class UIManipulateROIWindow:
def setup_ui(self, manipulate_roi_window_instance, rois, dataset_rtss,
roi_color, signal_roi_manipulated):
self.patient_dict_container = PatientDictContainer()
self.rois = rois
self.dataset_rtss = dataset_rtss
self.signal_roi_manipulated = signal_roi_manipulated
self.roi_color = roi_color
self.roi_names = [] # Names of selected ROIs
self.all_roi_names = [] # Names of all existing ROIs
for roi_id, roi_dict in self.rois.items():
self.all_roi_names.append(roi_dict['name'])
# Operation names
self.single_roi_operation_names = [
"Expand", "Contract", "Inner Rind (annulus)",
"Outer Rind (annulus)"
]
self.multiple_roi_operation_names = [
"Union", "Intersection", "Difference"
]
self.operation_names = self.multiple_roi_operation_names + \
self.single_roi_operation_names
self.new_ROI_contours = None
self.manipulate_roi_window_instance = manipulate_roi_window_instance
self.dicom_view = DicomAxialView(metadata_formatted=True,
is_four_view=True)
self.dicom_preview = DicomAxialView(metadata_formatted=True,
is_four_view=True)
self.dicom_view.slider.valueChanged.connect(
self.dicom_view_slider_value_changed)
self.dicom_preview.slider.valueChanged.connect(
self.dicom_preview_slider_value_changed)
self.init_layout()
QtCore.QMetaObject.connectSlotsByName(manipulate_roi_window_instance)
def retranslate_ui(self, manipulate_roi_window_instance):
_translate = QtCore.QCoreApplication.translate
manipulate_roi_window_instance.setWindowTitle(
_translate("ManipulateRoiWindowInstance",
"OnkoDICOM - Draw Region Of Interest"))
self.first_roi_name_label.setText(
_translate("FirstROINameLabel", "ROI 1: "))
self.first_roi_name_dropdown_list.setPlaceholderText("ROI 1")
self.first_roi_name_dropdown_list.addItems(self.all_roi_names)
self.operation_name_label.setText(
_translate("OperationNameLabel", "Operation"))
self.operation_name_dropdown_list.setPlaceholderText("Operation")
self.operation_name_dropdown_list.addItems(self.operation_names)
self.second_roi_name_label.setText(
_translate("SecondROINameLabel", "ROI 2: "))
self.second_roi_name_dropdown_list.setPlaceholderText("ROI 2")
self.second_roi_name_dropdown_list.addItems(self.all_roi_names)
self.manipulate_roi_window_instance_draw_button.setText(
_translate("ManipulateRoiWindowInstanceDrawButton", "Draw"))
self.manipulate_roi_window_instance_save_button.setText(
_translate("ManipulateRoiWindowInstanceSaveButton", "Save"))
self.manipulate_roi_window_instance_cancel_button.setText(
_translate("ManipulateRoiWindowInstanceCancelButton", "Cancel"))
self.margin_label.setText(_translate("MarginLabel", "Margin (mm): "))
self.new_roi_name_label.setText(
_translate("NewROINameLabel", "New ROI Name"))
self.ROI_view_box_label.setText("ROI")
self.preview_box_label.setText("Preview")
def init_layout(self):
"""
Initialize the layout for the DICOM View tab.
Add the view widget and the slider in the layout.
Add the whole container 'tab2_view' as a tab in the main page.
"""
# Initialise a ManipulateROIWindow
if platform.system() == 'Darwin':
self.stylesheet_path = "res/stylesheet.qss"
else:
self.stylesheet_path = "res/stylesheet-win-linux.qss"
stylesheet = open(resource_path(self.stylesheet_path)).read()
window_icon = QIcon()
window_icon.addPixmap(QPixmap(resource_path("res/images/icon.ico")),
QIcon.Normal, QIcon.Off)
self.manipulate_roi_window_instance.setObjectName(
"ManipulateRoiWindowInstance")
self.manipulate_roi_window_instance.setWindowIcon(window_icon)
# Creating a form box to hold all buttons and input fields
self.manipulate_roi_window_input_container_box = QFormLayout()
self.manipulate_roi_window_input_container_box.setObjectName(
"ManipulateRoiWindowInputContainerBox")
self.manipulate_roi_window_input_container_box.setLabelAlignment(
Qt.AlignLeft)
# Create a label for denoting the first ROI name
self.first_roi_name_label = QLabel()
self.first_roi_name_label.setObjectName("FirstROINameLabel")
self.first_roi_name_dropdown_list = QComboBox()
# Create an dropdown list for ROI name
self.first_roi_name_dropdown_list.setObjectName(
"FirstROINameDropdownList")
self.first_roi_name_dropdown_list.setSizePolicy(
QSizePolicy.Minimum, QSizePolicy.Minimum)
self.first_roi_name_dropdown_list.resize(
self.first_roi_name_dropdown_list.sizeHint().width(),
self.first_roi_name_dropdown_list.sizeHint().height())
self.first_roi_name_dropdown_list.activated.connect(
self.update_selected_rois)
self.manipulate_roi_window_input_container_box.addRow(
self.first_roi_name_label, self.first_roi_name_dropdown_list)
# Create a label for denoting the operation
self.operation_name_label = QLabel()
self.operation_name_label.setObjectName("OperationNameLabel")
self.operation_name_dropdown_list = QComboBox()
# Create an dropdown list for operation name
self.operation_name_dropdown_list.setObjectName(
"OperationNameDropdownList")
self.operation_name_dropdown_list.setSizePolicy(
QSizePolicy.Minimum, QSizePolicy.Minimum)
self.operation_name_dropdown_list.resize(
self.operation_name_dropdown_list.sizeHint().width(),
self.operation_name_dropdown_list.sizeHint().height())
self.operation_name_dropdown_list.activated.connect(
self.operation_changed)
self.manipulate_roi_window_input_container_box.addRow(
self.operation_name_label, self.operation_name_dropdown_list)
# Create a label for denoting the second ROI name
self.second_roi_name_label = QLabel()
self.second_roi_name_label.setObjectName("SecondROINameLabel")
self.second_roi_name_label.setVisible(False)
self.second_roi_name_dropdown_list = QComboBox()
# Create an dropdown list for ROI name
self.second_roi_name_dropdown_list.setObjectName(
"SecondROINameDropdownList")
self.second_roi_name_dropdown_list.setSizePolicy(
QSizePolicy.Minimum, QSizePolicy.Minimum)
self.second_roi_name_dropdown_list.resize(
self.second_roi_name_dropdown_list.sizeHint().width(),
self.second_roi_name_dropdown_list.sizeHint().height())
self.second_roi_name_dropdown_list.setVisible(False)
self.second_roi_name_dropdown_list.activated.connect(
self.update_selected_rois)
self.manipulate_roi_window_input_container_box.addRow(
self.second_roi_name_label, self.second_roi_name_dropdown_list)
# Create a label for denoting the margin
self.margin_label = QLabel()
self.margin_label.setObjectName("MarginLabel")
self.margin_label.setVisible(False)
# Create input for the new ROI name
self.margin_line_edit = QLineEdit()
self.margin_line_edit.setObjectName("MarginInput")
self.margin_line_edit.setSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.Minimum)
self.margin_line_edit.resize(self.margin_line_edit.sizeHint().width(),
self.margin_line_edit.sizeHint().height())
self.margin_line_edit.setVisible(False)
self.margin_line_edit.setValidator(
QRegularExpressionValidator(
QRegularExpression("^[0-9]*[.]?[0-9]*$")))
self.manipulate_roi_window_input_container_box.addRow(
self.margin_label, self.margin_line_edit)
# Create a label for denoting the new ROI name
self.new_roi_name_label = QLabel()
self.new_roi_name_label.setObjectName("NewROINameLabel")
# Create input for the new ROI name
self.new_roi_name_line_edit = QLineEdit()
self.new_roi_name_line_edit.setObjectName("NewROINameInput")
self.new_roi_name_line_edit.setSizePolicy(QSizePolicy.MinimumExpanding,
QSizePolicy.Minimum)
self.new_roi_name_line_edit.resize(
self.new_roi_name_line_edit.sizeHint().width(),
self.new_roi_name_line_edit.sizeHint().height())
self.manipulate_roi_window_input_container_box.addRow(
self.new_roi_name_label, self.new_roi_name_line_edit)
# Create a spacer between inputs and buttons
spacer = QWidget()
spacer.setSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding)
spacer.setFocusPolicy(Qt.NoFocus)
self.manipulate_roi_window_input_container_box.addRow(spacer)
# Create a warning message when missing inputs
self.warning_message = QWidget()
self.warning_message.setContentsMargins(8, 5, 8, 5)
warning_message_layout = QHBoxLayout()
warning_message_layout.setAlignment(QtCore.Qt.AlignLeft
| QtCore.Qt.AlignLeft)
warning_message_icon = QLabel()
warning_message_icon.setPixmap(
QtGui.QPixmap(
resource_path("res/images/btn-icons/alert_icon.png")))
warning_message_layout.addWidget(warning_message_icon)
self.warning_message_text = QLabel()
self.warning_message_text.setStyleSheet("color: red")
warning_message_layout.addWidget(self.warning_message_text)
self.warning_message.setLayout(warning_message_layout)
self.warning_message.setVisible(False)
self.manipulate_roi_window_input_container_box.addRow(
self.warning_message)
# Create a draw button
self.manipulate_roi_window_instance_draw_button = QPushButton()
self.manipulate_roi_window_instance_draw_button.setObjectName(
"ManipulateRoiWindowInstanceDrawButton")
self.manipulate_roi_window_instance_draw_button.setSizePolicy(
QSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.Minimum))
self.manipulate_roi_window_instance_draw_button.resize(
self.manipulate_roi_window_instance_draw_button.sizeHint().width(),
self.manipulate_roi_window_instance_draw_button.sizeHint().height(
))
self.manipulate_roi_window_instance_draw_button.setCursor(
QtGui.QCursor(QtCore.Qt.PointingHandCursor))
self.manipulate_roi_window_instance_draw_button.clicked.connect(
self.onDrawButtonClicked)
self.manipulate_roi_window_input_container_box.addRow(
self.manipulate_roi_window_instance_draw_button)
# Create a horizontal box for saving and cancel the drawing
self.manipulate_roi_window_cancel_save_box = QHBoxLayout()
self.manipulate_roi_window_cancel_save_box.setObjectName(
"ManipulateRoiWindowCancelSaveBox")
# Create an exit button to cancel the drawing
# Add a button to go back/exit from the application
self.manipulate_roi_window_instance_cancel_button = QPushButton()
self.manipulate_roi_window_instance_cancel_button.setObjectName(
"ManipulateRoiWindowInstanceCancelButton")
self.manipulate_roi_window_instance_cancel_button.setSizePolicy(
QSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.Minimum))
self.manipulate_roi_window_instance_cancel_button.resize(
self.manipulate_roi_window_instance_cancel_button.sizeHint().width(
),
self.manipulate_roi_window_instance_cancel_button.sizeHint().
height())
self.manipulate_roi_window_instance_cancel_button.setCursor(
QtGui.QCursor(QtCore.Qt.PointingHandCursor))
self.manipulate_roi_window_instance_cancel_button.clicked.connect(
self.onCancelButtonClicked)
self.manipulate_roi_window_instance_cancel_button.setProperty(
"QPushButtonClass", "fail-button")
icon_cancel = QtGui.QIcon()
icon_cancel.addPixmap(
QtGui.QPixmap(
resource_path('res/images/btn-icons/cancel_icon.png')))
self.manipulate_roi_window_instance_cancel_button.setIcon(icon_cancel)
self.manipulate_roi_window_cancel_save_box.addWidget(
self.manipulate_roi_window_instance_cancel_button)
# Create a save button to save all the changes
self.manipulate_roi_window_instance_save_button = QPushButton()
self.manipulate_roi_window_instance_save_button.setObjectName(
"ManipulateRoiWindowInstanceSaveButton")
self.manipulate_roi_window_instance_save_button.setSizePolicy(
QSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.Minimum))
self.manipulate_roi_window_instance_save_button.resize(
self.manipulate_roi_window_instance_save_button.sizeHint().width(),
self.manipulate_roi_window_instance_save_button.sizeHint().height(
))
self.manipulate_roi_window_instance_save_button.setProperty(
"QPushButtonClass", "success-button")
icon_save = QtGui.QIcon()
icon_save.addPixmap(
QtGui.QPixmap(resource_path('res/images/btn-icons/save_icon.png')))
self.manipulate_roi_window_instance_save_button.setIcon(icon_save)
self.manipulate_roi_window_instance_save_button.clicked.connect(
self.onSaveClicked)
self.manipulate_roi_window_cancel_save_box.addWidget(
self.manipulate_roi_window_instance_save_button)
self.manipulate_roi_window_input_container_box.addRow(
self.manipulate_roi_window_cancel_save_box)
# Creating a horizontal box to hold the ROI view and the preview
self.manipulate_roi_window_instance_view_box = QHBoxLayout()
self.manipulate_roi_window_instance_view_box.setObjectName(
"ManipulateRoiWindowInstanceViewBoxes")
# Font for the ROI view and preview's labels
font = QFont()
font.setBold(True)
font.setPixelSize(20)
# Creating the ROI view
self.ROI_view_box_layout = QVBoxLayout()
self.ROI_view_box_label = QLabel()
self.ROI_view_box_label.setFont(font)
self.ROI_view_box_label.setAlignment(Qt.AlignHCenter)
self.ROI_view_box_layout.addWidget(self.ROI_view_box_label)
self.ROI_view_box_layout.addWidget(self.dicom_view)
self.ROI_view_box_widget = QWidget()
self.ROI_view_box_widget.setLayout(self.ROI_view_box_layout)
# Creating the preview
self.preview_box_layout = QVBoxLayout()
self.preview_box_label = QLabel()
self.preview_box_label.setFont(font)
self.preview_box_label.setAlignment(Qt.AlignHCenter)
self.preview_box_layout.addWidget(self.preview_box_label)
self.preview_box_layout.addWidget(self.dicom_preview)
self.preview_box_widget = QWidget()
self.preview_box_widget.setLayout(self.preview_box_layout)
# Add View and Slider into horizontal box
self.manipulate_roi_window_instance_view_box.addWidget(
self.ROI_view_box_widget)
self.manipulate_roi_window_instance_view_box.addWidget(
self.preview_box_widget)
# Create a widget to hold the image slice box
self.manipulate_roi_window_instance_view_widget = QWidget()
self.manipulate_roi_window_instance_view_widget.setObjectName(
"ManipulateRoiWindowInstanceActionWidget")
self.manipulate_roi_window_instance_view_widget.setLayout(
self.manipulate_roi_window_instance_view_box)
# Create a horizontal box for containing the input fields and the
# viewports
self.manipulate_roi_window_main_box = QHBoxLayout()
self.manipulate_roi_window_main_box.setObjectName(
"ManipulateRoiWindowMainBox")
self.manipulate_roi_window_main_box.addLayout(
self.manipulate_roi_window_input_container_box, 1)
self.manipulate_roi_window_main_box.addWidget(
self.manipulate_roi_window_instance_view_widget, 11)
# Create a new central widget to hold the horizontal box layout
self.manipulate_roi_window_instance_central_widget = QWidget()
self.manipulate_roi_window_instance_central_widget.setObjectName(
"ManipulateRoiWindowInstanceCentralWidget")
self.manipulate_roi_window_instance_central_widget.setLayout(
self.manipulate_roi_window_main_box)
self.retranslate_ui(self.manipulate_roi_window_instance)
self.manipulate_roi_window_instance.setStyleSheet(stylesheet)
self.manipulate_roi_window_instance.setCentralWidget(
self.manipulate_roi_window_instance_central_widget)
QtCore.QMetaObject.connectSlotsByName(
self.manipulate_roi_window_instance)
def dicom_view_slider_value_changed(self):
"""
Display selected ROIs in dropbox when moving to another image slice
"""
self.display_selected_roi()
if self.dicom_preview.slider.value() != self.dicom_view.slider.value():
self.dicom_preview.slider.setValue(self.dicom_view.slider.value())
def dicom_preview_slider_value_changed(self):
"""
Display generated ROI when moving to another image slice
"""
self.draw_roi()
if self.dicom_preview.slider.value() != self.dicom_view.slider.value():
self.dicom_view.slider.setValue(self.dicom_preview.slider.value())
def onCancelButtonClicked(self):
"""
This function is used for canceling the drawing
"""
self.close()
def onDrawButtonClicked(self):
"""
Function triggered when the Draw button is pressed from the menu.
"""
# Hide warning message
self.warning_message.setVisible(False)
# Check inputs
selected_operation = self.operation_name_dropdown_list.currentText()
roi_1 = self.first_roi_name_dropdown_list.currentText()
roi_2 = self.second_roi_name_dropdown_list.currentText()
new_roi_name = self.new_roi_name_line_edit.text()
# Check the selected inputs and execute the operations
if roi_1 != "" and new_roi_name != "" and \
self.margin_line_edit.text() != "" and \
selected_operation in self.single_roi_operation_names:
# Single ROI operations
dict_rois_contours = ROI.get_roi_contour_pixel(
self.patient_dict_container.get("raw_contour"), [roi_1],
self.patient_dict_container.get("pixluts"))
roi_geometry = ROI.roi_to_geometry(dict_rois_contours[roi_1])
margin = float(self.margin_line_edit.text())
if selected_operation == self.single_roi_operation_names[0]:
new_geometry = ROI.scale_roi(roi_geometry, margin)
elif selected_operation == self.single_roi_operation_names[1]:
new_geometry = ROI.scale_roi(roi_geometry, -margin)
elif selected_operation == self.single_roi_operation_names[2]:
new_geometry = ROI.rind_roi(roi_geometry, -margin)
else:
new_geometry = ROI.rind_roi(roi_geometry, margin)
self.new_ROI_contours = ROI.geometry_to_roi(new_geometry)
self.draw_roi()
return True
elif roi_1 != "" and roi_2 != "" and new_roi_name != "" and \
selected_operation in self.multiple_roi_operation_names:
# Multiple ROI operations
dict_rois_contours = ROI.get_roi_contour_pixel(
self.patient_dict_container.get("raw_contour"), [roi_1, roi_2],
self.patient_dict_container.get("pixluts"))
roi_1_geometry = ROI.roi_to_geometry(dict_rois_contours[roi_1])
roi_2_geometry = ROI.roi_to_geometry(dict_rois_contours[roi_2])
# Execute the selected operation
new_geometry = ROI.manipulate_rois(roi_1_geometry, roi_2_geometry,
selected_operation.upper())
self.new_ROI_contours = ROI.geometry_to_roi(new_geometry)
self.draw_roi()
return True
self.warning_message_text.setText("Not all values are specified.")
self.warning_message.setVisible(True)
return False
def onSaveClicked(self):
""" Save the new ROI """
# Get the name of the new ROI
new_roi_name = self.new_roi_name_line_edit.text()
# If the new ROI hasn't been drawn, draw the new ROI. Then if the new
# ROI is drawn successfully, proceed to save the new ROI.
if self.new_ROI_contours is None:
if not self.onDrawButtonClicked():
return
# Get a dict to convert SOPInstanceUID to slice id
slice_ids_dict = get_dict_slice_to_uid(PatientDictContainer())
# Transform new_ROI_contours to a list of roi information
rois_to_save = {}
for uid, contour_sequence in self.new_ROI_contours.items():
slider_id = slice_ids_dict[uid]
location = self.patient_dict_container.filepaths[slider_id]
ds = pydicom.dcmread(location)
slice_info = {'coords': contour_sequence, 'ds': ds}
rois_to_save[slider_id] = slice_info
roi_list = ROI.convert_hull_list_to_contours_data(
rois_to_save, self.patient_dict_container)
connectSaveROIProgress(self, roi_list, self.dataset_rtss, new_roi_name,
self.roi_saved)
def draw_roi(self):
""" Draw the new ROI """
# Get the new ROI's name
new_roi_name = self.new_roi_name_line_edit.text()
# Check if the new ROI contour is None
if self.new_ROI_contours is None:
return
# Get the info required to draw the new ROI
slider_id = self.dicom_preview.slider.value()
curr_slice = self.patient_dict_container.get("dict_uid")[slider_id]
# Calculate the new ROI's polygon
dict_ROI_contours = {}
dict_ROI_contours[new_roi_name] = self.new_ROI_contours
polygons = ROI.calc_roi_polygon(new_roi_name, curr_slice,
dict_ROI_contours)
# Set the new ROI color
color = QtGui.QColor()
color.setRgb(90, 250, 175, 200)
pen_color = QtGui.QColor(color.red(), color.green(), color.blue())
pen = QtGui.QPen(pen_color)
pen.setStyle(QtCore.Qt.PenStyle(1))
pen.setWidthF(2.0)
# Draw the new ROI
self.dicom_preview.update_view()
for i in range(len(polygons)):
self.dicom_preview.scene.addPolygon(polygons[i], pen,
QtGui.QBrush(color))
def update_selected_rois(self):
""" Get the names of selected ROIs """
# Hide warning message
self.warning_message.setVisible(False)
self.roi_names = []
if self.first_roi_name_dropdown_list.currentText() != "":
self.roi_names.append(
self.first_roi_name_dropdown_list.currentText())
if self.second_roi_name_dropdown_list.currentText() != "" and \
self.second_roi_name_dropdown_list.isVisible():
self.roi_names.append(
self.second_roi_name_dropdown_list.currentText())
self.dict_rois_contours_axial = ROI.get_roi_contour_pixel(
self.patient_dict_container.get("raw_contour"), self.roi_names,
self.patient_dict_container.get("pixluts"))
self.display_selected_roi()
def display_selected_roi(self):
""" Display selected ROIs """
# Get the info required to display the selected ROIs
slider_id = self.dicom_view.slider.value()
curr_slice = self.patient_dict_container.get("dict_uid")[slider_id]
self.rois = self.patient_dict_container.get("rois")
# Display the selected ROIs
self.dicom_view.update_view()
for roi_id, roi_dict in self.rois.items():
roi_name = roi_dict['name']
if roi_name in self.roi_names:
polygons = ROI.calc_roi_polygon(roi_name, curr_slice,
self.dict_rois_contours_axial)
self.dicom_view.draw_roi_polygons(roi_id, polygons,
self.roi_color)
def operation_changed(self):
""" Change the form when users select different operations """
# Hide warning message
self.warning_message.setVisible(False)
selected_operation = self.operation_name_dropdown_list.currentText()
if selected_operation in self.single_roi_operation_names:
self.second_roi_name_label.setVisible(False)
self.second_roi_name_dropdown_list.setVisible(False)
self.margin_label.setVisible(True)
self.margin_line_edit.setVisible(True)
self.update_selected_rois()
else:
self.second_roi_name_label.setVisible(True)
self.second_roi_name_dropdown_list.setVisible(True)
self.margin_label.setVisible(False)
self.margin_line_edit.setVisible(False)
self.update_selected_rois()
def roi_saved(self, new_rtss):
""" Create a new ROI in Structure Tab and notify user """
new_roi_name = self.new_roi_name_line_edit.text()
self.signal_roi_manipulated.emit((new_rtss, {"draw": new_roi_name}))
QMessageBox.about(self.manipulate_roi_window_instance, "Saved",
"New contour successfully created!")
self.close()
class UIDrawROIWindow:
def setup_ui(self, draw_roi_window_instance, rois, dataset_rtss,
signal_roi_drawn):
"""
this function is responsible for setting up the UI
for DrawROIWindow
param draw_roi_window_instance: the current drawing
window instance.
:param rois: the rois to be drawn
:param dataset_rtss: the rtss to be written to
:param signal_roi_drawn: the signal to be triggered
when roi is drawn
"""
self.patient_dict_container = PatientDictContainer()
self.rois = rois
self.dataset_rtss = dataset_rtss
self.signal_roi_drawn = signal_roi_drawn
self.drawn_roi_list = {}
self.standard_organ_names = []
self.standard_volume_names = []
self.standard_names = [] # Combination of organ and volume
self.ROI_name = None # Selected ROI name
self.target_pixel_coords = [] # This will contain the new pixel
# coordinates specified by the min and max
self.drawingROI = None
self.slice_changed = False
self.drawing_tool_radius = INITIAL_DRAWING_TOOL_RADIUS
self.keep_empty_pixel = False
# pixel density
self.target_pixel_coords_single_array = [] # 1D array
self.draw_roi_window_instance = draw_roi_window_instance
self.colour = None
self.ds = None
self.zoom = 1.0
self.upper_limit = None
self.lower_limit = None
# is_four_view is set to True to stop the SUV2ROI button from appearing
self.dicom_view = DicomAxialView(is_four_view=True)
self.current_slice = self.dicom_view.slider.value()
self.dicom_view.slider.valueChanged.connect(self.slider_value_changed)
self.init_layout()
QtCore.QMetaObject.connectSlotsByName(draw_roi_window_instance)
def retranslate_ui(self, draw_roi_window_instance):
"""
this function retranslate the ui for draw roi window
:param draw_roi_window_instance: the current drawing
window instance.
"""
_translate = QtCore.QCoreApplication.translate
draw_roi_window_instance.setWindowTitle(
_translate("DrawRoiWindowInstance",
"OnkoDICOM - Draw Region Of Interest"))
self.roi_name_label.setText(
_translate("ROINameLabel", "Region of Interest: "))
self.roi_name_line_edit.setText(_translate("ROINameLineEdit", ""))
self.image_slice_number_label.setText(
_translate("ImageSliceNumberLabel", "Slice Number: "))
self.image_slice_number_line_edit.setText(
_translate("ImageSliceNumberLineEdit",
str(self.dicom_view.current_slice_number)))
self.image_slice_number_transect_button.setText(
_translate("ImageSliceNumberTransectButton", "Transect"))
self.image_slice_number_box_draw_button.setText(
_translate("ImageSliceNumberBoxDrawButton", "Set Bounds"))
self.image_slice_number_draw_button.setText(
_translate("ImageSliceNumberDrawButton", "Draw"))
self.image_slice_number_move_forward_button.setText(
_translate("ImageSliceNumberMoveForwardButton", ""))
self.image_slice_number_move_backward_button.setText(
_translate("ImageSliceNumberMoveBackwardButton", ""))
self.draw_roi_window_instance_save_button.setText(
_translate("DrawRoiWindowInstanceSaveButton", "Save"))
self.draw_roi_window_instance_cancel_button.setText(
_translate("DrawRoiWindowInstanceCancelButton", "Cancel"))
self.internal_hole_max_label.setText(
_translate("InternalHoleLabel",
"Maximum internal hole size (pixels): "))
self.internal_hole_max_line_edit.setText(
_translate("InternalHoleInput", "9"))
self.isthmus_width_max_label.setText(
_translate("IsthmusWidthLabel",
"Maximum isthmus width size (pixels): "))
self.isthmus_width_max_line_edit.setText(
_translate("IsthmusWidthInput", "5"))
self.min_pixel_density_label.setText(
_translate("MinPixelDensityLabel", "Minimum density (pixels): "))
self.min_pixel_density_line_edit.setText(
_translate("MinPixelDensityInput", ""))
self.max_pixel_density_label.setText(
_translate("MaxPixelDensityLabel", "Maximum density (pixels): "))
self.max_pixel_density_line_edit.setText(
_translate("MaxPixelDensityInput", ""))
self.toggle_keep_empty_pixel_label.setText(
_translate("ToggleKeepEmptyPixelLabel", "Keep empty pixel: "))
self.draw_roi_window_viewport_zoom_label.setText(
_translate("DrawRoiWindowViewportZoomLabel", "Zoom: "))
self.draw_roi_window_cursor_radius_change_label.setText(
_translate("DrawRoiWindowCursorRadiusChangeLabel",
"Cursor Radius: "))
self.draw_roi_window_instance_action_reset_button.setText(
_translate("DrawRoiWindowInstanceActionClearButton", "Reset"))
def init_layout(self):
"""
Initialize the layout for the DICOM View tab.
Add the view widget and the slider in the layout.
Add the whole container 'tab2_view' as a tab in the main page.
"""
# Initialise a DrawROIWindow
if platform.system() == 'Darwin':
self.stylesheet_path = "res/stylesheet.qss"
else:
self.stylesheet_path = "res/stylesheet-win-linux.qss"
stylesheet = open(resource_path(self.stylesheet_path)).read()
window_icon = QIcon()
window_icon.addPixmap(QPixmap(resource_path("res/images/icon.ico")),
QIcon.Normal, QIcon.Off)
self.draw_roi_window_instance.setObjectName("DrawRoiWindowInstance")
self.draw_roi_window_instance.setWindowIcon(window_icon)
# Creating a form box to hold all buttons and input fields
self.draw_roi_window_input_container_box = QFormLayout()
self.draw_roi_window_input_container_box. \
setObjectName("DrawRoiWindowInputContainerBox")
self.draw_roi_window_input_container_box. \
setLabelAlignment(Qt.AlignLeft)
# Create a label for denoting the ROI name
self.roi_name_label = QLabel()
self.roi_name_label.setObjectName("ROINameLabel")
self.roi_name_line_edit = QLineEdit()
# Create an input box for ROI name
self.roi_name_line_edit.setObjectName("ROINameLineEdit")
self.roi_name_line_edit.setSizePolicy(QSizePolicy.Minimum,
QSizePolicy.Minimum)
self.roi_name_line_edit.resize(
self.roi_name_line_edit.sizeHint().width(),
self.roi_name_line_edit.sizeHint().height())
self.roi_name_line_edit.setEnabled(False)
self.draw_roi_window_input_container_box. \
addRow(self.roi_name_label, self.roi_name_line_edit)
# Create horizontal box to store image slice number and backward,
# forward buttons
self.image_slice_number_box = QHBoxLayout()
self.image_slice_number_box.setObjectName("ImageSliceNumberBox")
# Create a label for denoting the Image Slice Number
self.image_slice_number_label = QLabel()
self.image_slice_number_label.setObjectName("ImageSliceNumberLabel")
self.image_slice_number_box.addWidget(self.image_slice_number_label)
# Create a line edit for containing the image slice number
self.image_slice_number_line_edit = QLineEdit()
self.image_slice_number_line_edit. \
setObjectName("ImageSliceNumberLineEdit")
self.image_slice_number_line_edit. \
setSizePolicy(QSizePolicy.Minimum, QSizePolicy.Minimum)
self.image_slice_number_line_edit.resize(
self.image_slice_number_line_edit.sizeHint().width(),
self.image_slice_number_line_edit.sizeHint().height())
self.image_slice_number_line_edit.setCursorPosition(0)
self.image_slice_number_line_edit.setEnabled(False)
self.image_slice_number_box. \
addWidget(self.image_slice_number_line_edit)
# Create a button to move backward to the previous image
self.image_slice_number_move_backward_button = QPushButton()
self.image_slice_number_move_backward_button. \
setObjectName("ImageSliceNumberMoveBackwardButton")
self.image_slice_number_move_backward_button.setSizePolicy(
QSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed))
self.image_slice_number_move_backward_button.resize(QSize(24, 24))
self.image_slice_number_move_backward_button.clicked. \
connect(self.onBackwardClicked)
icon_move_backward = QtGui.QIcon()
icon_move_backward.addPixmap(
QtGui.QPixmap(
resource_path('res/images/btn-icons/backward_slide_icon.png')))
self.image_slice_number_move_backward_button.setIcon(
icon_move_backward)
self.image_slice_number_box. \
addWidget(self.image_slice_number_move_backward_button)
# Create a button to move forward to the next image
self.image_slice_number_move_forward_button = QPushButton()
self.image_slice_number_move_forward_button. \
setObjectName("ImageSliceNumberMoveForwardButton")
self.image_slice_number_move_forward_button.setSizePolicy(
QSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed))
self.image_slice_number_move_forward_button.resize(QSize(24, 24))
self.image_slice_number_move_forward_button.clicked. \
connect(self.onForwardClicked)
icon_move_forward = QtGui.QIcon()
icon_move_forward.addPixmap(
QtGui.QPixmap(
resource_path('res/images/btn-icons/forward_slide_icon.png')))
self.image_slice_number_move_forward_button.setIcon(icon_move_forward)
self.image_slice_number_box. \
addWidget(self.image_slice_number_move_forward_button)
self.draw_roi_window_input_container_box. \
addRow(self.image_slice_number_box)
# Create a horizontal box for containing the zoom function
self.draw_roi_window_viewport_zoom_box = QHBoxLayout()
self.draw_roi_window_viewport_zoom_box.setObjectName(
"DrawRoiWindowViewportZoomBox")
# Create a label for zooming
self.draw_roi_window_viewport_zoom_label = QLabel()
self.draw_roi_window_viewport_zoom_label. \
setObjectName("DrawRoiWindowViewportZoomLabel")
# Create an input box for zoom factor
self.draw_roi_window_viewport_zoom_input = QLineEdit()
self.draw_roi_window_viewport_zoom_input. \
setObjectName("DrawRoiWindowViewportZoomInput")
self.draw_roi_window_viewport_zoom_input. \
setText("{:.2f}".format(self.zoom * 100) + "%")
self.draw_roi_window_viewport_zoom_input.setCursorPosition(0)
self.draw_roi_window_viewport_zoom_input.setEnabled(False)
self.draw_roi_window_viewport_zoom_input. \
setSizePolicy(QSizePolicy.Minimum, QSizePolicy.Minimum)
self.draw_roi_window_viewport_zoom_input.resize(
self.draw_roi_window_viewport_zoom_input.sizeHint().width(),
self.draw_roi_window_viewport_zoom_input.sizeHint().height())
# Create 2 buttons for zooming in and out
# Zoom In Button
self.draw_roi_window_viewport_zoom_in_button = QPushButton()
self.draw_roi_window_viewport_zoom_in_button. \
setObjectName("DrawRoiWindowViewportZoomInButton")
self.draw_roi_window_viewport_zoom_in_button.setSizePolicy(
QSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed))
self.draw_roi_window_viewport_zoom_in_button.resize(QSize(24, 24))
self.draw_roi_window_viewport_zoom_in_button. \
setProperty("QPushButtonClass", "zoom-button")
icon_zoom_in = QtGui.QIcon()
icon_zoom_in.addPixmap(
QtGui.QPixmap(
resource_path('res/images/btn-icons/zoom_in_icon.png')))
self.draw_roi_window_viewport_zoom_in_button.setIcon(icon_zoom_in)
self.draw_roi_window_viewport_zoom_in_button.clicked. \
connect(self.onZoomInClicked)
# Zoom Out Button
self.draw_roi_window_viewport_zoom_out_button = QPushButton()
self.draw_roi_window_viewport_zoom_out_button. \
setObjectName("DrawRoiWindowViewportZoomOutButton")
self.draw_roi_window_viewport_zoom_out_button.setSizePolicy(
QSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed))
self.draw_roi_window_viewport_zoom_out_button.resize(QSize(24, 24))
self.draw_roi_window_viewport_zoom_out_button. \
setProperty("QPushButtonClass", "zoom-button")
icon_zoom_out = QtGui.QIcon()
icon_zoom_out.addPixmap(
QtGui.QPixmap(
resource_path('res/images/btn-icons/zoom_out_icon.png')))
self.draw_roi_window_viewport_zoom_out_button.setIcon(icon_zoom_out)
self.draw_roi_window_viewport_zoom_out_button.clicked. \
connect(self.onZoomOutClicked)
self.draw_roi_window_viewport_zoom_box. \
addWidget(self.draw_roi_window_viewport_zoom_label)
self.draw_roi_window_viewport_zoom_box. \
addWidget(self.draw_roi_window_viewport_zoom_input)
self.draw_roi_window_viewport_zoom_box. \
addWidget(self.draw_roi_window_viewport_zoom_out_button)
self.draw_roi_window_viewport_zoom_box. \
addWidget(self.draw_roi_window_viewport_zoom_in_button)
self.draw_roi_window_input_container_box. \
addRow(self.draw_roi_window_viewport_zoom_box)
self.init_cursor_radius_change_box()
# Create field to toggle two options: Keep empty pixel or fill empty
# pixel when using draw cursor
self.toggle_keep_empty_pixel_box = QHBoxLayout()
self.toggle_keep_empty_pixel_label = QLabel()
self.toggle_keep_empty_pixel_label. \
setObjectName("ToggleKeepEmptyPixelLabel")
# Create input for min pixel size
self.toggle_keep_empty_pixel_combo_box = QComboBox()
self.toggle_keep_empty_pixel_combo_box.addItems(["Off", "On"])
self.toggle_keep_empty_pixel_combo_box.setCurrentIndex(0)
self.toggle_keep_empty_pixel_combo_box.setEnabled(False)
self.toggle_keep_empty_pixel_combo_box. \
setObjectName("ToggleKeepEmptyPixelComboBox")
self.toggle_keep_empty_pixel_combo_box. \
setSizePolicy(QSizePolicy.Minimum, QSizePolicy.Minimum)
self.toggle_keep_empty_pixel_combo_box.resize(
self.toggle_keep_empty_pixel_combo_box.sizeHint().width(),
self.toggle_keep_empty_pixel_combo_box.sizeHint().height())
self.toggle_keep_empty_pixel_combo_box.currentIndexChanged.connect(
self.toggle_keep_empty_pixel_box_index_changed)
self.toggle_keep_empty_pixel_box. \
addWidget(self.toggle_keep_empty_pixel_label)
self.toggle_keep_empty_pixel_box. \
addWidget(self.toggle_keep_empty_pixel_combo_box)
self.draw_roi_window_input_container_box. \
addRow(self.toggle_keep_empty_pixel_box)
# Create a horizontal box for transect and draw button
self.draw_roi_window_transect_draw_box = QHBoxLayout()
self.draw_roi_window_transect_draw_box. \
setObjectName("DrawRoiWindowTransectDrawBox")
# Create a transect button
self.image_slice_number_transect_button = QPushButton()
self.image_slice_number_transect_button. \
setObjectName("ImageSliceNumberTransectButton")
self.image_slice_number_transect_button.setSizePolicy(
QSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.Minimum))
self.image_slice_number_transect_button.resize(
self.image_slice_number_transect_button.sizeHint().width(),
self.image_slice_number_transect_button.sizeHint().height())
self.image_slice_number_transect_button.clicked. \
connect(self.transect_handler)
icon_transect = QtGui.QIcon()
icon_transect.addPixmap(
QtGui.QPixmap(
resource_path('res/images/btn-icons/transect_icon.png')))
self.image_slice_number_transect_button.setIcon(icon_transect)
self.draw_roi_window_transect_draw_box. \
addWidget(self.image_slice_number_transect_button)
# Create a bounding box button
self.image_slice_number_box_draw_button = QPushButton()
self.image_slice_number_box_draw_button. \
setObjectName("ImageSliceNumberBoxDrawButton")
self.image_slice_number_box_draw_button.setSizePolicy(
QSizePolicy.MinimumExpanding, QSizePolicy.Minimum)
self.image_slice_number_box_draw_button.resize(
self.image_slice_number_box_draw_button.sizeHint().width(),
self.image_slice_number_box_draw_button.sizeHint().height())
self.image_slice_number_box_draw_button.clicked. \
connect(self.onBoxDrawClicked)
icon_box_draw = QtGui.QIcon()
icon_box_draw.addPixmap(
QtGui.QPixmap(
resource_path('res/images/btn-icons/draw_bound_icon.png')))
self.image_slice_number_box_draw_button.setIcon(icon_box_draw)
self.draw_roi_window_transect_draw_box. \
addWidget(self.image_slice_number_box_draw_button)
# Create a draw button
self.image_slice_number_draw_button = QPushButton()
self.image_slice_number_draw_button. \
setObjectName("ImageSliceNumberDrawButton")
self.image_slice_number_draw_button.setSizePolicy(
QSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.Minimum))
self.image_slice_number_draw_button.resize(
self.image_slice_number_draw_button.sizeHint().width(),
self.image_slice_number_draw_button.sizeHint().height())
self.image_slice_number_draw_button.clicked.connect(self.onDrawClicked)
icon_draw = QtGui.QIcon()
icon_draw.addPixmap(
QtGui.QPixmap(resource_path('res/images/btn-icons/draw_icon.png')))
self.image_slice_number_draw_button.setIcon(icon_draw)
self.draw_roi_window_transect_draw_box. \
addWidget(self.image_slice_number_draw_button)
self.draw_roi_window_input_container_box. \
addRow(self.draw_roi_window_transect_draw_box)
# Create a contour preview button
self.row_preview_layout = QtWidgets.QHBoxLayout()
self.button_contour_preview = QtWidgets.QPushButton("Preview contour")
self.button_contour_preview.clicked.connect(self.onPreviewClicked)
self.row_preview_layout.addWidget(self.button_contour_preview)
self.draw_roi_window_input_container_box. \
addRow(self.row_preview_layout)
icon_preview = QtGui.QIcon()
icon_preview.addPixmap(
QtGui.QPixmap(
resource_path('res/images/btn-icons/preview_icon.png')))
self.button_contour_preview.setIcon(icon_preview)
# Create input line edit for alpha value
self.label_alpha_value = QtWidgets.QLabel("Alpha value:")
self.input_alpha_value = QtWidgets.QLineEdit("0.2")
self.input_alpha_value. \
setSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.Minimum)
self.input_alpha_value.resize(
self.input_alpha_value.sizeHint().width(),
self.input_alpha_value.sizeHint().height())
self.input_alpha_value.setValidator(
QRegularExpressionValidator(
QRegularExpression("^[0-9]*[.]?[0-9]*$")))
self.draw_roi_window_input_container_box. \
addRow(self.label_alpha_value, self.input_alpha_value)
# Create a label for denoting the max internal hole size
self.internal_hole_max_label = QLabel()
self.internal_hole_max_label.setObjectName("InternalHoleLabel")
# Create input for max internal hole size
self.internal_hole_max_line_edit = QLineEdit()
self.internal_hole_max_line_edit.setObjectName("InternalHoleInput")
self.internal_hole_max_line_edit. \
setSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.Minimum)
self.internal_hole_max_line_edit.resize(
self.internal_hole_max_line_edit.sizeHint().width(),
self.internal_hole_max_line_edit.sizeHint().height())
self.internal_hole_max_line_edit.setValidator(
QRegularExpressionValidator(
QRegularExpression("^[0-9]*[.]?[0-9]*$")))
self.draw_roi_window_input_container_box.addRow(
self.internal_hole_max_label, self.internal_hole_max_line_edit)
# Create a label for denoting the isthmus width size
self.isthmus_width_max_label = QLabel()
self.isthmus_width_max_label.setObjectName("IsthmusWidthLabel")
# Create input for max isthmus width size
self.isthmus_width_max_line_edit = QLineEdit()
self.isthmus_width_max_line_edit.setObjectName("IsthmusWidthInput")
self.isthmus_width_max_line_edit.setSizePolicy(
QSizePolicy.MinimumExpanding, QSizePolicy.Minimum)
self.isthmus_width_max_line_edit.resize(
self.isthmus_width_max_line_edit.sizeHint().width(),
self.isthmus_width_max_line_edit.sizeHint().height())
self.isthmus_width_max_line_edit.setValidator(
QRegularExpressionValidator(
QRegularExpression("^[0-9]*[.]?[0-9]*$")))
self.draw_roi_window_input_container_box.addRow(
self.isthmus_width_max_label, self.isthmus_width_max_line_edit)
# Create a label for denoting the minimum pixel density
self.min_pixel_density_label = QLabel()
self.min_pixel_density_label.setObjectName("MinPixelDensityLabel")
# Create input for min pixel size
self.min_pixel_density_line_edit = QLineEdit()
self.min_pixel_density_line_edit.setObjectName("MinPixelDensityInput")
self.min_pixel_density_line_edit.setSizePolicy(
QSizePolicy.MinimumExpanding, QSizePolicy.Minimum)
self.min_pixel_density_line_edit.resize(
self.min_pixel_density_line_edit.sizeHint().width(),
self.min_pixel_density_line_edit.sizeHint().height())
self.min_pixel_density_line_edit.setValidator(
QRegularExpressionValidator(
QRegularExpression("^[0-9]*[.]?[0-9]*$")))
self.draw_roi_window_input_container_box.addRow(
self.min_pixel_density_label, self.min_pixel_density_line_edit)
# Create a label for denoting the minimum pixel density
self.max_pixel_density_label = QLabel()
self.max_pixel_density_label.setObjectName("MaxPixelDensityLabel")
# Create input for min pixel size
self.max_pixel_density_line_edit = QLineEdit()
self.max_pixel_density_line_edit.setObjectName("MaxPixelDensityInput")
self.max_pixel_density_line_edit. \
setSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.Minimum)
self.max_pixel_density_line_edit.resize(
self.max_pixel_density_line_edit.sizeHint().width(),
self.max_pixel_density_line_edit.sizeHint().height())
self.max_pixel_density_line_edit.setValidator(
QRegularExpressionValidator(
QRegularExpression("^[0-9]*[.]?[0-9]*$")))
self.draw_roi_window_input_container_box.addRow(
self.max_pixel_density_label, self.max_pixel_density_line_edit)
# Create a button to clear the draw
self.draw_roi_window_instance_action_reset_button = QPushButton()
self.draw_roi_window_instance_action_reset_button. \
setObjectName("DrawRoiWindowInstanceActionClearButton")
self.draw_roi_window_instance_action_reset_button.setSizePolicy(
QSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.Minimum))
reset_button = self.draw_roi_window_instance_action_reset_button
self.draw_roi_window_instance_action_reset_button.resize(
reset_button.sizeHint().width(),
reset_button.sizeHint().height())
self.draw_roi_window_instance_action_reset_button.clicked. \
connect(self.onResetClicked)
self.draw_roi_window_instance_action_reset_button. \
setProperty("QPushButtonClass", "fail-button")
icon_clear_roi_draw = QtGui.QIcon()
icon_clear_roi_draw.addPixmap(
QtGui.QPixmap(
resource_path('res/images/btn-icons/reset_roi_draw_icon.png')))
self.draw_roi_window_instance_action_reset_button. \
setIcon(icon_clear_roi_draw)
self.draw_roi_window_input_container_box. \
addRow(self.draw_roi_window_instance_action_reset_button)
# Create a horizontal box for saving and cancel the drawing
self.draw_roi_window_cancel_save_box = QHBoxLayout()
self.draw_roi_window_cancel_save_box. \
setObjectName("DrawRoiWindowCancelSaveBox")
# Create an exit button to cancel the drawing
# Add a button to go back/exit from the application
self.draw_roi_window_instance_cancel_button = QPushButton()
self.draw_roi_window_instance_cancel_button. \
setObjectName("DrawRoiWindowInstanceCancelButton")
self.draw_roi_window_instance_cancel_button.setSizePolicy(
QSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.Minimum))
self.draw_roi_window_instance_cancel_button.resize(
self.draw_roi_window_instance_cancel_button.sizeHint().width(),
self.draw_roi_window_instance_cancel_button.sizeHint().height())
self.draw_roi_window_instance_cancel_button. \
setCursor(QtGui.QCursor(QtCore.Qt.PointingHandCursor))
self.draw_roi_window_instance_cancel_button.clicked. \
connect(self.onCancelButtonClicked)
self.draw_roi_window_instance_cancel_button. \
setProperty("QPushButtonClass", "fail-button")
icon_cancel = QtGui.QIcon()
icon_cancel.addPixmap(
QtGui.QPixmap(
resource_path('res/images/btn-icons/cancel_icon.png')))
self.draw_roi_window_instance_cancel_button.setIcon(icon_cancel)
self.draw_roi_window_cancel_save_box. \
addWidget(self.draw_roi_window_instance_cancel_button)
# Create a save button to save all the changes
self.draw_roi_window_instance_save_button = QPushButton()
self.draw_roi_window_instance_save_button. \
setObjectName("DrawRoiWindowInstanceSaveButton")
self.draw_roi_window_instance_save_button.setSizePolicy(
QSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.Minimum))
self.draw_roi_window_instance_save_button.resize(
self.draw_roi_window_instance_save_button.sizeHint().width(),
self.draw_roi_window_instance_save_button.sizeHint().height())
self.draw_roi_window_instance_save_button. \
setProperty("QPushButtonClass", "success-button")
icon_save = QtGui.QIcon()
icon_save.addPixmap(
QtGui.QPixmap(resource_path('res/images/btn-icons/save_icon.png')))
self.draw_roi_window_instance_save_button.setIcon(icon_save)
self.draw_roi_window_instance_save_button.clicked. \
connect(self.onSaveClicked)
self.draw_roi_window_cancel_save_box. \
addWidget(self.draw_roi_window_instance_save_button)
self.draw_roi_window_input_container_box. \
addRow(self.draw_roi_window_cancel_save_box)
# Creating a horizontal box to hold the ROI view and slider
self.draw_roi_window_instance_view_box = QHBoxLayout()
self.draw_roi_window_instance_view_box. \
setObjectName("DrawRoiWindowInstanceViewBox")
# Add View and Slider into horizontal box
self.draw_roi_window_instance_view_box.addWidget(self.dicom_view)
# Create a widget to hold the image slice box
self.draw_roi_window_instance_view_widget = QWidget()
self.draw_roi_window_instance_view_widget.setObjectName(
"DrawRoiWindowInstanceActionWidget")
self.draw_roi_window_instance_view_widget.setLayout(
self.draw_roi_window_instance_view_box)
# Create a horizontal box for containing the input fields and the
# viewport
self.draw_roi_window_main_box = QHBoxLayout()
self.draw_roi_window_main_box.setObjectName("DrawRoiWindowMainBox")
self.draw_roi_window_main_box. \
addLayout(self.draw_roi_window_input_container_box, 1)
self.draw_roi_window_main_box. \
addWidget(self.draw_roi_window_instance_view_widget, 11)
# Create a new central widget to hold the vertical box layout
self.draw_roi_window_instance_central_widget = QWidget()
self.draw_roi_window_instance_central_widget. \
setObjectName("DrawRoiWindowInstanceCentralWidget")
self.draw_roi_window_instance_central_widget.setLayout(
self.draw_roi_window_main_box)
self.retranslate_ui(self.draw_roi_window_instance)
self.draw_roi_window_instance.setStyleSheet(stylesheet)
self.draw_roi_window_instance. \
setCentralWidget(self.draw_roi_window_instance_central_widget)
QtCore.QMetaObject.connectSlotsByName(self.draw_roi_window_instance)
def slider_value_changed(self):
"""
actions to be taken when slider value changes
"""
image_slice_number = self.current_slice
# save progress
self.save_drawing_progress(image_slice_number)
self.set_current_slice(self.dicom_view.slider.value())
def set_current_slice(self, slice_number):
"""
set the current slice
:param slice_number: the slice number to be set
"""
self.image_slice_number_line_edit.setText(str(slice_number + 1))
self.current_slice = slice_number
self.dicom_view.update_view()
# check if this slice has any drawings before
if self.drawn_roi_list.get(self.current_slice) is not None:
self.drawingROI = self.drawn_roi_list[
self.current_slice]['drawingROI']
self.ds = self.drawn_roi_list[self.current_slice]['ds']
self.dicom_view.view.setScene(self.drawingROI)
self.enable_cursor_radius_change_box()
self.drawingROI.clear_cursor(self.drawing_tool_radius)
else:
self.disable_cursor_radius_change_box()
self.ds = None
def onZoomInClicked(self):
"""
This function is used for zooming in button
"""
self.dicom_view.zoom *= 1.05
self.dicom_view.update_view(zoom_change=True)
if self.drawingROI \
and self.drawingROI.current_slice == self.current_slice:
self.dicom_view.view.setScene(self.drawingROI)
self.draw_roi_window_viewport_zoom_input.setText(
"{:.2f}".format(self.dicom_view.zoom * 100) + "%")
self.draw_roi_window_viewport_zoom_input.setCursorPosition(0)
def onZoomOutClicked(self):
"""
This function is used for zooming out button
"""
self.dicom_view.zoom /= 1.05
self.dicom_view.update_view(zoom_change=True)
if self.drawingROI \
and self.drawingROI.current_slice == self.current_slice:
self.dicom_view.view.setScene(self.drawingROI)
self.draw_roi_window_viewport_zoom_input. \
setText("{:.2f}".format(self.dicom_view.zoom * 100) + "%")
self.draw_roi_window_viewport_zoom_input.setCursorPosition(0)
def toggle_keep_empty_pixel_box_index_changed(self):
self.keep_empty_pixel = self.toggle_keep_empty_pixel_combo_box. \
currentText() == "On"
self.drawingROI.keep_empty_pixel = self.keep_empty_pixel
def onCancelButtonClicked(self):
"""
This function is used for canceling the drawing
"""
self.closeWindow()
def onBackwardClicked(self):
"""
This function is used when backward button is clicked
"""
image_slice_number = self.current_slice
# save progress
if self.save_drawing_progress(image_slice_number):
# Backward will only execute if current image slice is above 0.
if int(image_slice_number) > 0:
# decrements slice by 1 and update slider to move to correct
# position
self.dicom_view.slider.setValue(image_slice_number - 1)
def onForwardClicked(self):
"""
This function is used when forward button is clicked
"""
image_slice_number = self.current_slice
# save progress
if self.save_drawing_progress(image_slice_number):
pixmaps = self.patient_dict_container.get("pixmaps_axial")
total_slices = len(pixmaps)
# Forward will only execute if current image slice is below the
# total number of slices.
if int(image_slice_number) < total_slices:
# increments slice by 1 and update slider to move to correct
# position
self.dicom_view.slider.setValue(image_slice_number + 1)
def onResetClicked(self):
"""
This function is used when reset button is clicked
"""
self.dicom_view.image_display()
self.dicom_view.update_view()
self.isthmus_width_max_line_edit.setText("5")
self.internal_hole_max_line_edit.setText("9")
self.min_pixel_density_line_edit.setText("")
self.max_pixel_density_line_edit.setText("")
if hasattr(self, 'bounds_box_draw'):
delattr(self, 'bounds_box_draw')
if hasattr(self, 'drawingROI'):
delattr(self, 'drawingROI')
self.ds = None
def transect_handler(self):
"""
Function triggered when the Transect button is pressed from the menu.
"""
pixmaps = self.patient_dict_container.get("pixmaps_axial")
id = self.current_slice
dt = self.patient_dict_container.dataset[id]
rowS = dt.PixelSpacing[0]
colS = dt.PixelSpacing[1]
dt.convert_pixel_data()
MainPageCallClass().run_transect(
self.draw_roi_window_instance,
self.dicom_view.view,
pixmaps[id],
dt._pixel_array.transpose(),
rowS,
colS,
is_roi_draw=True,
)
def save_drawing_progress(self, image_slice_number):
"""
this function saves the drawing progress on current slice
:param image_slice_number: the slice number to be saved
"""
if self.slice_changed:
if hasattr(self, 'drawingROI') and self.drawingROI \
and self.ds is not None \
and len(self.drawingROI.target_pixel_coords) != 0:
alpha = float(self.input_alpha_value.text())
pixel_hull_list = calculate_concave_hull_of_points(
self.drawingROI.target_pixel_coords, alpha)
coord_list = []
for pixel_hull in pixel_hull_list:
coord_list.append(pixel_hull)
self.drawn_roi_list[image_slice_number] = {
'coords': coord_list,
'ds': self.ds,
'drawingROI': self.drawingROI
}
self.slice_changed = False
return True
else:
return True
return True
def on_transect_close(self):
"""
Function triggered when transect is closed
"""
if self.upper_limit and self.lower_limit:
self.min_pixel_density_line_edit.setText(str(self.lower_limit))
self.max_pixel_density_line_edit.setText(str(self.upper_limit))
self.dicom_view.update_view()
def onDrawClicked(self):
"""
Function triggered when the Draw button is pressed from the menu.
"""
pixmaps = self.patient_dict_container.get("pixmaps_axial")
if self.min_pixel_density_line_edit.text() == "" \
or self.max_pixel_density_line_edit.text() == "":
QMessageBox.about(self.draw_roi_window_instance, "Not Enough Data",
"Not all values are specified or correct.")
else:
# Getting most updated selected slice
id = self.current_slice
dt = self.patient_dict_container.dataset[id]
dt.convert_pixel_data()
# Path to the selected .dcm file
location = self.patient_dict_container.filepaths[id]
self.ds = pydicom.dcmread(location)
min_pixel = self.min_pixel_density_line_edit.text()
max_pixel = self.max_pixel_density_line_edit.text()
# If they are number inputs
if min_pixel.isdecimal() and max_pixel.isdecimal():
min_pixel = int(min_pixel)
max_pixel = int(max_pixel)
if min_pixel >= max_pixel:
QMessageBox.about(
self.draw_roi_window_instance, "Incorrect Input",
"Please ensure maximum density is "
"atleast higher than minimum density.")
self.drawingROI = Drawing(
pixmaps[id], dt._pixel_array.transpose(), min_pixel,
max_pixel, self.patient_dict_container.dataset[id],
self.draw_roi_window_instance, self.slice_changed,
self.current_slice, self.drawing_tool_radius,
self.keep_empty_pixel, set())
self.slice_changed = True
self.dicom_view.view.setScene(self.drawingROI)
self.enable_cursor_radius_change_box()
else:
QMessageBox.about(self.draw_roi_window_instance,
"Not Enough Data",
"Not all values are specified or correct.")
def onBoxDrawClicked(self):
"""
Function triggered when bounding box button is pressed
"""
id = self.current_slice
dt = self.patient_dict_container.dataset[id]
dt.convert_pixel_data()
pixmaps = self.patient_dict_container.get("pixmaps_axial")
self.bounds_box_draw = DrawBoundingBox(pixmaps[id], dt)
self.dicom_view.view.setScene(self.bounds_box_draw)
self.disable_cursor_radius_change_box()
def onSaveClicked(self):
"""
Function triggered when Save button is clicked
"""
# Make sure the user has clicked Draw first
if self.save_drawing_progress(image_slice_number=self.current_slice):
self.saveROIList()
def saveROIList(self):
"""
Function triggered when saving ROI list
"""
roi_list = ROI.convert_hull_list_to_contours_data(
self.drawn_roi_list, self.patient_dict_container)
if len(roi_list) == 0:
QMessageBox.about(self.draw_roi_window_instance, "No ROI Detected",
"Please ensure you have drawn your ROI first.")
return
# The list of points will need to be converted into a
# single-dimensional array, as RTSTRUCT contour data is stored in
# such a way. i.e. [x, y, z, x, y, z, x, y, z, ..., ...] Create a
# popup window that modifies the RTSTRUCT and tells the user that
# processing is happening.
connectSaveROIProgress(self, roi_list, self.dataset_rtss,
self.ROI_name, self.roi_saved)
def roi_saved(self, new_rtss):
"""
Function to call save ROI and display progress
"""
self.signal_roi_drawn.emit((new_rtss, {"draw": self.ROI_name}))
QMessageBox.about(self.draw_roi_window_instance, "Saved",
"New contour successfully created!")
self.closeWindow()
def onPreviewClicked(self):
"""
function triggered when Preview button is clicked
"""
if hasattr(self, 'drawingROI') and self.drawingROI and len(
self.drawingROI.target_pixel_coords) > 0:
alpha = float(self.input_alpha_value.text())
polygon_list = calculate_concave_hull_of_points(
self.drawingROI.target_pixel_coords, alpha)
self.drawingROI.draw_contour_preview(polygon_list)
else:
QMessageBox.about(self.draw_roi_window_instance, "Not Enough Data",
"Please ensure you have drawn your ROI first.")
def set_selected_roi_name(self, roi_name):
"""
function to set selected roi name
:param roi_name: roi name selected
"""
roi_exists = False
patient_dict_container = PatientDictContainer()
existing_rois = patient_dict_container.get("rois")
number_of_rois = len(existing_rois)
# Check to see if the ROI already exists
for key, value in existing_rois.items():
if roi_name in value['name']:
roi_exists = True
if roi_exists:
QMessageBox.about(self.draw_roi_window_instance,
"ROI already exists in RTSS",
"Would you like to continue?")
self.ROI_name = roi_name
self.roi_name_line_edit.setText(self.ROI_name)
def onRadiusReduceClicked(self):
"""
function triggered when user reduce cursor radius
"""
self.drawing_tool_radius = max(self.drawing_tool_radius - 1, 4)
self.draw_roi_window_cursor_radius_change_input.setText(
str(self.drawing_tool_radius))
self.draw_roi_window_cursor_radius_change_input.setCursorPosition(0)
self.draw_cursor_when_radius_changed()
def onRadiusIncreaseClicked(self):
"""
function triggered when user increase cursor radius
"""
self.drawing_tool_radius = min(self.drawing_tool_radius + 1, 25)
self.draw_roi_window_cursor_radius_change_input.setText(
str(self.drawing_tool_radius))
self.draw_cursor_when_radius_changed()
def draw_cursor_when_radius_changed(self):
"""
function to update drawing cursor when radius changed
"""
if self.drawingROI.cursor:
self.drawingROI.draw_cursor(
self.drawingROI.current_cursor_x + self.drawing_tool_radius,
self.drawingROI.current_cursor_y + self.drawing_tool_radius,
self.drawing_tool_radius)
else:
self.drawingROI.draw_cursor(
(self.drawingROI.min_x + self.drawingROI.max_x) / 2,
(self.drawingROI.min_y + self.drawingROI.max_y) / 2,
self.drawing_tool_radius, True)
def init_cursor_radius_change_box(self):
"""
function to init cursor radius change box
"""
# Create a horizontal box for containing the cursor radius changing
# function
self.draw_roi_window_cursor_radius_change_box = QHBoxLayout()
self.draw_roi_window_cursor_radius_change_box.setObjectName(
"DrawRoiWindowCursorRadiusChangeBox")
# Create a label for cursor radius change
self.draw_roi_window_cursor_radius_change_label = QLabel()
self.draw_roi_window_cursor_radius_change_label.setObjectName(
"DrawRoiWindowCursorRadiusChangeLabel")
# Create an input box for cursor radius
self.draw_roi_window_cursor_radius_change_input = QLineEdit()
self.draw_roi_window_cursor_radius_change_input.setObjectName(
"DrawRoiWindowCursorRadiusChangeInput")
self.draw_roi_window_cursor_radius_change_input.setText(str(19))
self.draw_roi_window_cursor_radius_change_input.setCursorPosition(0)
self.draw_roi_window_cursor_radius_change_input.setEnabled(False)
self.draw_roi_window_cursor_radius_change_input.setSizePolicy(
QSizePolicy.Minimum, QSizePolicy.Minimum)
self.draw_roi_window_cursor_radius_change_input.resize(
self.draw_roi_window_cursor_radius_change_input.sizeHint().width(),
self.draw_roi_window_cursor_radius_change_input.sizeHint().height(
))
# Create 2 buttons for increasing and reducing cursor radius
# Increase Button
self.draw_roi_window_cursor_radius_change_increase_button = \
QPushButton()
self.draw_roi_window_cursor_radius_change_increase_button. \
setObjectName("DrawRoiWindowCursorRadiusIncreaseButton")
self.draw_roi_window_cursor_radius_change_increase_button. \
setSizePolicy(QSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed))
self.draw_roi_window_cursor_radius_change_increase_button.resize(
QSize(24, 24))
self.draw_roi_window_cursor_radius_change_increase_button.setProperty(
"QPushButtonClass", "zoom-button")
icon_zoom_in = QtGui.QIcon()
icon_zoom_in.addPixmap(
QtGui.QPixmap(
resource_path('res/images/btn-icons/zoom_in_icon.png')))
self.draw_roi_window_cursor_radius_change_increase_button.setIcon(
icon_zoom_in)
self.draw_roi_window_cursor_radius_change_increase_button.clicked. \
connect(self.onRadiusIncreaseClicked)
# Reduce Button
self.draw_roi_window_cursor_radius_change_reduce_button = QPushButton()
self.draw_roi_window_cursor_radius_change_reduce_button.setObjectName(
"DrawRoiWindowCursorRadiusReduceButton")
self.draw_roi_window_cursor_radius_change_reduce_button.setSizePolicy(
QSizePolicy(QSizePolicy.Fixed, QSizePolicy.Fixed))
self.draw_roi_window_cursor_radius_change_reduce_button.resize(
QSize(24, 24))
self.draw_roi_window_cursor_radius_change_reduce_button.setProperty(
"QPushButtonClass", "zoom-button")
icon_zoom_out = QtGui.QIcon()
icon_zoom_out.addPixmap(
QtGui.QPixmap(
resource_path('res/images/btn-icons/zoom_out_icon.png')))
self.draw_roi_window_cursor_radius_change_reduce_button.setIcon(
icon_zoom_out)
self.draw_roi_window_cursor_radius_change_reduce_button.clicked. \
connect(self.onRadiusReduceClicked)
self.draw_roi_window_cursor_radius_change_box.addWidget(
self.draw_roi_window_cursor_radius_change_label)
self.draw_roi_window_cursor_radius_change_box.addWidget(
self.draw_roi_window_cursor_radius_change_input)
self.draw_roi_window_cursor_radius_change_box.addWidget(
self.draw_roi_window_cursor_radius_change_reduce_button)
self.draw_roi_window_cursor_radius_change_box.addWidget(
self.draw_roi_window_cursor_radius_change_increase_button)
self.draw_roi_window_input_container_box.addRow(
self.draw_roi_window_cursor_radius_change_box)
self.draw_roi_window_cursor_radius_change_increase_button.setEnabled(
False)
self.draw_roi_window_cursor_radius_change_reduce_button.setEnabled(
False)
def disable_cursor_radius_change_box(self):
"""
function to disable cursor radius change box
"""
self.draw_roi_window_cursor_radius_change_reduce_button.setEnabled(
False)
self.draw_roi_window_cursor_radius_change_increase_button.setEnabled(
False)
self.toggle_keep_empty_pixel_combo_box.setEnabled(False)
def enable_cursor_radius_change_box(self):
"""
function to enable cursor radius change box
"""
self.draw_roi_window_cursor_radius_change_reduce_button.setEnabled(
True)
self.draw_roi_window_cursor_radius_change_increase_button.setEnabled(
True)
self.toggle_keep_empty_pixel_combo_box.setEnabled(True)
def closeWindow(self):
"""
function to close draw roi window
"""
self.drawn_roi_list = {}
if hasattr(self, 'bounds_box_draw'):
delattr(self, 'bounds_box_draw')
if hasattr(self, 'drawingROI'):
delattr(self, 'drawingROI')
self.ds = None
self.close()
class ImageFusionOptions(object):
"""
UI class that can be used by the AddOnOptions Class to allow the user
customise their input parameters for auto-registration.
"""
def __init__(self, window_options):
self.auto_image_fusion_frame = QtWidgets.QFrame()
self.window = window_options
self.moving_image = None
self.fixed_image = None
self.dict = {}
self.setupUi()
self.create_view()
self.get_patients_info()
def set_value(self, key, value):
"""
Stores values into a dictionary to the corresponding key.
Parameters
----------
key (Any):
value (Any):
"""
self.dict[key] = value
def create_view(self):
"""
Create a table to hold all the ROI creation by isodose entries.
"""
self.auto_image_fusion_frame.setVisible(False)
def setVisible(self, visibility):
"""
Custom setVisible function that will set the visibility of the GUI.
Args:
visibility (bool): flag for setting the GUI to visible
"""
self.auto_image_fusion_frame.setVisible(visibility)
def setupUi(self):
"""
Constructs the GUI and sets the limit of each input field.
"""
# Create a vertical Widget to hold Vertical Layout
self.vertical_layout_widget = QWidget()
self.vertical_layout = QtWidgets.QVBoxLayout()
# Create a Widget and set layout to a GridLayout
self.gridLayoutWidget = QWidget()
self.gridLayout = QtWidgets.QGridLayout(self.gridLayoutWidget)
self.gridLayout.setSizeConstraint(QLayout.SetDefaultConstraint)
self.gridLayout.setContentsMargins(0, 0, 0, 0)
self.gridLayout.setVerticalSpacing(0)
# Create horizontal spacer in the middle of the grid
hspacer = QtWidgets.QSpacerItem(QtWidgets.QSizePolicy.Expanding,
QtWidgets.QSizePolicy.Minimum)
self.gridLayout.addItem(hspacer, 0, 5, 16, 1)
# Labels
self.fixed_image_label = QLabel("Fixed Image: ")
fixed_image_sizePolicy = QSizePolicy(QSizePolicy.Maximum,
QSizePolicy.Preferred)
fixed_image_sizePolicy.setHorizontalStretch(0)
fixed_image_sizePolicy.setVerticalStretch(0)
fixed_image_sizePolicy.setHeightForWidth(
self.fixed_image_label.sizePolicy().hasHeightForWidth())
self.fixed_image_label.setAlignment(Qt.AlignRight | Qt.AlignTrailing
| Qt.AlignVCenter)
self.fixed_image_placeholder \
= QLabel("This is a placeholder for fixed image")
self.fixed_image_placeholder.setWordWrap(False)
self.fixed_image_placeholder.setText(str(self.fixed_image))
self.fixed_image_placeholder.setMaximumSize(200, 50)
self.moving_image_label = QLabel("Moving Image: ")
moving_image_label_sizePolicy = QSizePolicy(QSizePolicy.Maximum,
QSizePolicy.Maximum)
moving_image_label_sizePolicy.setHorizontalStretch(0)
moving_image_label_sizePolicy.setVerticalStretch(0)
moving_image_label_sizePolicy.setHeightForWidth(
self.moving_image_label.sizePolicy().hasHeightForWidth())
self.moving_image_label.setSizePolicy(moving_image_label_sizePolicy)
self.moving_image_placeholder = QLabel("This is a placeholder")
self.moving_image_placeholder.setWordWrap(False)
self.moving_image_placeholder.setText(str(self.moving_image))
self.moving_image_placeholder.setMaximumSize(200, 50)
self.gridLayout.addWidget(self.fixed_image_label, 0, 0)
self.gridLayout.addWidget(self.fixed_image_placeholder, 0, 1)
self.gridLayout.addWidget(self.moving_image_label, 0, 2)
self.gridLayout.addWidget(self.moving_image_placeholder, 0, 3)
# Default Numbers
self.default_numbers_label = QLabel("Default Numbers")
self.default_numbers_label.setAlignment(Qt.AlignLeft | Qt.AlignTrailing
| Qt.AlignVCenter)
self.gridLayout.addWidget(self.default_numbers_label, 1, 0)
self.default_number_spinBox = QSpinBox(self.gridLayoutWidget)
self.default_number_spinBox.setRange(-2147483648, 2147483647)
self.default_number_spinBox.setSizePolicy(QSizePolicy.Minimum,
QSizePolicy.Fixed)
self.default_number_spinBox.setToolTip(
"Default voxel value. Defaults to -1000.")
self.gridLayout.addWidget(self.default_number_spinBox, 1, 1)
# Final Interp
self.interp_order_label = QLabel("Final Interp")
self.interp_order_label.setAlignment(Qt.AlignLeft | Qt.AlignTrailing
| Qt.AlignVCenter)
self.gridLayout.addWidget(self.interp_order_label, 2, 0)
self.interp_order_spinbox = QSpinBox(self.gridLayoutWidget)
self.interp_order_spinbox.setSizePolicy(QSizePolicy.Minimum,
QSizePolicy.Fixed)
self.interp_order_spinbox.setToolTip("The final interpolation order.")
self.gridLayout.addWidget(self.interp_order_spinbox, 2, 1)
# Metric
self.metric_label = QLabel("Metric")
self.metric_label.setAlignment(QtCore.Qt.AlignLeft | Qt.AlignTrailing
| Qt.AlignVCenter)
self.gridLayout.addWidget(self.metric_label, 3, 0)
self.metric_comboBox = QComboBox()
self.metric_comboBox.addItem("correlation")
self.metric_comboBox.addItem("mean_squares")
self.metric_comboBox.addItem("mattes_mi")
self.metric_comboBox.addItem("joint_hist_mi")
self.metric_comboBox.setToolTip(
"The metric to be optimised during image registration.")
self.gridLayout.addWidget(self.metric_comboBox, 3, 1)
# Number of Iterations
self.no_of_iterations_label = QLabel("Number of Iterations")
self.no_of_iterations_label.setAlignment(Qt.AlignLeft
| Qt.AlignTrailing
| Qt.AlignVCenter)
self.gridLayout.addWidget(self.no_of_iterations_label, 4, 0)
self.no_of_iterations_spinBox = QSpinBox(self.gridLayoutWidget)
self.no_of_iterations_spinBox.setSizePolicy(QSizePolicy.Minimum,
QSizePolicy.Fixed)
self.no_of_iterations_spinBox.setRange(0, 100)
self.no_of_iterations_spinBox.setToolTip(
"Number of iterations in each multi-resolution step.")
self.gridLayout.addWidget(self.no_of_iterations_spinBox, 4, 1)
# Shrink Factor
self.shrink_factor_label = QLabel("Shrink Factor")
self.shrink_factor_label.setAlignment(Qt.AlignLeft | Qt.AlignTrailing
| Qt.AlignVCenter)
self.gridLayout.addWidget(self.shrink_factor_label, 5, 0)
self.shrink_factor_qLineEdit = QLineEdit()
self.shrink_factor_qLineEdit.resize(
self.shrink_factor_qLineEdit.sizeHint().width(),
self.shrink_factor_qLineEdit.sizeHint().height())
self.shrink_factor_qLineEdit.setValidator(
QRegularExpressionValidator(
QRegularExpression("^[0-9]*[,]?[0-9]*[,]?[0-9]")))
self.shrink_factor_qLineEdit.setToolTip(
"The multi-resolution downsampling factors. Can be up to three "
"integer elements in an array. Example [8, 2, 1]")
self.gridLayout.addWidget(self.shrink_factor_qLineEdit, 5, 1)
# Optimiser
self.optimiser_label = QLabel("Optimiser")
self.optimiser_label.setAlignment(Qt.AlignLeft | Qt.AlignTrailing
| Qt.AlignVCenter)
self.gridLayout.addWidget(self.optimiser_label, 1, 2)
self.optimiser_comboBox = QComboBox(self.gridLayoutWidget)
self.optimiser_comboBox.addItem("lbfgsb")
self.optimiser_comboBox.addItem("gradient_descent")
self.optimiser_comboBox.addItem("gradient_descent_line_search")
self.optimiser_comboBox.setToolTip(
"The optimiser algorithm used for image registration.")
self.gridLayout.addWidget(self.optimiser_comboBox, 1, 3)
# Reg Method
self.reg_method_label = QLabel("Reg Method")
self.reg_method_label.setAlignment(QtCore.Qt.AlignLeft
| Qt.AlignTrailing
| Qt.AlignVCenter)
self.gridLayout.addWidget(self.reg_method_label, 2, 2)
self.reg_method_comboBox = QComboBox()
self.reg_method_comboBox.addItem("translation")
self.reg_method_comboBox.addItem("rigid")
self.reg_method_comboBox.addItem("similarity")
self.reg_method_comboBox.addItem("affine")
self.reg_method_comboBox.addItem("scaleversor")
self.reg_method_comboBox.addItem("scaleskewversor")
self.reg_method_comboBox.setToolTip(
"The linear transformation model to be used for image "
"registration.")
self.gridLayout.addWidget(self.reg_method_comboBox, 2, 3)
# Sampling Rate
self.sampling_rate_label = QLabel("Sampling Rate")
self.sampling_rate_label.setAlignment(Qt.AlignLeft | Qt.AlignTrailing
| Qt.AlignVCenter)
self.gridLayout.addWidget(self.sampling_rate_label, 3, 2)
self.sampling_rate_spinBox = QDoubleSpinBox(self.gridLayoutWidget)
self.sampling_rate_spinBox.setMinimum(0)
self.sampling_rate_spinBox.setMaximum(1)
self.sampling_rate_spinBox.setSingleStep(0.01)
self.sampling_rate_spinBox.setSizePolicy(QSizePolicy.Minimum,
QSizePolicy.Fixed)
self.sampling_rate_spinBox.setToolTip("The fraction of voxels sampled "
"during each iteration.")
self.gridLayout.addWidget(self.sampling_rate_spinBox, 3, 3)
# Smooth Sigmas
self.smooth_sigma_label = QLabel("Smooth Sigma")
self.smooth_sigma_label.setAlignment(Qt.AlignLeft | Qt.AlignTrailing
| Qt.AlignVCenter)
self.gridLayout.addWidget(self.smooth_sigma_label, 4, 2)
self.smooth_sigmas_qLineEdit = QLineEdit()
self.smooth_sigmas_qLineEdit.resize(
self.smooth_sigmas_qLineEdit.sizeHint().width(),
self.smooth_sigmas_qLineEdit.sizeHint().height())
self.smooth_sigmas_qLineEdit.setValidator(
QRegularExpressionValidator(
QRegularExpression("^[0-9]*[,]?[0-9]*[,]?[0-9]")))
self.smooth_sigmas_qLineEdit.setToolTip(
"The multi-resolution smoothing kernal scale (Gaussian). Can be "
"up to three integer elements in an array. Example [4, 2, 1]")
self.gridLayout.addWidget(self.smooth_sigmas_qLineEdit, 4, 3)
# Label to hold warning labels.
self.warning_label = QLabel()
# Button for fast mode
self.fast_mode_button = QtWidgets.QPushButton("Fast Mode")
self.fast_mode_button.setCursor(
QtGui.QCursor(QtCore.Qt.PointingHandCursor))
self.fast_mode_button.clicked.connect(self.set_fast_mode)
# Add Widgets to the vertical layout
self.vertical_layout.addWidget(self.fast_mode_button)
self.vertical_layout.addWidget(self.gridLayoutWidget)
self.vertical_layout.addWidget(self.warning_label)
# Set layout of frame to the gridlayout widget
self.auto_image_fusion_frame.setLayout(self.vertical_layout)
def set_gridLayout(self):
"""
Set the UI based on the values taken from the JSON
"""
msg = ""
# If-Elif statements for setting the dict
# this can only be done in if-else statements.
if self.dict["reg_method"] == "translation":
self.reg_method_comboBox.setCurrentIndex(0)
elif self.dict["reg_method"] == "rigid":
self.reg_method_comboBox.setCurrentIndex(1)
elif self.dict["reg_method"] == "similarity":
self.reg_method_comboBox.setCurrentIndex(2)
elif self.dict["reg_method"] == "affine":
self.reg_method_comboBox.setCurrentIndex(3)
elif self.dict["reg_method"] == "scaleversor":
self.reg_method_comboBox.setCurrentIndex(4)
elif self.dict["reg_method"] == "scaleskewversor":
self.reg_method_comboBox.setCurrentIndex(5)
else:
msg += 'There was an error setting the reg_method value.\n'
self.warning_label.setText(msg)
if self.dict["metric"] == "coorelation":
self.metric_comboBox.setCurrentIndex(0)
elif self.dict["metric"] == "mean_squares":
self.metric_comboBox.setCurrentIndex(1)
elif self.dict["metric"] == "mattes_mi":
self.metric_comboBox.setCurrentIndex(2)
elif self.dict["metric"] == "joint_hist_mi":
self.metric_comboBox.setCurrentIndex(3)
else:
msg += 'There was an error setting the metric value.\n'
self.warning_label.setText(msg)
if self.dict["optimiser"] == "lbfgsb":
self.optimiser_comboBox.setCurrentIndex(0)
elif self.dict["optimiser"] == "gradient_descent":
self.optimiser_comboBox.setCurrentIndex(1)
elif self.dict["optimiser"] == "gradient_descent_line_search":
self.optimiser_comboBox.setCurrentIndex(2)
else:
msg += 'There was an error setting the optimiser value.\n'
self.warning_label.setText(msg)
# Check if all elements in list are ints
if all(isinstance(x, int) for x in self.dict["shrink_factors"]):
# Shrink_factors is stored as a list in JSON convert the list into
# a string.
shrink_factor_list_json = ', '.join(
str(e) for e in self.dict["shrink_factors"])
self.shrink_factor_qLineEdit.setText(shrink_factor_list_json)
else:
msg += 'There was an error setting the Shrink Factors value.\n'
self.warning_label.setText(msg)
# Check if all elements in list are ints
if all(isinstance(x, int) for x in self.dict["smooth_sigmas"]):
# Since smooth_sigma is stored as a list in JSON convert the list
# into a string.
smooth_sigma_list_json = ', '.join(
str(e) for e in self.dict["smooth_sigmas"])
self.smooth_sigmas_qLineEdit.setText(smooth_sigma_list_json)
else:
msg += 'There was an error setting the Smooth Sigmas value.\n'
self.warning_label.setText(msg)
try:
self.sampling_rate_spinBox.setValue(
float(self.dict["sampling_rate"]))
except ValueError:
msg += 'There was an error setting the Sampling Rate value.\n'
self.warning_label.setText(msg)
try:
self.interp_order_spinbox.setValue(int(self.dict["final_interp"]))
except ValueError:
msg += 'There was an error setting the Final Interp value.\n'
self.warning_label.setText(msg)
try:
self.no_of_iterations_spinBox.setValue(
int(self.dict["number_of_iterations"]))
except ValueError:
msg += 'There was an error setting the Number of iterations ' \
'value.\n'
self.warning_label.setText(msg)
try:
self.default_number_spinBox.setValue(
int(self.dict["default_value"]))
except ValueError:
msg += 'There was an error setting the Default Number'
self.warning_label.setText(msg)
def get_patients_info(self):
"""
Retrieve the patient's study description of the fixed image
and for the moving image (if it exists).
"""
patient_dict_container = PatientDictContainer()
if not patient_dict_container.is_empty():
filename = patient_dict_container.filepaths[0]
dicom_tree_slice = DicomTree(filename)
dict_tree = dicom_tree_slice.dict
try:
self.fixed_image = dict_tree["Series Instance UID"][0]
except:
self.fixed_image = ""
self.warning_label.setText(
'Couldn\'t find the series instance '
'UID for the Fixed Image.')
moving_dict_container = MovingDictContainer()
if not moving_dict_container.is_empty():
filename = moving_dict_container.filepaths[0]
dicom_tree_slice = DicomTree(filename)
dict_tree = dicom_tree_slice.dict
try:
self.moving_image = dict_tree["Series Instance UID"][0]
except:
self.moving_image = ""
self.warning_label.setText(
'Couldn\'t find the series instance '
'UID for the Moving Image.')
if moving_dict_container.is_empty() and self.moving_image != "":
self.moving_image = ""
self.fixed_image_placeholder.setText(str(self.fixed_image))
self.moving_image_placeholder.setText(str(self.moving_image))
def get_values_from_UI(self):
"""
Sets values from the GUI to the dict that will be used to store the
relevant parameters to imageFusion.json.
"""
self.dict["reg_method"] = str(self.reg_method_comboBox.currentText())
self.dict["metric"] = str(self.metric_comboBox.currentText())
self.dict["optimiser"] = str(self.optimiser_comboBox.currentText())
a_string = self.shrink_factor_qLineEdit.text().split(",")
a_int = list(map(int, a_string))
self.dict["shrink_factors"] = a_int
a_string = self.smooth_sigmas_qLineEdit.text().split(",")
a_int = list(map(int, a_string))
self.dict["smooth_sigmas"] = a_int
self.dict["sampling_rate"] = self.sampling_rate_spinBox.value()
self.dict["final_interp"] = self.interp_order_spinbox.value()
self.dict[
"number_of_iterations"] = self.no_of_iterations_spinBox.value()
self.dict["default_value"] = self.default_number_spinBox.value()
return self.dict
def check_parameter(self):
"""
Check the number of values of the smooth sigma and shrink factors of
that are parameters used for images fusion.
"""
len_smooth_sigmas = len(self.dict["smooth_sigmas"])
len_shrink_factor = len(self.dict["shrink_factors"])
if len_smooth_sigmas != len_shrink_factor:
raise ValueError
def set_fast_mode(self):
"""These settings are customised to be fast for images fusion."""
self.reg_method_comboBox.setCurrentIndex(1)
self.metric_comboBox.setCurrentIndex(1)
self.optimiser_comboBox.setCurrentIndex(1)
self.shrink_factor_qLineEdit.setText("8")
self.smooth_sigmas_qLineEdit.setText("10")
self.sampling_rate_spinBox.setValue(0.25)
self.interp_order_spinbox.setValue(2)
self.no_of_iterations_spinBox.setValue(50)
self.default_number_spinBox.setValue(-1000)