def __init__(self, parent: 'MainWindowView', dock: QDockWidget,
images: Images):
# enforce not showing a single image
assert images.data.ndim == 3, \
"Data does NOT have 3 dimensions! Dimensions found: {0}".format(images.data.ndim)
# We set the main window as the parent, the effect is the same as
# having no parent, the window will be inside the QDockWidget. If the
# dock is set as a parent the window will be an independent floating
# window
super(StackVisualiserView, self).__init__(parent, None)
self.central_widget = QWidget(self)
self.layout = QVBoxLayout(self)
self.central_widget.setLayout(self.layout)
self.setCentralWidget(self.central_widget)
self.parent_create_stack = self.parent().create_new_stack
self._main_window = parent
# capture the QDockWidget reference so that we can access the Qt widget
# and change things like the title
self.dock = dock
# Swap out the dock close event with our own provided close event. This
# is needed to manually delete the data reference, otherwise it is left
# hanging in the presenter
setattr(dock, 'closeEvent', self.closeEvent)
self.presenter = StackVisualiserPresenter(self, images)
self._actions = [
("Show history and metadata", self.show_image_metadata),
("Duplicate whole data",
lambda: self.presenter.notify(SVNotification.DUPE_STACK)),
("Duplicate current ROI of data",
lambda: self.presenter.notify(SVNotification.DUPE_STACK_ROI)),
("Mark as projections/sinograms", self.mark_as_sinograms),
("", None),
("Toggle show averaged image",
lambda: self.presenter.notify(SVNotification.TOGGLE_IMAGE_MODE)),
("Create sinograms from stack",
lambda: self.presenter.notify(SVNotification.SWAP_AXES)),
("Set ROI", self.set_roi),
("Copy ROI to clipboard", self.copy_roi_to_clipboard), ("", None),
("Change window name", self.change_window_name_clicked),
("Goto projection", self.goto_projection),
("Goto angle", self.goto_angle)
]
self._context_actions = self.build_context_menu()
self.image_view = MIImageView(self)
self.image_view.imageItem.menu = self._context_actions
self.actionCloseStack = QAction("Close window", self)
self.actionCloseStack.triggered.connect(self.close)
self.actionCloseStack.setShortcut("Ctrl+W")
self.dock.addAction(self.actionCloseStack)
self.image_view.setImage(self.presenter.images.data)
self.image_view.roi_changed_callback = self.roi_changed_callback
self.layout.addWidget(self.image_view)
def __init__(self, parent: 'MainWindowView', images: Images):
# enforce not showing a single image
assert images.data.ndim == 3, \
"Data does NOT have 3 dimensions! Dimensions found: {0}".format(images.data.ndim)
# We set the main window as the parent, the effect is the same as
# having no parent, the window will be inside the QDockWidget. If the
# dock is set as a parent the window will be an independent floating
# window
super().__init__(images.name, parent)
self.central_widget = QWidget(self)
self.layout = QVBoxLayout()
self.central_widget.setLayout(self.layout)
self.setWidget(self.central_widget)
self.parent_create_stack = self.parent().create_new_stack
self._main_window = parent
self.presenter = StackVisualiserPresenter(self, images)
self._actions = [
("Show history and metadata", self.show_image_metadata),
("Duplicate whole data",
lambda: self.presenter.notify(SVNotification.DUPE_STACK)),
("Duplicate current ROI of data",
lambda: self.presenter.notify(SVNotification.DUPE_STACK_ROI)),
("Mark as projections/sinograms", self.mark_as_sinograms),
("", None),
("Toggle averaged image",
lambda: self.presenter.notify(SVNotification.TOGGLE_IMAGE_MODE)),
("Create sinograms from stack",
lambda: self.presenter.notify(SVNotification.SWAP_AXES)),
("Set ROI", self.set_roi),
("Copy ROI to clipboard", self.copy_roi_to_clipboard), ("", None),
("Change window name", self.change_window_name_clicked),
("Goto projection", self.goto_projection),
("Goto angle", self.goto_angle)
]
self._context_actions = self.build_context_menu()
self.image_view = MIImageView(self)
self.image_view.imageItem.menu = self._context_actions
self.actionCloseStack = QAction("Close window", self)
self.actionCloseStack.triggered.connect(self.close)
self.actionCloseStack.setShortcut("Ctrl+W")
nan_check_menu = [
("Crop Coordinates", lambda: self._main_window.presenter.
show_operation("Crop Coordinates")),
("NaN Removal",
lambda: self._main_window.presenter.show_operation("NaN Removal"))
]
self.image_view.enable_nan_check(actions=nan_check_menu)
self.addAction(self.actionCloseStack)
self.image_view.setImage(self.presenter.images.data)
self.image_view.roi_changed_callback = self.roi_changed_callback
self.layout.addWidget(self.image_view)
def _setup_stack_for_view(self, stack: MIImageView, data: np.ndarray):
stack.setContentsMargins(4, 4, 4, 4)
stack.setImage(data)
stack.ui.menuBtn.hide()
stack.ui.roiBtn.hide()
stack.button_stack_right.hide()
stack.button_stack_left.hide()
details_size_policy = QSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.Preferred)
details_size_policy.setHorizontalStretch(1)
stack.details.setSizePolicy(details_size_policy)
self.roiButton.clicked.connect(stack.roiClicked)
class StackVisualiserView(BaseMainWindowView):
# Signal that signifies when the ROI is updated. Used to update previews in Filter views
roi_updated = pyqtSignal(SensibleROI)
image_view: MIImageView
presenter: StackVisualiserPresenter
dock: QDockWidget
layout: QVBoxLayout
def __init__(self, parent: 'MainWindowView', dock: QDockWidget,
images: Images):
# enforce not showing a single image
assert images.data.ndim == 3, \
"Data does NOT have 3 dimensions! Dimensions found: {0}".format(images.data.ndim)
# We set the main window as the parent, the effect is the same as
# having no parent, the window will be inside the QDockWidget. If the
# dock is set as a parent the window will be an independent floating
# window
super(StackVisualiserView, self).__init__(parent, None)
self.central_widget = QWidget(self)
self.layout = QVBoxLayout(self)
self.central_widget.setLayout(self.layout)
self.setCentralWidget(self.central_widget)
self.parent_create_stack = self.parent().create_new_stack
self._main_window = parent
# capture the QDockWidget reference so that we can access the Qt widget
# and change things like the title
self.dock = dock
# Swap out the dock close event with our own provided close event. This
# is needed to manually delete the data reference, otherwise it is left
# hanging in the presenter
setattr(dock, 'closeEvent', self.closeEvent)
self.presenter = StackVisualiserPresenter(self, images)
self._actions = [
("Show history and metadata", self.show_image_metadata),
("Duplicate whole data",
lambda: self.presenter.notify(SVNotification.DUPE_STACK)),
("Duplicate current ROI of data",
lambda: self.presenter.notify(SVNotification.DUPE_STACK_ROI)),
("Mark as projections/sinograms", self.mark_as_sinograms),
("", None),
("Toggle show averaged image",
lambda: self.presenter.notify(SVNotification.TOGGLE_IMAGE_MODE)),
("Create sinograms from stack",
lambda: self.presenter.notify(SVNotification.SWAP_AXES)),
("Set ROI", self.set_roi),
("Copy ROI to clipboard", self.copy_roi_to_clipboard), ("", None),
("Change window name", self.change_window_name_clicked),
("Goto projection", self.goto_projection),
("Goto angle", self.goto_angle)
]
self._context_actions = self.build_context_menu()
self.image_view = MIImageView(self)
self.image_view.imageItem.menu = self._context_actions
self.actionCloseStack = QAction("Close window", self)
self.actionCloseStack.triggered.connect(self.close)
self.actionCloseStack.setShortcut("Ctrl+W")
self.dock.addAction(self.actionCloseStack)
self.image_view.setImage(self.presenter.images.data)
self.image_view.roi_changed_callback = self.roi_changed_callback
self.layout.addWidget(self.image_view)
@property
def name(self):
return self.dock.windowTitle()
@name.setter
def name(self, name: str):
self.dock.setWindowTitle(name)
@property
def current_roi(self) -> SensibleROI:
return SensibleROI.from_points(*self.image_view.get_roi())
@property
def image(self):
return self.image_view.imageItem
@image.setter
def image(self, to_display):
self.image_view.setImage(to_display)
@property
def main_window(self) -> 'MainWindowView':
return self._main_window
@property
def context_actions(self):
return self._context_actions
@property
def actions(self):
return self._actions
def closeEvent(self, event):
window: 'MainWindowView' = self.window()
stacks_with_proj180 = window.get_all_stack_visualisers_with_180deg_proj(
)
for stack in stacks_with_proj180:
if stack.presenter.images.proj180deg is self.presenter.images:
if not self.ask_confirmation(
"Caution: If you close this then the 180 degree projection will "
"not be available for COR correlation, and the middle of the image stack will be used."
):
event.ignore()
return
else:
stack.presenter.images.clear_proj180deg()
with operation_in_progress("Closing image view",
"Freeing image memory"):
self.dock.setFloating(False)
self.hide()
self.image_view.close()
# this removes all references to the data, allowing it to be GC'ed
# otherwise there is a hanging reference
self.presenter.delete_data()
window.remove_stack(self)
self.deleteLater()
# refers to the QDockWidget within which the stack is contained
self.dock.deleteLater()
def roi_changed_callback(self, roi: SensibleROI):
self.roi_updated.emit(roi)
def build_context_menu(self) -> QMenu:
menu = QMenu(self)
populate_menu(menu, self.actions)
return menu
def goto_projection(self):
projection_to_goto, accepted = QInputDialog.getInt(
self,
"Enter Projection",
"Projection",
0, # Default value
0, # Min projection value
self.presenter.get_num_images(), # Max possible value
)
if accepted:
self.image_view.set_selected_image(projection_to_goto)
def goto_angle(self):
projection_to_goto, accepted = QInputDialog.getDouble(
self,
"Enter Angle",
"Angle in Degrees",
0, # Default value
0, # Min projection value
2147483647, # Max possible value
4, # Digits/decimals
)
if accepted:
self.image_view.set_selected_image(
self.presenter.find_image_from_angle(projection_to_goto))
def set_roi(self):
roi, accepted = QInputDialog.getText(
self,
"Manual ROI",
"Enter ROI in order left, top, right, bottom, with commas in-between each number",
text="0, 0, 50, 50")
if accepted:
roi = [int(r.strip()) for r in roi.split(",")]
self.image_view.roi.setPos((roi[0], roi[1]), update=False)
self.image_view.roi.setSize((roi[2] - roi[0], roi[3] - roi[1]))
self.image_view.roi.show()
self.image_view.roiChanged()
def copy_roi_to_clipboard(self):
pos, size = self.image_view.get_roi()
QGuiApplication.clipboard().setText(
f"{pos.x}, {pos.y}, {pos.x + size.x}, {pos.y + size.y}")
def change_window_name_clicked(self):
input_window = QInputDialog()
new_window_name, ok = input_window.getText(self,
"Change window name",
"Name:",
text=self.name)
if ok:
if new_window_name not in self.main_window.stack_names:
self.main_window.rename_stack(self.name, new_window_name)
else:
error = QMessageBox(self)
error.setWindowTitle("Stack name conflict")
error.setText(
f"There is already a window named {new_window_name}")
error.exec()
def show_image_metadata(self):
dialog = MetadataDialog(self, self.presenter.images)
dialog.show()
def show_op_history_copy_dialog(self):
dialog = OpHistoryCopyDialogView(self, self.presenter.images,
self.main_window)
dialog.show()
def mark_as_sinograms(self):
# 1 is position of sinograms, 0 is projections
current = 1 if self.presenter.images._is_sinograms else 0
item, accepted = QInputDialog.getItem(
self, "Select if projections or sinograms", "Images are:",
["projections", "sinograms"], current)
if accepted:
self.presenter.images._is_sinograms = False if item == "projections" else True
def ask_confirmation(self, msg: str):
response = QMessageBox.question(self, "Confirm action", msg,
QMessageBox.Ok
| QMessageBox.Cancel) # type:ignore
return response == QMessageBox.Ok
def __init__(self, original_stack: Images, new_stack: Images,
presenter: Union['StackComparePresenter',
'StackChoicePresenter'],
parent: Optional[QMainWindow]):
super().__init__(parent, "gui/ui/stack_choice_window.ui")
self.presenter = presenter
self.setWindowTitle("Choose the stack you want to keep")
self.setWindowModality(Qt.WindowModality.ApplicationModal)
# Create stacks and place them in the choice window
self.original_stack = MIImageView(detailsSpanAllCols=True)
self.original_stack.name = "Original Stack"
self.original_stack.enable_nan_check(True)
self.new_stack = MIImageView(detailsSpanAllCols=True)
self.new_stack.name = "New Stack"
self.new_stack.enable_nan_check(True)
self._setup_stack_for_view(self.original_stack, original_stack.data)
self._setup_stack_for_view(self.new_stack, new_stack.data)
self.topVerticalOriginal.addWidget(self.original_stack)
self.topVerticalNew.addWidget(self.new_stack)
self.shifting_through_images = False
self.original_stack.sigTimeChanged.connect(
self._sync_timelines_for_new_stack_with_old_stack)
self.new_stack.sigTimeChanged.connect(
self._sync_timelines_for_old_stack_with_new_stack)
# Hook nav buttons into original stack (new stack not needed as the timelines are synced)
self.leftButton.pressed.connect(
self.original_stack.button_stack_left.pressed)
self.leftButton.released.connect(
self.original_stack.button_stack_left.released)
self.rightButton.pressed.connect(
self.original_stack.button_stack_right.pressed)
self.rightButton.released.connect(
self.original_stack.button_stack_right.released)
# Hook the choice buttons
self.originalDataButton.clicked.connect(
lambda: self.presenter.notify(Notification.CHOOSE_ORIGINAL))
self.newDataButton.clicked.connect(
lambda: self.presenter.notify(Notification.CHOOSE_NEW_DATA))
# Hooks the lock histograms checkbox
self.lockHistograms.clicked.connect(
lambda: self.presenter.notify(Notification.TOGGLE_LOCK_HISTOGRAMS))
# Hook ROI button into both stacks
self.roiButton.clicked.connect(self._toggle_roi)
# Hook the two plot ROIs together so that any changes are synced
self.original_stack.roi.sigRegionChanged.connect(
self._sync_roi_plot_for_new_stack_with_old_stack)
self.new_stack.roi.sigRegionChanged.connect(
self._sync_roi_plot_for_old_stack_with_new_stack)
self._sync_both_image_axis()
self._ensure_range_is_the_same()
self.choice_made = False
self.roi_shown = False
class StackChoiceView(BaseMainWindowView):
originalDataButton: QPushButton
newDataButton: QPushButton
lockHistograms: QCheckBox
def __init__(self, original_stack: Images, new_stack: Images,
presenter: Union['StackComparePresenter',
'StackChoicePresenter'],
parent: Optional[QMainWindow]):
super().__init__(parent, "gui/ui/stack_choice_window.ui")
self.presenter = presenter
self.setWindowTitle("Choose the stack you want to keep")
self.setWindowModality(Qt.WindowModality.ApplicationModal)
# Create stacks and place them in the choice window
self.original_stack = MIImageView(detailsSpanAllCols=True)
self.original_stack.name = "Original Stack"
self.original_stack.enable_nan_check(True)
self.new_stack = MIImageView(detailsSpanAllCols=True)
self.new_stack.name = "New Stack"
self.new_stack.enable_nan_check(True)
self._setup_stack_for_view(self.original_stack, original_stack.data)
self._setup_stack_for_view(self.new_stack, new_stack.data)
self.topVerticalOriginal.addWidget(self.original_stack)
self.topVerticalNew.addWidget(self.new_stack)
self.shifting_through_images = False
self.original_stack.sigTimeChanged.connect(
self._sync_timelines_for_new_stack_with_old_stack)
self.new_stack.sigTimeChanged.connect(
self._sync_timelines_for_old_stack_with_new_stack)
# Hook nav buttons into original stack (new stack not needed as the timelines are synced)
self.leftButton.pressed.connect(
self.original_stack.button_stack_left.pressed)
self.leftButton.released.connect(
self.original_stack.button_stack_left.released)
self.rightButton.pressed.connect(
self.original_stack.button_stack_right.pressed)
self.rightButton.released.connect(
self.original_stack.button_stack_right.released)
# Hook the choice buttons
self.originalDataButton.clicked.connect(
lambda: self.presenter.notify(Notification.CHOOSE_ORIGINAL))
self.newDataButton.clicked.connect(
lambda: self.presenter.notify(Notification.CHOOSE_NEW_DATA))
# Hooks the lock histograms checkbox
self.lockHistograms.clicked.connect(
lambda: self.presenter.notify(Notification.TOGGLE_LOCK_HISTOGRAMS))
# Hook ROI button into both stacks
self.roiButton.clicked.connect(self._toggle_roi)
# Hook the two plot ROIs together so that any changes are synced
self.original_stack.roi.sigRegionChanged.connect(
self._sync_roi_plot_for_new_stack_with_old_stack)
self.new_stack.roi.sigRegionChanged.connect(
self._sync_roi_plot_for_old_stack_with_new_stack)
self._sync_both_image_axis()
self._ensure_range_is_the_same()
self.choice_made = False
self.roi_shown = False
def _ensure_range_is_the_same(self):
new_range = self.new_stack.ui.histogram.getLevels()
original_range = self.original_stack.ui.histogram.getLevels()
new_max_y = max(new_range[0], new_range[1])
new_min_y = min(new_range[0], new_range[1])
original_max_y = max(original_range[0], original_range[1])
original_min_y = min(original_range[0], original_range[1])
y_range_min = min(new_min_y, original_min_y)
y_range_max = max(new_max_y, original_max_y)
self.new_stack.ui.histogram.vb.setRange(yRange=(y_range_min,
y_range_max))
self.original_stack.ui.histogram.vb.setRange(yRange=(y_range_min,
y_range_max))
def _toggle_roi(self):
if self.roi_shown:
self.roi_shown = False
self.original_stack.ui.roiBtn.setChecked(False)
self.new_stack.ui.roiBtn.setChecked(False)
self.original_stack.roiClicked()
self.new_stack.roiClicked()
else:
self.roi_shown = True
self.original_stack.ui.roiBtn.setChecked(True)
self.new_stack.ui.roiBtn.setChecked(True)
self.original_stack.roiClicked()
self.new_stack.roiClicked()
def _setup_stack_for_view(self, stack: MIImageView, data: np.ndarray):
stack.setContentsMargins(4, 4, 4, 4)
stack.setImage(data)
stack.ui.menuBtn.hide()
stack.ui.roiBtn.hide()
stack.button_stack_right.hide()
stack.button_stack_left.hide()
details_size_policy = QSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.Preferred)
details_size_policy.setHorizontalStretch(1)
stack.details.setSizePolicy(details_size_policy)
self.roiButton.clicked.connect(stack.roiClicked)
def _sync_roi_plot_for_new_stack_with_old_stack(self):
self.new_stack.roi.sigRegionChanged.disconnect(
self._sync_roi_plot_for_old_stack_with_new_stack)
self.new_stack.roi.setPos(self.original_stack.roi.pos())
self.new_stack.roi.setSize(self.original_stack.roi.size())
self.new_stack.roi.sigRegionChanged.connect(
self._sync_roi_plot_for_old_stack_with_new_stack)
def _sync_roi_plot_for_old_stack_with_new_stack(self):
self.original_stack.roi.sigRegionChanged.disconnect(
self._sync_roi_plot_for_new_stack_with_old_stack)
self.original_stack.roi.setPos(self.new_stack.roi.pos())
self.original_stack.roi.setSize(self.new_stack.roi.size())
self.original_stack.roi.sigRegionChanged.connect(
self._sync_roi_plot_for_new_stack_with_old_stack)
def _sync_timelines_for_new_stack_with_old_stack(self, index, _):
self.new_stack.sigTimeChanged.disconnect(
self._sync_timelines_for_old_stack_with_new_stack)
self.new_stack.setCurrentIndex(index)
self.new_stack.sigTimeChanged.connect(
self._sync_timelines_for_old_stack_with_new_stack)
def _sync_timelines_for_old_stack_with_new_stack(self, index, _):
self.original_stack.sigTimeChanged.disconnect(
self._sync_timelines_for_new_stack_with_old_stack)
self.original_stack.setCurrentIndex(index)
self.original_stack.sigTimeChanged.connect(
self._sync_timelines_for_new_stack_with_old_stack)
def _sync_both_image_axis(self):
self.original_stack.view.linkView(ViewBox.XAxis, self.new_stack.view)
self.original_stack.view.linkView(ViewBox.YAxis, self.new_stack.view)
def closeEvent(self, e):
# Confirm exit is actually wanted as it will lead to data loss
if not self.choice_made:
response = QMessageBox.warning(
self, "Data Loss! Are you sure?",
"You will lose the original stack if you close this window! Are you sure?",
QMessageBox.Ok | QMessageBox.Cancel)
if response == QMessageBox.Ok:
self.presenter.notify(Notification.CHOOSE_NEW_DATA)
else:
e.ignore()
return
self.original_stack.close()
self.new_stack.close()
def _set_from_old_to_new(self):
"""
Signal triggered when the histograms are locked and the contrast values changed.
"""
levels: Tuple[float,
float] = self.original_stack.ui.histogram.getLevels()
self.new_stack.ui.histogram.setLevels(*levels)
def _set_from_new_to_old(self):
"""
Signal triggered when the histograms are locked and the contrast values changed.
"""
levels: Tuple[float, float] = self.new_stack.ui.histogram.getLevels()
self.original_stack.ui.histogram.setLevels(*levels)
def connect_histogram_changes(self):
self._set_from_old_to_new()
self.original_stack.ui.histogram.sigLevelsChanged.connect(
self._set_from_old_to_new)
self.new_stack.ui.histogram.sigLevelsChanged.connect(
self._set_from_new_to_old)
self.new_stack.ui.histogram.vb.linkView(
ViewBox.YAxis, self.original_stack.ui.histogram.vb)
self.new_stack.ui.histogram.vb.linkView(
ViewBox.XAxis, self.original_stack.ui.histogram.vb)
def disconnect_histogram_changes(self):
self.original_stack.ui.histogram.sigLevelsChanged.disconnect(
self._set_from_old_to_new)
self.new_stack.ui.histogram.sigLevelsChanged.disconnect(
self._set_from_new_to_old)
self.new_stack.ui.histogram.vb.linkView(ViewBox.YAxis, None)
self.new_stack.ui.histogram.vb.linkView(ViewBox.XAxis, None)
class FiltersWindowView(BaseMainWindowView):
auto_update_triggered = pyqtSignal()
filter_applied = pyqtSignal()
splitter: QSplitter
collapseToggleButton: QPushButton
linkImages: QCheckBox
invertDifference: QCheckBox
overlayDifference: QCheckBox
lockScaleCheckBox: QCheckBox
lockZoomCheckBox: QCheckBox
previewsLayout: QVBoxLayout
previews: FilterPreviews
stackSelector: StackSelectorWidgetView
notification_icon: QLabel
notification_text: QLabel
presenter: FiltersWindowPresenter
applyButton: QPushButton
applyToAllButton: QPushButton
filterSelector: QComboBox
def __init__(self, main_window: 'MainWindowView'):
super().__init__(main_window, 'gui/ui/filters_window.ui')
self.main_window = main_window
self.presenter = FiltersWindowPresenter(self, main_window)
self.roi_view = None
self.roi_view_averaged = False
self.splitter.setSizes([200, 9999])
self.splitter.setStretchFactor(0, 1)
# Populate list of operations and handle filter selection
self.filterSelector.addItems(self.presenter.model.filter_names)
self.filterSelector.currentTextChanged.connect(
self.handle_filter_selection)
self.filterSelector.currentTextChanged.connect(
self._update_apply_all_button)
# Handle stack selection
self.stackSelector.stack_selected_uuid.connect(
self.presenter.set_stack_uuid)
self.stackSelector.stack_selected_uuid.connect(
self.auto_update_triggered.emit)
# Handle apply filter
self.applyButton.clicked.connect(
lambda: self.presenter.notify(PresNotification.APPLY_FILTER))
self.applyToAllButton.clicked.connect(lambda: self.presenter.notify(
PresNotification.APPLY_FILTER_TO_ALL))
self.previews = FilterPreviews(self)
self.previews.setSizePolicy(QSizePolicy.Expanding,
QSizePolicy.Expanding)
self.previewsLayout.addWidget(self.previews)
self.clear_previews()
self.linkImages.stateChanged.connect(self.link_images_changed)
# set here to trigger the changed event
self.linkImages.setChecked(True)
self.invertDifference.stateChanged.connect(
lambda: self.presenter.notify(PresNotification.UPDATE_PREVIEWS))
self.overlayDifference.stateChanged.connect(
lambda: self.presenter.notify(PresNotification.UPDATE_PREVIEWS))
# Handle preview index selection
self.previewImageIndex.valueChanged[int].connect(
self.presenter.set_preview_image_index)
# Preview update triggers
self.auto_update_triggered.connect(self.on_auto_update_triggered)
self.updatePreviewButton.clicked.connect(
lambda: self.presenter.notify(PresNotification.UPDATE_PREVIEWS))
self.stackSelector.subscribe_to_main_window(main_window)
self.stackSelector.select_eligible_stack()
# Handle help button pressed
self.filterHelpButton.pressed.connect(self.open_help_webpage)
self.collapseToggleButton.pressed.connect(self.toggle_filters_section)
self.handle_filter_selection("")
def closeEvent(self, e):
if self.presenter.filter_is_running:
e.ignore()
else:
super().closeEvent(e)
def cleanup(self):
self.stackSelector.unsubscribe_from_main_window()
if self.roi_view is not None:
self.roi_view.close()
self.roi_view = None
self.auto_update_triggered.disconnect()
self.main_window.filters = None
self.presenter = None
def show(self):
super().show()
self.auto_update_triggered.emit()
def handle_filter_selection(self, filter_name: str):
"""
Handle selection of a filter from the drop down list.
"""
# If a divider select the one below the divider.
if filter_name == self.presenter.divider:
self.filterSelector.setCurrentIndex(
self.filterSelector.currentIndex() + 1)
# Changing the selection triggers a second run through of this method that results in unwanted popups
# Terminating the original call here ensures that the presenter is only notified once
return
# Remove all existing items from the properties layout
delete_all_widgets_from_layout(self.filterPropertiesLayout)
# Do registration of new filter
self.presenter.notify(PresNotification.REGISTER_ACTIVE_FILTER)
# Update preview on filter selection (on the off chance the default
# options are valid)
self.auto_update_triggered.emit()
def on_auto_update_triggered(self):
"""
Called when the signal indicating the filter, filter properties or data
has changed such that the previews are now out of date.
"""
# Disable the preview image box widget as it can misbehave if making a preview takes too long
self.previewImageIndex.setEnabled(False)
self.clear_notification_dialog()
if self.previewAutoUpdate.isChecked() and self.isVisible():
self.presenter.notify(PresNotification.UPDATE_PREVIEWS)
# Enable the spinbox widget once the preview has been created
self.previewImageIndex.setEnabled(True)
def clear_previews(self, clear_before: bool = True):
self.previews.clear_items(clear_before=clear_before)
def link_images_changed(self):
if self.linkImages.isChecked():
self.previews.link_all_views()
else:
self.previews.unlink_all_views()
@property
def preview_image_before(self) -> ImageItem:
return self.previews.imageview_before
@property
def preview_image_after(self) -> ImageItem:
return self.previews.imageview_after
@property
def preview_image_difference(self) -> ImageItem:
return self.previews.imageview_difference
def show_error_dialog(self, msg=""):
self.notification_text.show()
self.notification_icon.setPixmap(QApplication.style().standardPixmap(
QStyle.SP_MessageBoxCritical))
self.notification_text.setText(str(msg))
def clear_notification_dialog(self):
self.notification_icon.clear()
self.notification_text.clear()
self.notification_text.hide()
def show_operation_completed(self, operation_name):
self.notification_text.show()
self.notification_icon.setPixmap(QApplication.style().standardPixmap(
QStyle.SP_DialogYesButton))
self.notification_text.setText(
f"{operation_name} completed successfully!")
def show_operation_cancelled(self, operation_name):
self.notification_text.show()
self.notification_icon.setPixmap(QApplication.style().standardPixmap(
QStyle.SP_DialogYesButton))
self.notification_text.setText(
f"{operation_name} cancelled, original data restored")
def open_help_webpage(self):
filter_name = self.filterSelector.currentText()
try:
open_user_operation_docs(filter_name)
except RuntimeError as err:
self.show_error_dialog(str(err))
def ask_confirmation(self, msg: str):
response = QMessageBox.question(self, "Confirm action", msg,
QMessageBox.Ok
| QMessageBox.Cancel) # type:ignore
return response == QMessageBox.Ok
def _update_apply_all_button(self, filter_name):
list_of_apply_single_stack = ["ROI Normalisation", "Flat-fielding"]
if filter_name in list_of_apply_single_stack:
self.applyToAllButton.setEnabled(False)
else:
self.applyToAllButton.setEnabled(True)
def roi_visualiser(self, roi_field):
# Start the stack visualiser and ensure that it uses the ROI from here in the rest of this
try:
images = self.presenter.stack.presenter.get_image(
self.presenter.model.preview_image_idx)
except Exception:
# Happens if nothing has been loaded, so do nothing as nothing can't be visualised
return
window = QMainWindow(self)
window.setWindowTitle("Select ROI")
window.setMinimumHeight(600)
window.setMinimumWidth(600)
self.roi_view = MIImageView(window)
window.setCentralWidget(self.roi_view)
self.roi_view.setWindowTitle("Select ROI for operation")
def set_averaged_image():
averaged_images = np.sum(
self.presenter.stack.presenter.images.data, axis=0)
self.roi_view.setImage(
averaged_images.reshape(
(1, averaged_images.shape[0], averaged_images.shape[1])))
self.roi_view_averaged = True
def toggle_average_images(images_):
if self.roi_view_averaged:
self.roi_view.setImage(images_.data)
self.roi_view_averaged = False
else:
set_averaged_image()
self.roi_view.roi.show()
self.roi_view.ui.roiPlot.hide()
# Add context menu bits:
menu = QMenu(self.roi_view)
toggle_show_averaged_image = QAction("Toggle show averaged image",
menu)
toggle_show_averaged_image.triggered.connect(
lambda: toggle_average_images(images))
menu.addAction(toggle_show_averaged_image)
menu.addSeparator()
self.roi_view.imageItem.menu = menu
set_averaged_image()
def roi_changed_callback(callback):
roi_field.setText(callback.to_list_string())
roi_field.editingFinished.emit()
self.roi_view.roi_changed_callback = lambda callback: roi_changed_callback(
callback)
# prep the MIImageView to display in this context
self.roi_view.ui.roiBtn.hide()
self.roi_view.ui.histogram.hide()
self.roi_view.ui.menuBtn.hide()
self.roi_view.ui.roiPlot.hide()
self.roi_view.roi.show()
self.roi_view.ui.gridLayout.setRowStretch(1, 5)
self.roi_view.ui.gridLayout.setRowStretch(0, 95)
self.roi_view.button_stack_right.hide()
self.roi_view.button_stack_left.hide()
button = QPushButton("OK", window)
button.clicked.connect(lambda: window.close())
self.roi_view.ui.gridLayout.addWidget(button)
window.show()
def toggle_filters_section(self):
if self.collapseToggleButton.text() == "<<":
self.splitter.setSizes([0, 9999])
self.collapseToggleButton.setText(">>")
else:
self.splitter.setSizes([200, 9999])
self.collapseToggleButton.setText("<<")
def roi_visualiser(self, roi_field):
# Start the stack visualiser and ensure that it uses the ROI from here in the rest of this
try:
images = self.presenter.stack.presenter.get_image(
self.presenter.model.preview_image_idx)
except Exception:
# Happens if nothing has been loaded, so do nothing as nothing can't be visualised
return
window = QMainWindow(self)
window.setWindowTitle("Select ROI")
window.setMinimumHeight(600)
window.setMinimumWidth(600)
self.roi_view = MIImageView(window)
window.setCentralWidget(self.roi_view)
self.roi_view.setWindowTitle("Select ROI for operation")
def set_averaged_image():
averaged_images = np.sum(
self.presenter.stack.presenter.images.data, axis=0)
self.roi_view.setImage(
averaged_images.reshape(
(1, averaged_images.shape[0], averaged_images.shape[1])))
self.roi_view_averaged = True
def toggle_average_images(images_):
if self.roi_view_averaged:
self.roi_view.setImage(images_.data)
self.roi_view_averaged = False
else:
set_averaged_image()
self.roi_view.roi.show()
self.roi_view.ui.roiPlot.hide()
# Add context menu bits:
menu = QMenu(self.roi_view)
toggle_show_averaged_image = QAction("Toggle show averaged image",
menu)
toggle_show_averaged_image.triggered.connect(
lambda: toggle_average_images(images))
menu.addAction(toggle_show_averaged_image)
menu.addSeparator()
self.roi_view.imageItem.menu = menu
set_averaged_image()
def roi_changed_callback(callback):
roi_field.setText(callback.to_list_string())
roi_field.editingFinished.emit()
self.roi_view.roi_changed_callback = lambda callback: roi_changed_callback(
callback)
# prep the MIImageView to display in this context
self.roi_view.ui.roiBtn.hide()
self.roi_view.ui.histogram.hide()
self.roi_view.ui.menuBtn.hide()
self.roi_view.ui.roiPlot.hide()
self.roi_view.roi.show()
self.roi_view.ui.gridLayout.setRowStretch(1, 5)
self.roi_view.ui.gridLayout.setRowStretch(0, 95)
self.roi_view.button_stack_right.hide()
self.roi_view.button_stack_left.hide()
button = QPushButton("OK", window)
button.clicked.connect(lambda: window.close())
self.roi_view.ui.gridLayout.addWidget(button)
window.show()