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 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 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 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