(
"xxxx_cnapy_test_reaction")
self.parent.appdata.project.cobra_py_model.remove_reactions(
[test_reaction], remove_orphans=True)
except KeyError:
pass
return ok
def validate_lowerbound(self):
try:
_x = float(self.lower_bound.text())
except ValueError:
turn_red(self.lower_bound)
return False
else:
turn_white(self.lower_bound)
return True
def validate_upperbound(self):
try:
_x = float(self.upper_bound.text())
except ValueError:
turn_red(self.upper_bound)
return False
else:
turn_white(self.upper_bound)
return True
def validate_coefficient(self):
try:
_x = float(self.coefficent.text())
except ValueError:
turn_red(self.coefficent)
return False
else:
turn_white(self.coefficent)
return True
def validate_gene_reaction_rule(self):
try:
_x = float(self.gene_reaction_rule.text())
except ValueError:
turn_red(self.gene_reaction_rule)
return False
else:
turn_white(self.gene_reaction_rule)
return True
def validate_mask(self):
valid_id = self.validate_id()
valid_name = self.validate_name()
valid_equation = self.validate_equation()
valid_lb = self.validate_lowerbound()
valid_ub = self.validate_upperbound()
valid_coefficient = self.validate_coefficient()
if valid_id & valid_name & valid_equation & valid_lb & valid_ub & valid_coefficient:
self.is_valid = True
else:
self.is_valid = False
def reaction_data_changed(self):
self.changed = True
self.validate_mask()
if self.is_valid:
self.apply()
self.update_state()
def update_state(self):
self.jump_list.clear()
for name, m in self.parent.appdata.project.maps.items():
if self.id.text() in m["boxes"]:
self.jump_list.add(name)
self.metabolites.clear()
if self.parent.appdata.project.cobra_py_model.reactions.has_id(self.id.text()):
reaction = self.parent.appdata.project.cobra_py_model.reactions.get_by_id(
self.id.text())
for m in reaction.metabolites:
item = QTreeWidgetItem(self.metabolites)
item.setText(0, m.id)
item.setText(1, m.name)
item.setData(2, 0, m)
text = "Id: " + m.id + "\nName: " + m.name
item.setToolTip(1, text)
def emit_jump_to_map(self, name):
self.jumpToMap.emit(name, self.id.text())
def emit_jump_to_metabolite(self, metabolite):
self.jumpToMetabolite.emit(str(metabolite.data(2, 0)))
jumpToMap = Signal(str, str)
jumpToMetabolite = Signal(str)
reactionChanged = Signal(cobra.Reaction)
reactionDeleted = Signal(cobra.Reaction)
class MCSDialog(QDialog):
"""A dialog to perform minimal cut set computation"""
def __init__(self, appdata: CnaData, centralwidget):
QDialog.__init__(self)
self.setWindowTitle("Minimal Cut Sets Computation")
self.appdata = appdata
self.centralwidget = centralwidget
self.eng = appdata.engine
self.out = io.StringIO()
self.err = io.StringIO()
self.layout = QVBoxLayout()
l1 = QLabel("Target Region(s)")
self.layout.addWidget(l1)
s1 = QHBoxLayout()
completer = QCompleter(
self.appdata.project.cobra_py_model.reactions.list_attr("id"), self)
completer.setCaseSensitivity(Qt.CaseInsensitive)
self.target_list = QTableWidget(1, 4)
self.target_list.setHorizontalHeaderLabels(
["region no", "T", "≥/≤", "t"])
self.target_list.horizontalHeader().setSectionResizeMode(QHeaderView.Stretch)
self.target_list.horizontalHeader().setSectionResizeMode(0, QHeaderView.Fixed)
self.target_list.horizontalHeader().resizeSection(0, 100)
self.target_list.horizontalHeader().setSectionResizeMode(2, QHeaderView.Fixed)
self.target_list.horizontalHeader().resizeSection(2, 50)
item = QLineEdit("1")
self.target_list.setCellWidget(0, 0, item)
item2 = QLineEdit("")
item2.setCompleter(completer)
self.target_list.setCellWidget(0, 1, item2)
combo = QComboBox(self.target_list)
combo.insertItem(1, "≤")
combo.insertItem(2, "≥")
self.target_list.setCellWidget(0, 2, combo)
item = QLineEdit("0")
self.target_list.setCellWidget(0, 3, item)
s1.addWidget(self.target_list)
s11 = QVBoxLayout()
self.add_target = QPushButton("+")
self.add_target.clicked.connect(self.add_target_region)
self.rem_target = QPushButton("-")
self.rem_target.clicked.connect(self.rem_target_region)
s11.addWidget(self.add_target)
s11.addWidget(self.rem_target)
s1.addItem(s11)
self.layout.addItem(s1)
l2 = QLabel("Desired Region(s)")
self.layout.addWidget(l2)
s2 = QHBoxLayout()
self.desired_list = QTableWidget(1, 4)
self.desired_list.setHorizontalHeaderLabels(
["region no", "D", "≥/≤", "d"])
self.desired_list.horizontalHeader().setSectionResizeMode(QHeaderView.Stretch)
self.desired_list.horizontalHeader().setSectionResizeMode(0, QHeaderView.Fixed)
self.desired_list.horizontalHeader().resizeSection(0, 100)
self.desired_list.horizontalHeader().setSectionResizeMode(2, QHeaderView.Fixed)
self.desired_list.horizontalHeader().resizeSection(2, 50)
item = QLineEdit("1")
self.desired_list.setCellWidget(0, 0, item)
item2 = QLineEdit("")
item2.setCompleter(completer)
self.desired_list.setCellWidget(0, 1, item2)
combo = QComboBox(self.desired_list)
combo.insertItem(1, "≤")
combo.insertItem(2, "≥")
self.desired_list.setCellWidget(0, 2, combo)
item = QLineEdit("0")
self.desired_list.setCellWidget(0, 3, item)
s2.addWidget(self.desired_list)
s21 = QVBoxLayout()
self.add_desire = QPushButton("+")
self.add_desire.clicked.connect(self.add_desired_region)
self.rem_desire = QPushButton("-")
self.rem_desire.clicked.connect(self.rem_desired_region)
s21.addWidget(self.add_desire)
s21.addWidget(self.rem_desire)
s2.addItem(s21)
self.layout.addItem(s2)
s3 = QHBoxLayout()
sgx = QVBoxLayout()
self.gen_kos = QCheckBox("Gene KOs")
self.exclude_boundary = QCheckBox(
"Exclude boundary\nreactions as cuts")
sg1 = QHBoxLayout()
s31 = QVBoxLayout()
l = QLabel("Max. Solutions")
s31.addWidget(l)
l = QLabel("Max. Size")
s31.addWidget(l)
l = QLabel("Time Limit [sec]")
s31.addWidget(l)
sg1.addItem(s31)
s32 = QVBoxLayout()
self.max_solu = QLineEdit("inf")
self.max_solu.setMaximumWidth(50)
s32.addWidget(self.max_solu)
self.max_size = QLineEdit("7")
self.max_size.setMaximumWidth(50)
s32.addWidget(self.max_size)
self.time_limit = QLineEdit("inf")
self.time_limit.setMaximumWidth(50)
s32.addWidget(self.time_limit)
sg1.addItem(s32)
sgx.addWidget(self.gen_kos)
sgx.addWidget(self.exclude_boundary)
sgx.addItem(sg1)
s3.addItem(sgx)
g3 = QGroupBox("Solver")
s33 = QVBoxLayout()
self.bg1 = QButtonGroup()
optlang_solver_name = interface_to_str(
appdata.project.cobra_py_model.problem)
self.solver_optlang = QRadioButton(f"{optlang_solver_name} (optlang)")
self.solver_optlang.setToolTip(
"Uses the solver specified by the current model.")
s33.addWidget(self.solver_optlang)
self.bg1.addButton(self.solver_optlang)
self.solver_cplex_matlab = QRadioButton("CPLEX (MATLAB)")
self.solver_cplex_matlab.setToolTip(
"Only enabled with MATLAB and CPLEX")
s33.addWidget(self.solver_cplex_matlab)
self.bg1.addButton(self.solver_cplex_matlab)
self.solver_cplex_java = QRadioButton("CPLEX (Octave)")
self.solver_cplex_java.setToolTip("Only enabled with Octave and CPLEX")
s33.addWidget(self.solver_cplex_java)
self.bg1.addButton(self.solver_cplex_java)
self.solver_intlinprog = QRadioButton("intlinprog (MATLAB)")
self.solver_intlinprog.setToolTip("Only enabled with MATLAB")
s33.addWidget(self.solver_intlinprog)
self.bg1.addButton(self.solver_intlinprog)
self.solver_glpk = QRadioButton("GLPK (Octave/MATLAB)")
s33.addWidget(self.solver_glpk)
self.bg1.addButton(self.solver_glpk)
self.bg1.buttonClicked.connect(self.configure_solver_options)
g3.setLayout(s33)
s3.addWidget(g3)
g4 = QGroupBox("MCS search")
s34 = QVBoxLayout()
self.bg2 = QButtonGroup()
self.any_mcs = QRadioButton("any MCS (fast)")
self.any_mcs.setChecked(True)
s34.addWidget(self.any_mcs)
self.bg2.addButton(self.any_mcs)
# Search type: by cardinality only with CPLEX possible
self.mcs_by_cardinality = QRadioButton("by cardinality")
s34.addWidget(self.mcs_by_cardinality)
self.bg2.addButton(self.mcs_by_cardinality)
self.smalles_mcs_first = QRadioButton("smallest MCS first")
s34.addWidget(self.smalles_mcs_first)
self.bg2.addButton(self.smalles_mcs_first)
g4.setLayout(s34)
s3.addWidget(g4)
self.layout.addItem(s3)
# Disable incompatible combinations
if appdata.selected_engine == 'None':
self.solver_optlang.setChecked(True)
self.solver_cplex_matlab.setEnabled(False)
self.solver_cplex_java.setEnabled(False)
self.solver_glpk.setEnabled(False)
self.solver_intlinprog.setEnabled(False)
if optlang_solver_name != 'cplex':
self.mcs_by_cardinality.setEnabled(False)
else:
self.solver_glpk.setChecked(True)
if not self.eng.is_cplex_matlab_ready():
self.solver_cplex_matlab.setEnabled(False)
if not self.eng.is_cplex_java_ready():
self.solver_cplex_java.setEnabled(False)
if self.appdata.is_matlab_set():
self.solver_cplex_java.setEnabled(False)
if not self.appdata.is_matlab_set():
self.solver_cplex_matlab.setEnabled(False)
self.solver_intlinprog.setEnabled(False)
self.configure_solver_options()
s4 = QVBoxLayout()
self.consider_scenario = QCheckBox(
"Consider constraint given by scenario")
s4.addWidget(self.consider_scenario)
self.advanced = QCheckBox(
"Advanced: Define knockout/addition costs for genes/reactions")
self.advanced.setEnabled(False)
s4.addWidget(self.advanced)
self.layout.addItem(s4)
buttons = QHBoxLayout()
# self.save = QPushButton("save")
# buttons.addWidget(self.save)
# self.load = QPushButton("load")
# buttons.addWidget(self.load)
self.compute_mcs = QPushButton("Compute MCS")
buttons.addWidget(self.compute_mcs)
# self.compute_mcs2 = QPushButton("Compute MCS2")
# buttons.addWidget(self.compute_mcs2)
self.cancel = QPushButton("Close")
buttons.addWidget(self.cancel)
self.layout.addItem(buttons)
# max width for buttons
self.add_target.setMaximumWidth(20)
self.rem_target.setMaximumWidth(20)
self.add_desire.setMaximumWidth(20)
self.rem_desire.setMaximumWidth(20)
self.setLayout(self.layout)
# Connecting the signal
self.cancel.clicked.connect(self.reject)
self.compute_mcs.clicked.connect(self.compute)
@Slot()
def configure_solver_options(self):
optlang_solver_name = interface_to_str(
self.appdata.project.cobra_py_model.problem)
if self.solver_optlang.isChecked():
self.gen_kos.setChecked(False)
self.gen_kos.setEnabled(False)
self.exclude_boundary.setEnabled(True)
if optlang_solver_name != 'cplex':
if self.mcs_by_cardinality.isChecked():
self.mcs_by_cardinality.setChecked(False)
self.any_mcs.setChecked(True)
self.mcs_by_cardinality.setEnabled(False)
self.mcs_by_cardinality.setChecked(False)
else:
self.gen_kos.setEnabled(True)
self.exclude_boundary.setChecked(False)
self.exclude_boundary.setEnabled(False)
self.mcs_by_cardinality.setEnabled(True)
def add_target_region(self):
i = self.target_list.rowCount()
self.target_list.insertRow(i)
completer = QCompleter(
self.appdata.project.cobra_py_model.reactions.list_attr("id"), self)
completer.setCaseSensitivity(Qt.CaseInsensitive)
item = QLineEdit("1")
self.target_list.setCellWidget(i, 0, item)
item2 = QLineEdit("")
item2.setCompleter(completer)
self.target_list.setCellWidget(i, 1, item2)
combo = QComboBox(self.target_list)
combo.insertItem(1, "≤")
combo.insertItem(2, "≥")
self.target_list.setCellWidget(i, 2, combo)
item = QLineEdit("0")
self.target_list.setCellWidget(i, 3, item)
def add_desired_region(self):
i = self.desired_list.rowCount()
self.desired_list.insertRow(i)
completer = QCompleter(
self.appdata.project.cobra_py_model.reactions.list_attr("id"), self)
completer.setCaseSensitivity(Qt.CaseInsensitive)
item = QLineEdit("1")
self.desired_list.setCellWidget(i, 0, item)
item2 = QLineEdit("")
item2.setCompleter(completer)
self.desired_list.setCellWidget(i, 1, item2)
combo = QComboBox(self.desired_list)
combo.insertItem(1, "≤")
combo.insertItem(2, "≥")
self.desired_list.setCellWidget(i, 2, combo)
item = QLineEdit("0")
self.desired_list.setCellWidget(i, 3, item)
def rem_target_region(self):
i = self.target_list.rowCount()
self.target_list.removeRow(i-1)
def rem_desired_region(self):
i = self.desired_list.rowCount()
self.desired_list.removeRow(i-1)
def compute(self):
if self.solver_optlang.isChecked():
self.compute_optlang()
else:
self.compute_legacy()
def compute_legacy(self):
self.setCursor(Qt.BusyCursor)
# create CobraModel for matlab
with self.appdata.project.cobra_py_model as model:
if self.consider_scenario.isChecked(): # integrate scenario into model bounds
for r in self.appdata.project.scen_values.keys():
model.reactions.get_by_id(
r).bounds = self.appdata.project.scen_values[r]
cobra.io.save_matlab_model(model, os.path.join(
self.appdata.cna_path, "cobra_model.mat"), varname="cbmodel")
self.eng.eval("load('cobra_model.mat')",
nargout=0)
try:
self.eng.eval("cnap = CNAcobra2cna(cbmodel);",
nargout=0,
stdout=self.out, stderr=self.err)
except Exception:
output = io.StringIO()
traceback.print_exc(file=output)
exstr = output.getvalue()
print(exstr)
QMessageBox.warning(self, 'Unknown exception occured!',
exstr+'\nPlease report the problem to:\n\
\nhttps://github.com/cnapy-org/CNApy/issues')
return
self.eng.eval("genes = [];", nargout=0,
stdout=self.out, stderr=self.err)
cmd = "maxSolutions = " + str(float(self.max_solu.text())) + ";"
self.eng.eval(cmd, nargout=0, stdout=self.out, stderr=self.err)
cmd = "maxSize = " + str(int(self.max_size.text())) + ";"
self.eng.eval(cmd, nargout=0, stdout=self.out, stderr=self.err)
cmd = "milp_time_limit = " + str(float(self.time_limit.text())) + ";"
self.eng.eval(cmd, nargout=0, stdout=self.out, stderr=self.err)
if self.gen_kos.isChecked():
self.eng.eval("gKOs = 1;", nargout=0)
else:
self.eng.eval("gKOs = 0;", nargout=0)
if self.advanced.isChecked():
self.eng.eval("advanced_on = 1;", nargout=0)
else:
self.eng.eval("advanced_on = 0;", nargout=0)
if self.solver_intlinprog.isChecked():
self.eng.eval("solver = 'intlinprog';", nargout=0)
if self.solver_cplex_java.isChecked():
self.eng.eval("solver = 'java_cplex_new';", nargout=0)
if self.solver_cplex_matlab.isChecked():
self.eng.eval("solver = 'matlab_cplex';", nargout=0)
if self.solver_glpk.isChecked():
self.eng.eval("solver = 'glpk';", nargout=0)
if self.any_mcs.isChecked():
self.eng.eval("mcs_search_mode = 'search_1';", nargout=0)
elif self.mcs_by_cardinality.isChecked():
self.eng.eval("mcs_search_mode = 'search_2';", nargout=0)
elif self.smalles_mcs_first.isChecked():
self.eng.eval("mcs_search_mode = 'search_3';", nargout=0)
rows = self.target_list.rowCount()
for i in range(0, rows):
p1 = self.target_list.cellWidget(i, 0).text()
p2 = self.target_list.cellWidget(i, 1).text()
if self.target_list.cellWidget(i, 2).currentText() == '≤':
p3 = "<="
else:
p3 = ">="
p4 = self.target_list.cellWidget(i, 3).text()
cmd = "dg_T = {[" + p1+"], '" + p2 + \
"', '" + p3 + "', [" + p4 + "']};"
self.eng.eval(cmd, nargout=0,
stdout=self.out, stderr=self.err)
rows = self.desired_list.rowCount()
for i in range(0, rows):
p1 = self.desired_list.cellWidget(i, 0).text()
p2 = self.desired_list.cellWidget(i, 1).text()
if self.desired_list.cellWidget(i, 2).currentText() == '≤':
p3 = "<="
else:
p3 = ">="
p4 = self.desired_list.cellWidget(i, 3).text()
cmd = "dg_D = {[" + p1+"], '" + p2 + \
"', '" + p3 + "', [" + p4 + "']};"
self.eng.eval(cmd, nargout=0)
# get some data
self.eng.eval("reac_id = cellstr(cnap.reacID).';",
nargout=0, stdout=self.out, stderr=self.err)
mcs = []
values = []
reactions = []
reac_id = []
if self.appdata.is_matlab_set():
reac_id = self.eng.workspace['reac_id']
try:
self.eng.eval("[mcs] = cnapy_compute_mcs(cnap, genes, maxSolutions, maxSize, milp_time_limit, gKOs, advanced_on, solver, mcs_search_mode, dg_T,dg_D);",
nargout=0)
except Exception:
output = io.StringIO()
traceback.print_exc(file=output)
exstr = output.getvalue()
print(exstr)
QMessageBox.warning(self, 'Unknown exception occured!',
exstr+'\nPlease report the problem to:\n\
\nhttps://github.com/cnapy-org/CNApy/issues')
return
else:
self.eng.eval("[reaction, mcs, value] = find(mcs);", nargout=0,
stdout=self.out, stderr=self.err)
reactions = self.eng.workspace['reaction']
mcs = self.eng.workspace['mcs']
values = self.eng.workspace['value']
elif self.appdata.is_octave_ready():
reac_id = self.eng.pull('reac_id')
reac_id = reac_id[0]
try:
self.eng.eval("[mcs] = cnapy_compute_mcs(cnap, genes, maxSolutions, maxSize, milp_time_limit, gKOs, advanced_on, solver, mcs_search_mode, dg_T,dg_D);",
nargout=0)
except Exception:
output = io.StringIO()
traceback.print_exc(file=output)
exstr = output.getvalue()
print(exstr)
QMessageBox.warning(self, 'Unknown exception occured!',
exstr+'\nPlease report the problem to:\n\
\nhttps://github.com/cnapy-org/CNApy/issues')
return
else:
self.eng.eval("[reaction, mcs, value] = find(mcs);", nargout=0,
stdout=self.out, stderr=self.err)
reactions = self.eng.pull('reaction')
mcs = self.eng.pull('mcs')
values = self.eng.pull('value')
if len(mcs) == 0:
QMessageBox.information(self, 'No cut sets',
'Cut sets have not been calculated or do not exist.')
else:
last_mcs = 1
omcs = []
current_mcs = {}
for i in range(0, len(reactions)):
reacid = int(reactions[i][0])
reaction = reac_id[reacid-1]
c_mcs = int(mcs[i][0])
c_value = int(values[i][0])
if c_value == -1: # -1 stands for removed which is 0 in the ui
c_value = 0
if c_mcs > last_mcs:
omcs.append(current_mcs)
last_mcs = c_mcs
current_mcs = {}
current_mcs[reaction] = c_value
omcs.append(current_mcs)
self.appdata.project.modes = omcs
self.centralwidget.mode_navigator.current = 0
QMessageBox.information(self, 'Cut sets found',
str(len(omcs))+' Cut sets have been calculated.')
self.centralwidget.update_mode()
self.centralwidget.mode_navigator.title.setText("MCS Navigation")
self.setCursor(Qt.ArrowCursor)
def compute_optlang(self):
self.setCursor(Qt.BusyCursor)
max_mcs_num = float(self.max_solu.text())
max_mcs_size = int(self.max_size.text())
timeout = float(self.time_limit.text())
if timeout is float('inf'):
timeout = None
# if self.gen_kos.isChecked():
# self.eng.eval("gKOs = 1;", nargout=0)
# else:
# self.eng.eval("gKOs = 0;", nargout=0)
# if self.advanced.isChecked():
# self.eng.eval("advanced_on = 1;", nargout=0)
# else:
# self.eng.eval("advanced_on = 0;", nargout=0)
if self.smalles_mcs_first.isChecked():
enum_method = 1
elif self.mcs_by_cardinality.isChecked():
enum_method = 2
elif self.any_mcs.isChecked():
enum_method = 3
with self.appdata.project.cobra_py_model as model:
if self.consider_scenario.isChecked(): # integrate scenario into model bounds
for r in self.appdata.project.scen_values.keys():
model.reactions.get_by_id(
r).bounds = self.appdata.project.scen_values[r]
reac_id = model.reactions.list_attr("id")
reac_id_symbols = cMCS_enumerator.get_reac_id_symbols(reac_id)
rows = self.target_list.rowCount()
targets = dict()
for i in range(0, rows):
p1 = self.target_list.cellWidget(i, 0).text()
p2 = self.target_list.cellWidget(i, 1).text()
if len(p1) > 0 and len(p2) > 0:
if self.target_list.cellWidget(i, 2).currentText() == '≤':
p3 = "<="
else:
p3 = ">="
p4 = float(self.target_list.cellWidget(i, 3).text())
targets.setdefault(p1, []).append((p2, p3, p4))
targets = list(targets.values())
targets = [cMCS_enumerator.relations2leq_matrix(cMCS_enumerator.parse_relations(
t, reac_id_symbols=reac_id_symbols), reac_id) for t in targets]
rows = self.desired_list.rowCount()
desired = dict()
for i in range(0, rows):
p1 = self.desired_list.cellWidget(i, 0).text()
p2 = self.desired_list.cellWidget(i, 1).text()
if len(p1) > 0 and len(p2) > 0:
if self.desired_list.cellWidget(i, 2).currentText() == '≤':
p3 = "<="
else:
p3 = ">="
p4 = float(self.desired_list.cellWidget(i, 3).text())
desired.setdefault(p1, []).append((p2, p3, p4))
desired = list(desired.values())
desired = [cMCS_enumerator.relations2leq_matrix(cMCS_enumerator.parse_relations(
d, reac_id_symbols=reac_id_symbols), reac_id) for d in desired]
try:
mcs = cMCS_enumerator.compute_mcs(model,
targets=targets,
desired=desired,
enum_method=enum_method,
max_mcs_size=max_mcs_size,
max_mcs_num=max_mcs_num,
timeout=timeout,
exclude_boundary_reactions_as_cuts=self.exclude_boundary.isChecked())
except cMCS_enumerator.InfeasibleRegion as e:
QMessageBox.warning(self, 'Cannot calculate MCS', str(e))
return targets, desired
except Exception:
output = io.StringIO()
traceback.print_exc(file=output)
exstr = output.getvalue()
print(exstr)
QMessageBox.warning(self, 'An exception has occured!',
exstr+'\nPlease report the problem to:\n\
\nhttps://github.com/cnapy-org/CNApy/issues')
return targets, desired
finally:
self.setCursor(Qt.ArrowCursor)
if len(mcs) == 0:
QMessageBox.information(self, 'No cut sets',
'Cut sets have not been calculated or do not exist.')
return targets, desired
omcs = [{reac_id[i]: 0 for i in m} for m in mcs]
self.appdata.project.modes = omcs
self.centralwidget.mode_navigator.current = 0
QMessageBox.information(self, 'Cut sets found',
str(len(omcs))+' Cut sets have been calculated.')
self.centralwidget.update_mode()
self.centralwidget.mode_navigator.title.setText("MCS Navigation")
class LogViewerDialog(DialogBase):
"""Logger widget."""
def __init__(
self,
parent=None,
log_folder=LOG_FOLDER,
log_filename=LOG_FILENAME,
):
"""
Logger widget.
Parameters
----------
log_folder: str
Folder where logs are located
log_filename: str
Basic name for the rotating log files.
"""
super(LogViewerDialog, self).__init__(parent=parent)
self._data = None
self._columns = ['level', 'time', 'module', 'method', 'message']
self._headers = [c.capitalize() for c in self._columns]
self._log_filename = log_filename
self._log_folder = log_folder
# Widgets
self.label = QLabel('Select log file:')
self.combobox = ComboBoxBase()
self.table_logs = QTableWidget(self)
self.button_copy = ButtonPrimary('Copy')
self.text_search = LineEditSearch()
# Widget setup
self.table_logs.setAttribute(Qt.WA_LayoutUsesWidgetRect, True)
horizontal_header = self.table_logs.horizontalHeader()
vertical_header = self.table_logs.verticalHeader()
horizontal_header.setStretchLastSection(True)
horizontal_header.setSectionResizeMode(QHeaderView.Fixed)
vertical_header.setSectionResizeMode(QHeaderView.Fixed)
self.table_logs.setSelectionBehavior(QTableWidget.SelectRows)
self.table_logs.setEditTriggers(QTableWidget.NoEditTriggers)
self.setWindowTitle('Log Viewer')
self.setMinimumWidth(800)
self.setMinimumHeight(500)
self.text_search.setPlaceholderText("Search...")
# Layouts
top_layout = QHBoxLayout()
top_layout.addWidget(self.label)
top_layout.addWidget(SpacerHorizontal())
top_layout.addWidget(self.combobox)
top_layout.addStretch()
top_layout.addWidget(SpacerHorizontal())
top_layout.addWidget(self.text_search)
top_layout.addWidget(SpacerHorizontal())
top_layout.addWidget(self.button_copy)
layout = QVBoxLayout()
layout.addLayout(top_layout)
layout.addWidget(SpacerVertical())
layout.addWidget(self.table_logs)
self.setLayout(layout)
# Signals
self.combobox.currentIndexChanged.connect(self.update_text)
self.button_copy.clicked.connect(self.copy_item)
self.text_search.textChanged.connect(self.filter_text)
# Setup()
self.setup()
self.update_style_sheet()
def update_style_sheet(self, style_sheet=None):
"""Update custom CSS stylesheet."""
if style_sheet is None:
style_sheet = load_style_sheet()
self.setStyleSheet(style_sheet)
def setup(self):
"""Setup widget content."""
self.combobox.clear()
paths = log_files(
log_folder=self._log_folder,
log_filename=self._log_filename,
)
files = [os.path.basename(p) for p in paths]
self.combobox.addItems(files)
def filter_text(self):
"""Search for text in the selected log file."""
search = self.text_search.text().lower()
for i, data in enumerate(self._data):
if any(search in str(d).lower() for d in data.values()):
self.table_logs.showRow(i)
else:
self.table_logs.hideRow(i)
def row_data(self, row):
"""Give the current row data concatenated with spaces."""
data = {}
if self._data:
length = len(self._data)
if 0 >= row < length:
data = self._data[row]
return data
def update_text(self, index):
"""Update logs based on combobox selection."""
path = os.path.join(self._log_folder, self.combobox.currentText())
self._data = load_log(path)
self.table_logs.clear()
self.table_logs.setSortingEnabled(False)
self.table_logs.setRowCount(len(self._data))
self.table_logs.setColumnCount(len(self._columns))
self.table_logs.setHorizontalHeaderLabels(self._headers)
for row, data in enumerate(self._data):
for col, col_key in enumerate(self._columns):
item = QTableWidgetItem(data.get(col_key, ''))
self.table_logs.setItem(row, col, item)
for c in [0, 2, 3]:
self.table_logs.resizeColumnToContents(c)
self.table_logs.resizeRowsToContents()
self.table_logs.setSortingEnabled(True)
self.table_logs.scrollToBottom()
self.table_logs.scrollToTop()
self.table_logs.sortByColumn(1, Qt.AscendingOrder)
# Make sure there is always a selected row
self.table_logs.setCurrentCell(0, 0)
def copy_item(self):
"""Copy selected item to clipboard in markdown format."""
app = QApplication.instance()
items = self.table_logs.selectedIndexes()
if items:
rows = set(sorted(i.row() for i in items))
if self._data:
all_data = [self._data[row] for row in rows]
dump = json.dumps(all_data, sort_keys=True, indent=4)
app.clipboard().setText('```json\n' + dump + '\n```')
def add_table(self):
"""Add table with info about files to be recovered."""
table = QTableWidget(len(self.data), 3, self)
self.table = table
labels = [_('Original file'), _('Autosave file'), _('Actions')]
table.setHorizontalHeaderLabels(labels)
table.verticalHeader().hide()
table.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
table.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
table.setSelectionMode(QTableWidget.NoSelection)
# Show horizontal grid lines
table.setShowGrid(False)
table.setStyleSheet('::item { border-bottom: 1px solid gray }')
for idx, (original, autosave) in enumerate(self.data):
self.add_label_to_table(idx, 0, file_data_to_str(original))
self.add_label_to_table(idx, 1, file_data_to_str(autosave))
widget = QWidget()
layout = QHBoxLayout()
tooltip = _('Recover the autosave file to its original location, '
'replacing the original if it exists.')
button = QPushButton(_('Restore'))
button.setToolTip(tooltip)
button.clicked.connect(
lambda checked, my_idx=idx: self.restore(my_idx))
layout.addWidget(button)
tooltip = _('Delete the autosave file.')
button = QPushButton(_('Discard'))
button.setToolTip(tooltip)
button.clicked.connect(
lambda checked, my_idx=idx: self.discard(my_idx))
layout.addWidget(button)
tooltip = _('Display the autosave file (and the original, if it '
'exists) in Spyder\'s Editor. You will have to move '
'or delete it manually.')
button = QPushButton(_('Open'))
button.setToolTip(tooltip)
button.clicked.connect(
lambda checked, my_idx=idx: self.open_files(my_idx))
layout.addWidget(button)
widget.setLayout(layout)
self.table.setCellWidget(idx, 2, widget)
table.resizeRowsToContents()
table.resizeColumnsToContents()
# Need to add the "+ 2" because otherwise the table scrolls a tiny
# amount; no idea why
width = table.horizontalHeader().length() + 2
height = (table.verticalHeader().length() +
table.horizontalHeader().height() + 2)
table.setFixedSize(width, height)
self.layout.addWidget(table)
class ShortcutEditor(QWidget):
"""Widget to edit keybindings for napari."""
valueChanged = Signal(dict)
VIEWER_KEYBINDINGS = trans._('Viewer key bindings')
def __init__(
self,
parent: QWidget = None,
description: str = "",
value: dict = None,
):
super().__init__(parent=parent)
# Flag to not run _set_keybinding method after setting special symbols.
# When changing line edit to special symbols, the _set_keybinding
# method will be called again (and breaks) and is not needed.
self._skip = False
layers = [
Image,
Labels,
Points,
Shapes,
Surface,
Vectors,
]
self.key_bindings_strs = OrderedDict()
# widgets
self.layer_combo_box = QComboBox(self)
self._label = QLabel(self)
self._table = QTableWidget(self)
self._table.setSelectionBehavior(QAbstractItemView.SelectItems)
self._table.setSelectionMode(QAbstractItemView.SingleSelection)
self._table.setShowGrid(False)
self._restore_button = QPushButton(trans._("Reset All Keybindings"))
# Set up dictionary for layers and associated actions.
all_actions = action_manager._actions.copy()
self.key_bindings_strs[self.VIEWER_KEYBINDINGS] = []
for layer in layers:
if len(layer.class_keymap) == 0:
actions = []
else:
actions = action_manager._get_layer_actions(layer)
for name, action in actions.items():
all_actions.pop(name)
self.key_bindings_strs[f"{layer.__name__} layer"] = actions
# Left over actions can go here.
self.key_bindings_strs[self.VIEWER_KEYBINDINGS] = all_actions
# Widget set up
self.layer_combo_box.addItems(list(self.key_bindings_strs))
self.layer_combo_box.activated[str].connect(self._set_table)
self.layer_combo_box.setCurrentText(self.VIEWER_KEYBINDINGS)
self._set_table()
self._label.setText("Group")
self._restore_button.clicked.connect(self.restore_defaults)
# layout
hlayout1 = QHBoxLayout()
hlayout1.addWidget(self._label)
hlayout1.addWidget(self.layer_combo_box)
hlayout1.setContentsMargins(0, 0, 0, 0)
hlayout1.setSpacing(20)
hlayout1.addStretch(0)
hlayout2 = QHBoxLayout()
hlayout2.addLayout(hlayout1)
hlayout2.addWidget(self._restore_button)
layout = QVBoxLayout()
layout.addLayout(hlayout2)
layout.addWidget(self._table)
self.setLayout(layout)
def restore_defaults(self):
"""Launches dialog to confirm restore choice."""
self._reset_dialog = ConfirmDialog(
parent=self,
text=trans._(
"Are you sure you want to restore default shortcuts?"
),
)
self._reset_dialog.valueChanged.connect(self._reset_shortcuts)
self._reset_dialog.exec_()
def _reset_shortcuts(self, event=None):
"""Reset shortcuts to default settings.
Parameters
----------
event: Bool
Event will indicate whether user confirmed resetting shortcuts.
"""
# event is True if the user confirmed reset shortcuts
if event is True:
get_settings().reset(sections=['shortcuts'])
for (
action,
shortcuts,
) in get_settings().shortcuts.shortcuts.items():
action_manager.unbind_shortcut(action)
for shortcut in shortcuts:
action_manager.bind_shortcut(action, shortcut)
self._set_table(layer_str=self.layer_combo_box.currentText())
def _set_table(self, layer_str=''):
"""Builds and populates keybindings table.
Parameters
----------
layer_str = str
If layer_str is not empty, then show the specified layers'
keybinding shortcut table.
"""
# Keep track of what is in each column.
self._action_name_col = 0
self._icon_col = 1
self._shortcut_col = 2
self._action_col = 3
# Set header strings for table.
header_strs = ['', '', '', '']
header_strs[self._action_name_col] = trans._('Action')
header_strs[self._shortcut_col] = trans._('Keybinding')
# If no layer_str, then set the page to the viewer keybindings page.
if layer_str == '':
layer_str = self.VIEWER_KEYBINDINGS
# If rebuilding the table, then need to disconnect the connection made
# previously as well as clear the table contents.
try:
self._table.cellChanged.disconnect(self._set_keybinding)
except TypeError:
# if building the first time, the cells are not yet connected so this would fail.
pass
except RuntimeError:
# Needed to pass some tests.
pass
self._table.clearContents()
# Table styling set up.
self._table.horizontalHeader().setStretchLastSection(True)
self._table.horizontalHeader().setStyleSheet(
'border-bottom: 2px solid white;'
)
# Get all actions for the layer.
actions = self.key_bindings_strs[layer_str]
if len(actions) > 0:
# Set up table based on number of actions and needed columns.
self._table.setRowCount(len(actions))
self._table.setColumnCount(4)
# Set up delegate in order to capture keybindings.
self._table.setItemDelegateForColumn(
self._shortcut_col, ShortcutDelegate(self._table)
)
self._table.setHorizontalHeaderLabels(header_strs)
self._table.verticalHeader().setVisible(False)
# Hide the column with action names. These are kept here for reference when needed.
self._table.setColumnHidden(self._action_col, True)
# Column set up.
self._table.setColumnWidth(self._action_name_col, 250)
self._table.setColumnWidth(self._shortcut_col, 200)
self._table.setColumnWidth(self._icon_col, 50)
# Go through all the actions in the layer and add them to the table.
for row, (action_name, action) in enumerate(actions.items()):
shortcuts = action_manager._shortcuts.get(action_name, [])
# Set action description. Make sure its not selectable/editable.
item = QTableWidgetItem(action.description)
item.setFlags(Qt.NoItemFlags)
self._table.setItem(row, self._action_name_col, item)
# Create empty item in order to make sure this column is not
# selectable/editable.
item = QTableWidgetItem("")
item.setFlags(Qt.NoItemFlags)
self._table.setItem(row, self._icon_col, item)
# Set the shortcuts in table.
item_shortcut = QTableWidgetItem(
Shortcut(list(shortcuts)[0]).platform if shortcuts else ""
)
self._table.setItem(row, self._shortcut_col, item_shortcut)
# action_name is stored in the table to use later, but is not shown on dialog.
item_action = QTableWidgetItem(action_name)
self._table.setItem(row, self._action_col, item_action)
# If a cell is changed, run .set_keybinding.
self._table.cellChanged.connect(self._set_keybinding)
else:
# Display that there are no actions for this layer.
self._table.setRowCount(1)
self._table.setColumnCount(4)
self._table.setHorizontalHeaderLabels(header_strs)
self._table.verticalHeader().setVisible(False)
self._table.setColumnHidden(self._action_col, True)
item = QTableWidgetItem('No key bindings')
item.setFlags(Qt.NoItemFlags)
self._table.setItem(0, 0, item)
def _set_keybinding(self, row, col):
"""Checks the new keybinding to determine if it can be set.
Parameters
----------
row: int
Row in keybindings table that is being edited.
col: int
Column being edited (shortcut column).
"""
if self._skip is True:
# Do nothing if the text is setting to a symbol.
# Its already been handled.
self._skip = False
return
if col == self._shortcut_col:
# Get all layer actions and viewer actions in order to determine
# the new shortcut is not already set to an action.
current_layer_text = self.layer_combo_box.currentText()
layer_actions = self.key_bindings_strs[current_layer_text]
actions_all = layer_actions.copy()
if current_layer_text is not self.VIEWER_KEYBINDINGS:
viewer_actions = self.key_bindings_strs[
self.VIEWER_KEYBINDINGS
]
actions_all.update(viewer_actions)
# get the current item from shortcuts column
current_item = self._table.currentItem()
new_shortcut = current_item.text()
new_shortcut = new_shortcut[0].upper() + new_shortcut[1:]
# get the current action name
current_action = self._table.item(row, self._action_col).text()
# get the original shortcutS
current_shortcuts = list(
action_manager._shortcuts.get(current_action, {})
)
# Flag to indicate whether to set the new shortcut.
replace = True
# Go through all layer actions to determine if the new shortcut is already here.
for row1, (action_name, action) in enumerate(actions_all.items()):
shortcuts = action_manager._shortcuts.get(action_name, [])
if new_shortcut in shortcuts:
# Shortcut is here (either same action or not), don't replace in settings.
replace = False
if action_name != current_action:
# the shortcut is saved to a different action
# show warning symbols
self._show_warning_icons([row, row1])
# show warning message
message = trans._(
"The keybinding <b>{new_shortcut}</b> "
+ "is already assigned to <b>{action_description}</b>; change or clear "
+ "that shortcut before assigning <b>{new_shortcut}</b> to this one.",
new_shortcut=new_shortcut,
action_description=action.description,
)
self._show_warning(new_shortcut, action, row, message)
if len(current_shortcuts) > 0:
# If there was a shortcut set originally, then format it and reset the text.
format_shortcut = Shortcut(
current_shortcuts[0]
).platform
if format_shortcut != current_shortcuts[0]:
# only skip the next round if there are special symbols
self._skip = True
current_item.setText(format_shortcut)
else:
# There wasn't a shortcut here.
current_item.setText("")
self._cleanup_warning_icons([row, row1])
break
else:
# This shortcut was here. Reformat and reset text.
format_shortcut = Shortcut(new_shortcut).platform
if format_shortcut != new_shortcut:
# Only skip the next round if there are special symbols in shortcut.
self._skip = True
current_item.setText(format_shortcut)
if replace is True:
# This shortcut is not taken.
# Unbind current action from shortcuts in action manager.
action_manager.unbind_shortcut(current_action)
if new_shortcut != "":
# Bind the new shortcut.
try:
action_manager.bind_shortcut(
current_action, new_shortcut
)
except TypeError:
# Shortcut is not valid.
action_manager._shortcuts[current_action] = set()
# need to rebind the old shortcut
action_manager.unbind_shortcut(current_action)
action_manager.bind_shortcut(
current_action, current_shortcuts[0]
)
# Show warning message to let user know this shortcut is invalid.
self._show_warning_icons([row])
message = trans._(
"<b>{new_shortcut}</b> is not a valid keybinding.",
new_shortcut=new_shortcut,
)
self._show_warning(new_shortcut, action, row, message)
self._cleanup_warning_icons([row])
format_shortcut = Shortcut(
current_shortcuts[0]
).platform
if format_shortcut != current_shortcuts[0]:
# Skip the next round if there are special symbols.
self._skip = True
# Update text to formated shortcut.
current_item.setText(format_shortcut)
return
# The new shortcut is valid and can be displayed in widget.
# Keep track of what changed.
new_value_dict = {current_action: [new_shortcut]}
# Format new shortcut.
format_shortcut = Shortcut(new_shortcut).platform
if format_shortcut != new_shortcut:
# Skip the next round because there are special symbols.
self._skip = True
# Update text to formated shortcut.
current_item.setText(format_shortcut)
else:
# There is not a new shortcut to bind. Keep track of it.
if action_manager._shortcuts[current_action] != "":
new_value_dict = {current_action: [""]}
if new_value_dict:
# Emit signal when new value set for shortcut.
self.valueChanged.emit(new_value_dict)
def _show_warning_icons(self, rows):
"""Creates and displays the warning icons.
Parameters
----------
rows: list[int]
List of row numbers that should have the icon.
"""
for row in rows:
self.warning_indicator = QLabel(self)
self.warning_indicator.setObjectName("error_label")
self._table.setCellWidget(
row, self._icon_col, self.warning_indicator
)
def _cleanup_warning_icons(self, rows):
"""Remove the warning icons from the shortcut table.
Paramters
---------
rows: list[int]
List of row numbers to remove warning icon from.
"""
for row in rows:
self._table.setCellWidget(row, self._icon_col, QLabel(""))
def _show_warning(self, new_shortcut='', action=None, row=0, message=''):
"""Creates and displays warning message when shortcut is already assigned.
Parameters
----------
new_shortcut: str
The new shortcut attempting to be set.
action: Action
Action that is already assigned with the shortcut.
row: int
Row in table where the shortcut is attempting to be set.
message: str
Message to be displayed in warning pop up.
"""
# Determine placement of warning message.
delta_y = 105
delta_x = 10
global_point = self.mapToGlobal(
QPoint(
self._table.columnViewportPosition(self._shortcut_col)
+ delta_x,
self._table.rowViewportPosition(row) + delta_y,
)
)
# Create warning pop up and move it to desired position.
self._warn_dialog = KeyBindWarnPopup(
text=message,
)
self._warn_dialog.move(global_point)
# Styling adjustments.
self._warn_dialog.resize(250, self._warn_dialog.sizeHint().height())
self._warn_dialog._message.resize(
200, self._warn_dialog._message.sizeHint().height()
)
self._warn_dialog.exec_()
def value(self):
"""Return the actions and shortcuts currently assigned in action manager.
Returns
-------
value: dict
Dictionary of action names and shortcuts assigned to them.
"""
value = {}
for row, (action_name, action) in enumerate(
action_manager._actions.items()
):
shortcuts = action_manager._shortcuts.get(action_name, [])
value[action_name] = list(shortcuts)
return value
class PMGTableShow(BaseExtendedWidget):
default_bg = QTableWidgetItem().background()
default_fg = QTableWidgetItem().foreground()
def __init__(self,
layout_dir: str,
title: List[str],
initial_value: List[List[Union[int, float, str]]],
size_restricted=False,
header_adaption_h=False,
header_adaption_v=False,
background_color: List[List[Union[str]]] = None,
foreground_color: List[List[Union[str]]] = None):
super().__init__(layout_dir=layout_dir)
self.maximum_rows = 100
self.size_restricted = size_restricted
self.header_adaption_h = header_adaption_h
self.header_adaption_v = header_adaption_v
self.background_color = background_color if background_color is not None else ''
self.foreground_color = foreground_color if foreground_color is not None else ''
self.char_width = 15
self.on_check_callback = None
self.title_list = title
entryLayout = QHBoxLayout()
entryLayout.setContentsMargins(0, 0, 0, 0)
self.ctrl = QTableWidget()
self.ctrl.verticalHeader().setVisible(False)
self.set_params(size_restricted, header_adaption_h, header_adaption_v)
self.ctrl.setColumnCount(len(title))
self.ctrl.setHorizontalScrollBarPolicy(Qt.ScrollBarAsNeeded)
for i, text in enumerate(title):
self.ctrl.setColumnWidth(i, len(text) * self.char_width + 10)
self.ctrl.setHorizontalHeaderItem(i, QTableWidgetItem(text))
self.central_layout.addLayout(entryLayout)
entryLayout.addWidget(self.ctrl)
if initial_value is not None:
for sublist in initial_value:
assert len(sublist) == len(title), \
'title is not as long as sublist,%s,%s' % (repr(title), sublist)
self.ctrl.setRowCount(len(initial_value))
self.set_value(initial_value)
def set_params(self,
size_restricted=False,
header_adaption_h=False,
header_adaption_v=False):
self.size_restricted = size_restricted
self.header_adaption_h = header_adaption_h
self.header_adaption_v = header_adaption_v
if header_adaption_h:
self.ctrl.horizontalHeader().setSectionResizeMode(
QHeaderView.Stretch)
if header_adaption_v:
self.ctrl.verticalHeader().setSectionResizeMode(
QHeaderView.Stretch)
def check_data(self, value: List[List[Union[int, float, str]]]):
for sublist in value:
assert len(sublist) == len(self.title_list),\
'%s,%s' % (repr(sublist), repr(self.title_list))
def set_value(self, value: List[List[Union[int, float, str]]]):
self.check_data(value)
self.ctrl.setRowCount(len(value))
cols = len(value[0])
if isinstance(self.foreground_color, str):
fg = [[self.foreground_color for i in range(cols)]
for j in range(len(value))]
else:
fg = self.foreground_color
if isinstance(self.background_color, str):
bg = [[self.background_color for i in range(cols)]
for j in range(len(value))]
else:
bg = self.background_color
for row, row_list in enumerate(value):
for col, content in enumerate(row_list):
if len(str(content)) * self.char_width > self.ctrl.columnWidth(
col):
self.ctrl.setColumnWidth(
col,
len(str(content)) * self.char_width + 10)
table_item = QTableWidgetItem(str(content))
table_item.setTextAlignment(Qt.AlignCenter)
# 字体颜色（红色）
if fg[row][col] == '':
table_item.setForeground(self.default_fg)
else:
table_item.setForeground(
QBrush(QColor(*color_str2tup(fg[row][col]))))
# 背景颜色（红色）
if bg[row][col] == '':
table_item.setBackground(self.default_bg)
else:
table_item.setBackground(
QBrush(QColor(*color_str2tup(bg[row][col]))))
self.ctrl.setItem(row, col, table_item)
if self.size_restricted:
if self.header_adaption_h:
self.ctrl.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
scrollbar_area_width = 0
else:
self.ctrl.setHorizontalScrollBarPolicy(Qt.ScrollBarAsNeeded)
scrollbar_area_width = 10
self.ctrl.setMaximumHeight((self.ctrl.rowCount() + 1) * 30 +
scrollbar_area_width)
self.setMaximumHeight((self.ctrl.rowCount() + 1) * 30 +
scrollbar_area_width)
def alert(self, alert_level: int):
self.ctrl.alert(alert_level)
def add_row(self, row: List):
assert len(row) == self.ctrl.columnCount()
rc = self.ctrl.rowCount()
self.ctrl.setRowCount(rc + 1)
for i, val in enumerate(row):
self.ctrl.setItem(rc, i, QTableWidgetItem(str(val)))
if self.ctrl.rowCount() > self.maximum_rows:
self.ctrl.removeRow(0)
class DialogSelectQuantStandard(QDialog):
def __init__(self, parent=None):
super().__init__(parent)
self._qe_param_built_in = []
self._qe_param_custom = []
self._qe_standard_selected = None
self._qe_param = [] # The list of all standards
self._custom_label = [] # The list of booleans: True - the standard is custom, False -built-in
self.setWindowTitle("Load Quantitative Standard")
self.setMinimumHeight(500)
self.setMinimumWidth(600)
self.resize(600, 500)
self.selected_standard_index = -1
labels = ("C", "Serial #", "Name", "Description")
col_stretch = (
QHeaderView.ResizeToContents,
QHeaderView.ResizeToContents,
QHeaderView.ResizeToContents,
QHeaderView.Stretch,
)
self.table = QTableWidget()
set_tooltip(
self.table,
"To <b> load the sta"
"ndard</b>, double-click on the table row or "
"select the table row and then click <b>Ok</b> button.",
)
self.table.setMinimumHeight(200)
self.table.setColumnCount(len(labels))
self.table.verticalHeader().hide()
self.table.setHorizontalHeaderLabels(labels)
self.table.setSelectionBehavior(QTableWidget.SelectRows)
self.table.setSelectionMode(QTableWidget.SingleSelection)
self.table.itemSelectionChanged.connect(self.item_selection_changed)
self.table.itemDoubleClicked.connect(self.item_double_clicked)
self.table.setStyleSheet(
"QTableWidget::item{color: black;}"
"QTableWidget::item:selected{background-color: red;}"
"QTableWidget::item:selected{color: white;}"
)
header = self.table.horizontalHeader()
for n, col_stretch in enumerate(col_stretch):
# Set stretching for the columns
header.setSectionResizeMode(n, col_stretch)
self.lb_info = QLabel()
self.lb_info.setText("Column 'C': * means that the standard is user-defined.")
button_box = QDialogButtonBox(QDialogButtonBox.Open | QDialogButtonBox.Cancel)
button_box.button(QDialogButtonBox.Cancel).setDefault(True)
button_box.accepted.connect(self.accept)
button_box.rejected.connect(self.reject)
self.pb_open = button_box.button(QDialogButtonBox.Open)
self.pb_open.setEnabled(False)
vbox = QVBoxLayout()
vbox.addWidget(self.table)
vbox.addWidget(self.lb_info)
vbox.addWidget(button_box)
self.setLayout(vbox)
def _fill_table(self, table_contents):
self.table.setRowCount(len(table_contents))
for nr, row in enumerate(table_contents):
for nc, entry in enumerate(row):
s = textwrap.fill(entry, width=40)
item = QTableWidgetItem(s)
item.setFlags(item.flags() & ~Qt.ItemIsEditable)
if not nc:
item.setTextAlignment(Qt.AlignHCenter | Qt.AlignVCenter)
self.table.setItem(nr, nc, item)
self.table.resizeRowsToContents()
brightness = 220
for nr in range(self.table.rowCount()):
for nc in range(self.table.columnCount()):
self.table.item(nr, nc)
if nr % 2:
color = QColor(255, brightness, brightness)
else:
color = QColor(brightness, 255, brightness)
self.table.item(nr, nc).setBackground(QBrush(color))
try:
index = self._qe_param.index(self._qe_standard_selected)
self.selected_standard_index = index
n_columns = self.table.columnCount()
self.table.setRangeSelected(QTableWidgetSelectionRange(index, 0, index, n_columns - 1), True)
except ValueError:
pass
def item_selection_changed(self):
sel_ranges = self.table.selectedRanges()
# The table is configured to have one or no selected ranges
# 'Open' button should be enabled only if a range (row) is selected
if sel_ranges:
self.selected_standard_index = sel_ranges[0].topRow()
self.pb_open.setEnabled(True)
else:
self.selected_standard_index = -1
self.pb_open.setEnabled(False)
def item_double_clicked(self):
self.accept()
def set_standards(self, qe_param_built_in, qe_param_custom, qe_standard_selected):
self._qe_standard_selected = qe_standard_selected
self._qe_param = qe_param_custom + qe_param_built_in
custom_label = [True] * len(qe_param_custom) + [False] * len(qe_param_built_in)
table_contents = []
for n, param in enumerate(self._qe_param):
custom = "*" if custom_label[n] else ""
serial = param["serial"]
name = param["name"]
description = param["description"]
table_contents.append([custom, serial, name, description])
self._fill_table(table_contents)
def get_selected_standard(self):
if self.selected_standard_index >= 0:
return self._qe_param[self.selected_standard_index]
else:
return None
