class SimpleMeasurements(QWidget):
def __init__(self, settings: StackSettings, parent=None):
super().__init__(parent)
self.settings = settings
self.calculate_btn = QPushButton("Calculate")
self.calculate_btn.clicked.connect(self.calculate)
self.result_view = QTableWidget()
self.channel_select = ChannelComboBox()
self.units_select = EnumComboBox(Units)
self.units_select.set_value(self.settings.get("simple_measurements.units", Units.nm))
self.units_select.currentIndexChanged.connect(self.change_units)
layout = QHBoxLayout()
self.measurement_layout = QVBoxLayout()
l1 = QHBoxLayout()
l1.addWidget(QLabel("Units"))
l1.addWidget(self.units_select)
self.measurement_layout.addLayout(l1)
l2 = QHBoxLayout()
l2.addWidget(QLabel("Channel"))
l2.addWidget(self.channel_select)
self.measurement_layout.addLayout(l2)
layout.addLayout(self.measurement_layout)
result_layout = QVBoxLayout()
result_layout.addWidget(self.result_view)
result_layout.addWidget(self.calculate_btn)
layout.addLayout(result_layout)
self.setLayout(layout)
self.setWindowTitle("Measurement")
if self.window() == self:
try:
geometry = self.settings.get_from_profile("simple_measurement_window_geometry")
self.restoreGeometry(QByteArray.fromHex(bytes(geometry, "ascii")))
except KeyError:
pass
def closeEvent(self, event: QCloseEvent) -> None:
"""
Save geometry if widget is used as standalone window.
"""
if self.window() == self:
self.settings.set_in_profile(
"simple_measurement_window_geometry", self.saveGeometry().toHex().data().decode("ascii")
)
super().closeEvent(event)
def calculate(self):
if self.settings.segmentation is None:
QMessageBox.warning(self, "No segmentation", "need segmentation to work")
return
to_calculate = []
for i in range(2, self.measurement_layout.count()):
# noinspection PyTypeChecker
chk: QCheckBox = self.measurement_layout.itemAt(i).widget()
if chk.isChecked():
leaf: Leaf = MEASUREMENT_DICT[chk.text()].get_starting_leaf()
to_calculate.append(leaf.replace_(per_component=PerComponent.Yes, area=AreaType.ROI))
if not to_calculate:
QMessageBox.warning(self, "No measurement", "Select at least one measurement")
return
profile = MeasurementProfile("", [MeasurementEntry(x.name, x) for x in to_calculate])
dial = ExecuteFunctionDialog(
profile.calculate,
kwargs={
"channel": self.settings.image.get_channel(self.channel_select.get_value()),
"segmentation": self.settings.segmentation,
"mask": None,
"voxel_size": self.settings.image.spacing,
"result_units": self.units_select.get_value(),
},
)
dial.exec()
result: MeasurementResult = dial.get_result()
values = result.get_separated()
labels = result.get_labels()
self.result_view.clear()
self.result_view.setColumnCount(len(values) + 1)
self.result_view.setRowCount(len(labels))
for i, val in enumerate(labels):
self.result_view.setItem(i, 0, QTableWidgetItem(val))
for j, values_list in enumerate(values):
for i, val in enumerate(values_list):
self.result_view.setItem(i, j + 1, QTableWidgetItem(str(val)))
def _clean_measurements(self):
selected = set()
for _ in range(self.measurement_layout.count() - 2):
# noinspection PyTypeChecker
chk: QCheckBox = self.measurement_layout.takeAt(2).widget()
if chk.isChecked():
selected.add(chk.text())
chk.deleteLater()
return selected
def event(self, event: QEvent) -> bool:
if event.type() == QEvent.WindowActivate:
self.channel_select.change_channels_num(self.settings.image.channels)
selected = self._clean_measurements()
for val in MEASUREMENT_DICT.values():
area = val.get_starting_leaf().area
pc = val.get_starting_leaf().per_component
if (
val.get_fields()
or (area is not None and area != AreaType.ROI)
or (pc is not None and pc != PerComponent.Yes)
):
continue
text = val.get_name()
chk = QCheckBox(text)
if text in selected:
chk.setChecked(True)
self.measurement_layout.addWidget(chk)
return super().event(event)
def change_units(self):
self.settings.set("simple_measurements.units", self.units_select.get_value())
class SimpleMeasurements(QWidget):
def __init__(self, settings: StackSettings, parent=None):
super().__init__(parent)
self.settings = settings
self.calculate_btn = QPushButton("Calculate")
self.calculate_btn.clicked.connect(self.calculate)
self.result_view = QTableWidget()
self.channel_select = ChannelComboBox()
self.units_select = QEnumComboBox(enum_class=Units)
self.units_select.setCurrentEnum(
self.settings.get("simple_measurements.units", Units.nm))
self.units_select.currentIndexChanged.connect(self.change_units)
self._shift = 2
layout = QHBoxLayout()
self.measurement_layout = QVBoxLayout()
l1 = QHBoxLayout()
l1.addWidget(QLabel("Units"))
l1.addWidget(self.units_select)
self.measurement_layout.addLayout(l1)
l2 = QHBoxLayout()
l2.addWidget(QLabel("Channel"))
l2.addWidget(self.channel_select)
self.measurement_layout.addLayout(l2)
layout.addLayout(self.measurement_layout)
result_layout = QVBoxLayout()
result_layout.addWidget(self.result_view)
result_layout.addWidget(self.calculate_btn)
layout.addLayout(result_layout)
self.setLayout(layout)
self.setWindowTitle("Measurement")
if self.window() == self:
with suppress(KeyError):
geometry = self.settings.get_from_profile(
"simple_measurement_window_geometry")
self.restoreGeometry(
QByteArray.fromHex(bytes(geometry, "ascii")))
def closeEvent(self, event: QCloseEvent) -> None:
"""
Save geometry if widget is used as standalone window.
"""
if self.window() == self:
self.settings.set_in_profile(
"simple_measurement_window_geometry",
self.saveGeometry().toHex().data().decode("ascii"))
super().closeEvent(event)
def calculate(self):
if self.settings.roi is None:
QMessageBox.warning(self, "No segmentation",
"need segmentation to work")
return
to_calculate = []
for i in range(self._shift, self.measurement_layout.count()):
# noinspection PyTypeChecker
chk: QCheckBox = self.measurement_layout.itemAt(i).widget()
if chk.isChecked():
leaf: Leaf = MEASUREMENT_DICT[chk.text()].get_starting_leaf()
to_calculate.append(
leaf.replace_(per_component=PerComponent.Yes,
area=AreaType.ROI))
if not to_calculate:
QMessageBox.warning(self, "No measurement",
"Select at least one measurement")
return
profile = MeasurementProfile(
"", [MeasurementEntry(x.name, x) for x in to_calculate])
dial = ExecuteFunctionDialog(
profile.calculate,
kwargs={
"image": self.settings.image,
"channel_num": self.channel_select.get_value(),
"roi": self.settings.roi_info,
"result_units": self.units_select.currentEnum(),
},
)
dial.exec_()
result: MeasurementResult = dial.get_result()
values = result.get_separated()
labels = result.get_labels()
self.result_view.clear()
self.result_view.setColumnCount(len(values) + 1)
self.result_view.setRowCount(len(labels))
for i, val in enumerate(labels):
self.result_view.setItem(i, 0, QTableWidgetItem(val))
for j, values_list in enumerate(values):
for i, val in enumerate(values_list):
self.result_view.setItem(i, j + 1, QTableWidgetItem(str(val)))
def _clean_measurements(self):
selected = set()
for _ in range(self.measurement_layout.count() - self._shift):
# noinspection PyTypeChecker
chk: QCheckBox = self.measurement_layout.takeAt(
self._shift).widget()
if chk.isChecked():
selected.add(chk.text())
chk.deleteLater()
return selected
def refresh_measurements(self):
selected = self._clean_measurements()
for val in MEASUREMENT_DICT.values():
area = val.get_starting_leaf().area
pc = val.get_starting_leaf().per_component
if (val.get_fields() or (area is not None and area != AreaType.ROI)
or (pc is not None and pc != PerComponent.Yes)):
continue
text = val.get_name()
chk = QCheckBox(text)
if text in selected:
chk.setChecked(True)
self.measurement_layout.addWidget(chk)
def keyPressEvent(self, e: QKeyEvent):
if not e.modifiers() & Qt.ControlModifier:
return
selected = self.result_view.selectedRanges()
if e.key() == Qt.Key_C: # copy
s = ""
for r in range(selected[0].topRow(), selected[0].bottomRow() + 1):
for c in range(selected[0].leftColumn(),
selected[0].rightColumn() + 1):
try:
s += str(self.result_view.item(r, c).text()) + "\t"
except AttributeError:
s += "\t"
s = s[:-1] + "\n" # eliminate last '\t'
QApplication.clipboard().setText(s)
def event(self, event: QEvent) -> bool:
if event.type() == QEvent.WindowActivate:
if self.settings.image is not None:
self.channel_select.change_channels_num(
self.settings.image.channels)
self.refresh_measurements()
return super().event(event)
def change_units(self):
self.settings.set("simple_measurements.units",
self.units_select.currentEnum())
class MeasurementWidget(QWidget):
"""
:type settings: Settings
:type segment: Segment
"""
def __init__(self, settings: PartSettings, segment=None):
super().__init__()
self.settings = settings
self.segment = segment
self.measurements_storage = MeasurementsStorage()
self.recalculate_button = QPushButton(
"Recalculate and\n replace measurement", self)
self.recalculate_button.clicked.connect(
self.replace_measurement_result)
self.recalculate_append_button = QPushButton(
"Recalculate and\n append measurement", self)
self.recalculate_append_button.clicked.connect(
self.append_measurement_result)
self.copy_button = QPushButton("Copy to clipboard", self)
self.copy_button.setToolTip(
"You cacn copy also with 'Ctrl+C'. To get raw copy copy with 'Ctrl+Shit+C'"
)
self.horizontal_measurement_present = QCheckBox(
"Horizontal view", self)
self.no_header = QCheckBox("No header", self)
self.no_units = QCheckBox("No units", self)
self.no_units.setChecked(True)
self.no_units.clicked.connect(self.refresh_view)
self.expand_mode = QCheckBox("Expand", self)
self.expand_mode.setToolTip(
"Shows results for each component in separate entry")
self.file_names = EnumComboBox(FileNamesEnum)
self.file_names_label = QLabel("Add file name:")
self.file_names.currentIndexChanged.connect(self.refresh_view)
self.horizontal_measurement_present.stateChanged.connect(
self.refresh_view)
self.expand_mode.stateChanged.connect(self.refresh_view)
self.copy_button.clicked.connect(self.copy_to_clipboard)
self.measurement_type = SearchCombBox(self)
# noinspection PyUnresolvedReferences
self.measurement_type.currentIndexChanged.connect(
self.measurement_profile_selection_changed)
self.measurement_type.addItem("<none>")
self.measurement_type.addItems(
list(sorted(self.settings.measurement_profiles.keys())))
self.measurement_type.setToolTip(
'You can create new measurement profile in advanced window, in tab "Measurement settings"'
)
self.channels_chose = ChannelComboBox()
self.units_choose = EnumComboBox(Units)
self.units_choose.set_value(self.settings.get("units_value", Units.nm))
self.info_field = QTableWidget(self)
self.info_field.setColumnCount(3)
self.info_field.setHorizontalHeaderLabels(["Name", "Value", "Units"])
self.measurement_add_shift = 0
layout = QVBoxLayout()
# layout.addWidget(self.recalculate_button)
v_butt_layout = QVBoxLayout()
v_butt_layout.setSpacing(1)
self.up_butt_layout = QHBoxLayout()
self.up_butt_layout.addWidget(self.recalculate_button)
self.up_butt_layout.addWidget(self.recalculate_append_button)
self.butt_layout = QHBoxLayout()
# self.butt_layout.setMargin(0)
# self.butt_layout.setSpacing(10)
self.butt_layout.addWidget(self.horizontal_measurement_present, 1)
self.butt_layout.addWidget(self.no_header, 1)
self.butt_layout.addWidget(self.no_units, 1)
self.butt_layout.addWidget(self.expand_mode, 1)
self.butt_layout.addWidget(self.file_names_label)
self.butt_layout.addWidget(self.file_names, 1)
self.butt_layout.addWidget(self.copy_button, 2)
self.butt_layout2 = QHBoxLayout()
self.butt_layout3 = QHBoxLayout()
self.butt_layout3.addWidget(QLabel("Channel:"))
self.butt_layout3.addWidget(self.channels_chose)
self.butt_layout3.addWidget(QLabel("Units:"))
self.butt_layout3.addWidget(self.units_choose)
# self.butt_layout3.addWidget(QLabel("Noise removal:"))
# self.butt_layout3.addWidget(self.noise_removal_method)
self.butt_layout3.addWidget(QLabel("Measurement set:"))
self.butt_layout3.addWidget(self.measurement_type, 2)
v_butt_layout.addLayout(self.up_butt_layout)
v_butt_layout.addLayout(self.butt_layout)
v_butt_layout.addLayout(self.butt_layout2)
v_butt_layout.addLayout(self.butt_layout3)
layout.addLayout(v_butt_layout)
# layout.addLayout(self.butt_layout)
layout.addWidget(self.info_field)
self.setLayout(layout)
# noinspection PyArgumentList
self.clip = QApplication.clipboard()
self.settings.image_changed[int].connect(self.image_changed)
self.previous_profile = None
def check_if_measurement_can_be_calculated(self, name):
if name == "<none>":
return "<none>"
profile: MeasurementProfile = self.settings.measurement_profiles.get(
name)
if profile.is_any_mask_measurement() and self.settings.mask is None:
QMessageBox.information(
self, "Need mask",
"To use this measurement set please use data with mask loaded",
QMessageBox.Ok)
self.measurement_type.setCurrentIndex(0)
return "<none>"
if self.settings.roi is None:
QMessageBox.information(
self,
"Need segmentation",
'Before calculating please create segmentation ("Execute" button)',
QMessageBox.Ok,
)
self.measurement_type.setCurrentIndex(0)
return "<none>"
return name
def image_changed(self, channels_num):
self.channels_chose.change_channels_num(channels_num)
def measurement_profile_selection_changed(self, index):
text = self.measurement_type.itemText(index)
text = self.check_if_measurement_can_be_calculated(text)
try:
stat = self.settings.measurement_profiles[text]
is_mask = stat.is_any_mask_measurement()
disable = is_mask and (self.settings.mask is None)
except KeyError:
disable = True
self.recalculate_button.setDisabled(disable)
self.recalculate_append_button.setDisabled(disable)
if disable:
self.recalculate_button.setToolTip(
"Measurement profile contains mask measurements when mask is not loaded"
)
self.recalculate_append_button.setToolTip(
"Measurement profile contains mask measurements when mask is not loaded"
)
else:
self.recalculate_button.setToolTip("")
self.recalculate_append_button.setToolTip("")
def copy_to_clipboard(self):
s = ""
for r in range(self.info_field.rowCount()):
for c in range(self.info_field.columnCount()):
try:
s += str(self.info_field.item(r, c).text()) + "\t"
except AttributeError:
s += "\t"
s = s[:-1] + "\n" # eliminate last '\t'
self.clip.setText(s)
def replace_measurement_result(self):
self.measurements_storage.clear()
self.previous_profile = ""
self.append_measurement_result()
def refresh_view(self):
self.measurements_storage.set_expand(self.expand_mode.isChecked())
self.measurements_storage.set_show_units(not self.no_units.isChecked())
self.info_field.clear()
save_orientation = self.horizontal_measurement_present.isChecked()
columns, rows = self.measurements_storage.get_size(save_orientation)
self.info_field.setColumnCount(columns)
self.info_field.setRowCount(rows)
self.info_field.setHorizontalHeaderLabels(
self.measurements_storage.get_header(save_orientation))
self.info_field.setVerticalHeaderLabels(
self.measurements_storage.get_rows(save_orientation))
for x in range(rows):
for y in range(columns):
self.info_field.setItem(
x, y,
QTableWidgetItem(
self.measurements_storage.get_val_as_str(
x, y, save_orientation)))
if self.file_names.get_value() == FileNamesEnum.No:
if save_orientation:
self.info_field.removeColumn(0)
else:
self.info_field.removeRow(0)
elif self.file_names.get_value() == FileNamesEnum.Short:
if save_orientation:
columns = 1
else:
rows = 1
for x in range(rows):
for y in range(columns):
item = self.info_field.item(x, y)
item.setText(os.path.basename(item.text()))
self.info_field.setEditTriggers(QAbstractItemView.NoEditTriggers)
def append_measurement_result(self):
try:
compute_class = self.settings.measurement_profiles[
self.measurement_type.currentText()]
except KeyError:
QMessageBox.warning(
self,
"Measurement profile not found",
f"Measurement profile '{self.measurement_type.currentText()}' not found'",
)
return
if self.settings.roi is None:
return
units = self.units_choose.get_value()
# FIXME find which errors should be displayed as warning
# def exception_hook(exception):
# QMessageBox.warning(self, "Calculation error", f"Error during calculation: {exception}")
for num in compute_class.get_channels_num():
if num >= self.settings.image.channels:
QMessageBox.warning(
self,
"Measurement error",
"Cannot calculate this measurement because "
f"image do not have channel {num+1}",
)
return
thread = ExecuteFunctionThread(
compute_class.calculate,
[
self.settings.image,
self.channels_chose.currentIndex(), self.settings.roi_info,
units
],
)
dial = WaitingDialog(
thread,
"Measurement calculation") # , exception_hook=exception_hook)
dial.exec()
stat: MeasurementResult = thread.result
if stat is None:
return
stat.set_filename(self.settings.image_path)
self.measurements_storage.add_measurements(stat)
self.previous_profile = compute_class.name
self.refresh_view()
def keyPressEvent(self, e: QKeyEvent):
if e.modifiers() & Qt.ControlModifier:
selected = self.info_field.selectedRanges()
if e.key() == Qt.Key_C: # copy
s = ""
for r in range(selected[0].topRow(),
selected[0].bottomRow() + 1):
for c in range(selected[0].leftColumn(),
selected[0].rightColumn() + 1):
try:
s += str(self.info_field.item(r, c).text()) + "\t"
except AttributeError:
s += "\t"
s = s[:-1] + "\n" # eliminate last '\t'
self.clip.setText(s)
def update_measurement_list(self):
self.measurement_type.blockSignals(True)
available = list(sorted(self.settings.measurement_profiles.keys()))
text = self.measurement_type.currentText()
try:
index = available.index(text) + 1
except ValueError:
index = 0
self.measurement_type.clear()
self.measurement_type.addItem("<none>")
self.measurement_type.addItems(available)
self.measurement_type.setCurrentIndex(index)
self.measurement_type.blockSignals(False)
def showEvent(self, _):
self.update_measurement_list()
def event(self, event: QEvent):
if event.type() == QEvent.WindowActivate:
self.update_measurement_list()
return super().event(event)
@staticmethod
def _move_widgets(widgets_list: List[Tuple[QWidget, int]],
layout1: QBoxLayout, layout2: QBoxLayout):
for el in widgets_list:
layout1.removeWidget(el[0])
layout2.addWidget(el[0], el[1])
def resizeEvent(self, _event: QResizeEvent) -> None:
if self.width() < 800 and self.butt_layout2.count() == 0:
self._move_widgets(
[(self.file_names_label, 1), (self.file_names, 1),
(self.copy_button, 2)],
self.butt_layout,
self.butt_layout2,
)
elif self.width() > 800 and self.butt_layout2.count() != 0:
self._move_widgets(
[(self.file_names_label, 1), (self.file_names, 1),
(self.copy_button, 2)],
self.butt_layout2,
self.butt_layout,
)
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```')
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()
