def create(self):
super(WindowLevelEffectOptions,self).create()
#self.thresholdPaint.hide()
#self.paintOver.hide()
#self.threshold.hide()
#self.thresholdLabel.hide()
# add the selection whether it should work as regular w/l control,
# or as a rectangle
self.normalMode = qt.QRadioButton('Normal mode')
self.rectangleMode = qt.QRadioButton('Rectangle mode')
self.rectangleMode.setChecked(1)
label = qt.QLabel('Mode of operation:')
self.frame.layout().addWidget(label)
self.viewGroup = qt.QButtonGroup()
self.viewGroup.addButton(self.normalMode,1)
self.viewGroup.addButton(self.rectangleMode,2)
self.frame.layout().addWidget(self.normalMode)
self.frame.layout().addWidget(self.rectangleMode)
self.viewGroup.connect('buttonClicked(int)',self.updateMRMLFromGUI)
label = qt.QLabel('Layers affected:')
self.bgSelector = qt.QCheckBox('Background')
self.fgSelector = qt.QCheckBox('Foreground')
self.bgSelector.checked = 1
self.fgSelector.checked = 1
self.frame.layout().addWidget(label)
self.frame.layout().addWidget(self.bgSelector)
self.frame.layout().addWidget(self.fgSelector)
self.bgSelector.connect('stateChanged(int)',self.updateMRMLFromGUI)
self.fgSelector.connect('stateChanged(int)',self.updateMRMLFromGUI)
EditorLib.HelpButton(self.frame, "Use this tool to change window/level of background/foreground volumes based on the intensity range of the selected rectangle.\n\nNormal mode: use primary mouse button to adjust window level. Depending on the selection, Foreground, Background or both layers are affected.\n\nRectangle mode: Left Click and Drag: sweep out an outline that will draw when the button is released. The outline will define the rectangle for calculating the new window/level settings for the selected layers.\n\n")
# step4Layout.addRow(self.normalMode, rectangleMode)
# Add vertical spacer
self.frame.layout().addStretch(1)
# set effect-specific parameters
if self.parameterNode.GetParameter('WindowLevelEffect,wlmode') == '':
self.parameterNode.SetParameter('WindowLevelEffect,wlmode', 'Rectangle')
if self.parameterNode.GetParameter('WindowLevelEffect,changeBg') == '':
self.parameterNode.SetParameter('WindowLevelEffect,changeBg','1')
if self.parameterNode.GetParameter('WindowLevelEffect,changeFg') == '':
self.parameterNode.SetParameter('WindowLevelEffect,changeFg','1')
if self.parameterNode.GetParameter('Effect,scope') == '':
self.parameterNode.SetParameter('Effect,scope','')
def create(self, registationState):
"""Make the plugin-specific user interface"""
super(LocalBRAINSFitPlugin, self).create(registationState)
self.LocalBRAINSFitMode = "Small"
self.VerboseMode = "Quiet"
#
# Local Refinment Pane - initially hidden
# - interface options for linear registration
#
self.LocalBRAINSFitCollapsibleButton = ctk.ctkCollapsibleButton()
self.LocalBRAINSFitCollapsibleButton.text = "Local BRAINSFit"
LocalBRAINSFitFormLayout = qt.QFormLayout()
self.LocalBRAINSFitCollapsibleButton.setLayout(
LocalBRAINSFitFormLayout)
self.widgets.append(self.LocalBRAINSFitCollapsibleButton)
buttonLayout = qt.QVBoxLayout()
self.LocalBRAINSFitModeButtons = {}
self.LocalBRAINSFitModes = ("Small", "Large")
for mode in self.LocalBRAINSFitModes:
self.LocalBRAINSFitModeButtons[mode] = qt.QRadioButton()
self.LocalBRAINSFitModeButtons[mode].text = mode
self.LocalBRAINSFitModeButtons[mode].setToolTip(
"Run the refinement in a %s local region." % mode.lower())
buttonLayout.addWidget(self.LocalBRAINSFitModeButtons[mode])
self.widgets.append(self.LocalBRAINSFitModeButtons[mode])
self.LocalBRAINSFitModeButtons[mode].connect(
'clicked()', lambda m=mode: self.onLocalBRAINSFitMode(m))
self.LocalBRAINSFitModeButtons[self.LocalBRAINSFitMode].checked = True
LocalBRAINSFitFormLayout.addRow("Local BRAINSFit Mode ", buttonLayout)
buttonLayout = qt.QVBoxLayout()
self.VerboseModeButtons = {}
self.VerboseModes = ("Quiet", "Verbose")
for mode in self.VerboseModes:
self.VerboseModeButtons[mode] = qt.QRadioButton()
self.VerboseModeButtons[mode].text = mode
self.VerboseModeButtons[mode].setToolTip(
"Run the refinement in %s mode." % mode.lower())
buttonLayout.addWidget(self.VerboseModeButtons[mode])
self.widgets.append(self.VerboseModeButtons[mode])
self.VerboseModeButtons[mode].connect(
'clicked()', lambda m=mode: self.onVerboseMode(m))
self.VerboseModeButtons[self.VerboseMode].checked = True
LocalBRAINSFitFormLayout.addRow("Verbose Mode ", buttonLayout)
self.parent.layout().addWidget(self.LocalBRAINSFitCollapsibleButton)
def create(self, registationState):
"""Make the plugin-specific user interface"""
super(AffinePlugin, self).create(registationState)
self.linearMode = "Rigid"
#
# Linear Registration Pane - initially hidden
# - interface options for linear registration
# - TODO: move registration code into separate plugins
#
self.linearCollapsibleButton = ctk.ctkCollapsibleButton()
self.linearCollapsibleButton.text = "Linear Registration"
linearFormLayout = qt.QFormLayout()
self.linearCollapsibleButton.setLayout(linearFormLayout)
self.widgets.append(self.linearCollapsibleButton)
buttonLayout = qt.QVBoxLayout()
self.linearModeButtons = {}
self.linearModes = ("Rigid", "Similarity", "Affine")
for mode in self.linearModes:
self.linearModeButtons[mode] = qt.QRadioButton()
self.linearModeButtons[mode].text = mode
self.linearModeButtons[mode].setToolTip(
"Run the registration in %s mode." % mode)
buttonLayout.addWidget(self.linearModeButtons[mode])
self.widgets.append(self.linearModeButtons[mode])
self.linearModeButtons[mode].connect(
'clicked()', lambda m=mode: self.onLinearTransform(m))
self.linearModeButtons[self.linearMode].checked = True
linearFormLayout.addRow("Registration Mode ", buttonLayout)
self.parent.layout().addWidget(self.linearCollapsibleButton)
def createUserInterface(self):
font = qt.QFont("Sans Serif", 12, qt.QFont.Bold)
self.__layout = qt.QFormLayout(self)
self.trayectoriaLibreButton = qt.QRadioButton('Trayectoria libre')
self.trayectoriaProgramadaButton = qt.QRadioButton(
'Trayectoria programada')
self.__layout.addRow("", qt.QWidget())
self.__layout.addRow("", qt.QWidget())
self.__layout.addRow("", qt.QWidget())
self.trayectoriaLibreButton.setFont(font)
self.trayectoriaProgramadaButton.setFont(font)
self.__layout.addRow(self.trayectoriaLibreButton)
self.__layout.addRow(self.trayectoriaProgramadaButton)
def create(self):
super(MorphologyEffectOptions,self).create()
# TODO: provide an entry for label to replace with (defaults to zero)
self.eightNeighbors = qt.QRadioButton("Eight Neighbors", self.frame)
self.eightNeighbors.setToolTip("Treat diagonally adjacent voxels as neighbors.")
self.frame.layout().addWidget(self.eightNeighbors)
self.widgets.append(self.eightNeighbors)
self.fourNeighbors = qt.QRadioButton("Four Neighbors", self.frame)
self.fourNeighbors.setToolTip("Do not treat diagonally adjacent voxels as neighbors.")
self.frame.layout().addWidget(self.fourNeighbors)
self.widgets.append(self.fourNeighbors)
# TODO: fill option not yet supported
# TODO: iterations option not yet supported
self.connections.append( (self.eightNeighbors, 'clicked()', self.updateMRMLFromGUI) )
self.connections.append( (self.fourNeighbors, 'clicked()', self.updateMRMLFromGUI) )
def createUserInterface(self):
font =qt.QFont("Sans Serif", 12, qt.QFont.Bold)
self.__layout = qt.QFormLayout( self )
self.anadirTrayectoriaButton = qt.QRadioButton('Anadir trayectoria')
self.calificarButton = qt.QRadioButton('Calificar trayectoria de alumnos')
self.verActividadButton = qt.QRadioButton('Ver actividad de alumnos')
self.__layout.addRow("",qt.QWidget())
self.__layout.addRow("",qt.QWidget())
self.__layout.addRow("",qt.QWidget())
self.anadirTrayectoriaButton.setFont(font)
self.calificarButton.setFont(font)
self.verActividadButton.setFont(font)
self.__layout.addRow(self.anadirTrayectoriaButton)
self.__layout.addRow(self.calificarButton)
self.__layout.addRow(self.verActividadButton)
def makeTransformationTypeWidgets(self):
self.trsfTypeTab = qt.QWidget()
self.parametersTabWidget.addTab(self.trsfTypeTab,
'Transformation type')
trsfTypeLayout = qt.QHBoxLayout(self.trsfTypeTab)
self.trsfTypeRadioButtons = []
for trsfType in TRANSFORMATIONS_MAP:
radioButton = qt.QRadioButton(trsfType)
radioButton.clicked.connect(self.onTransformationTypeChanged)
self.trsfTypeRadioButtons.append(radioButton)
trsfTypeLayout.addWidget(radioButton)
self.trsfTypeRadioButtons[0].setChecked(True)
def createUserInterface(self):
font = qt.QFont("Sans Serif", 12, qt.QFont.Bold)
self.__layout = qt.QFormLayout(self)
self.__layout.addRow(" ", qt.QWidget())
self.__layout.addRow(" ", qt.QWidget())
self.nombreBienvenida = qt.QLabel("Quien eres?")
self.nombreBienvenida.setFont(font)
self.__layout.addRow(self.nombreBienvenida)
self.__layout.addRow(" ", qt.QWidget())
self.__layout.addRow(" ", qt.QWidget())
self.EstudianteButton = qt.QRadioButton('Soy estudiante')
self.EstudianteButton.setFont(font)
self.ProfesorButton = qt.QRadioButton('Soy profesor')
self.ProfesorButton.setFont(font)
self.soyNuevoButton = qt.QRadioButton('Soy nuevo')
self.soyNuevoButton.setFont(font)
self.__layout.addRow(self.EstudianteButton)
self.__layout.addRow(" ", qt.QWidget())
self.__layout.addRow(self.ProfesorButton)
self.__layout.addRow(" ", qt.QWidget())
self.__layout.addRow(self.soyNuevoButton)
def setup(self):
frame = qt.QFrame()
frameLayout = qt.QFormLayout()
frame.setLayout(frameLayout)
self.parent.layout().addWidget(frame)
# Choose directory button to choose the folder for saving the registered image
self.directoryButton = qt.QPushButton(
"Choose folder with the segmented images")
self.directoryButton.setFont(qt.QFont(self.font_type, self.font_size))
self.directoryButton.toolTip = "Choose a folder of .nii or .img/.hdr images of the segmented bones."
frameLayout.addWidget(self.directoryButton)
self.directoryButton.connect('clicked()', self.onDirectoryButtonClick)
frameLayout.addRow(self.directoryButton)
# Choose the Output folder button to choose the folder for saving the registered image
self.outputDirectoryButton = qt.QPushButton(
"Choose folder to save the output training data to")
self.outputDirectoryButton.setFont(
qt.QFont(self.font_type, self.font_size))
self.outputDirectoryButton.toolTip = "Choose a folder to save the output"
frameLayout.addWidget(self.outputDirectoryButton)
self.outputDirectoryButton.connect('clicked()',
self.onOutputDirectoryButtonClick)
frameLayout.addRow(self.outputDirectoryButton)
# ICP Registration Collapse button
self.ICPCollapsibleButton = ctk.ctkCollapsibleButton()
self.ICPCollapsibleButton.setFont(
qt.QFont(self.font_type, self.font_size))
self.ICPCollapsibleButton.text = "Iterative Closest Point Registration"
self.ICPCollapsibleButton.collapsed = True # Default is to not show
frameLayout.addWidget(self.ICPCollapsibleButton)
# Layout within the ICP collapsible button
self.ICPFormLayout = qt.QFormLayout(self.ICPCollapsibleButton)
# Slider for Maximum Iteration Number for ICP registration
self.label = qt.QLabel()
self.label.setFont(qt.QFont(self.font_type, self.font_size))
self.label.setText("Maximum Iteration Number: ")
self.label.setToolTip(
"Select the maximum iteration number for the ICP registration.")
self.IterationSlider = ctk.ctkSliderWidget()
self.IterationSlider.setToolTip(
"Select the maximum iteration number for the ICP registration.")
self.IterationSlider.minimum = 1
self.IterationSlider.maximum = 200
self.IterationSlider.value = 100
self.IterationSlider.singleStep = 5
self.IterationSlider.tickInterval = 1
self.IterationSlider.decimals = 0
self.IterationSlider.connect('valueChanged(double)',
self.onIterationSliderChange)
self.ICPFormLayout.addRow(self.label, self.IterationSlider)
self.IterationNumber = self.IterationSlider.value # Set default value
# Slider for Number of Landmarks for ICP
self.label = qt.QLabel()
self.label.setFont(qt.QFont(self.font_type, self.font_size))
self.label.setText("ICP Landmark Number: ")
self.label.setToolTip(
"Select the number of landmarks per surface for the ICP registration."
)
self.LandmarkSlider = ctk.ctkSliderWidget()
self.LandmarkSlider.setToolTip(
"Select the number of landmarks per surface for the ICP registration."
)
self.LandmarkSlider.minimum = 50
self.LandmarkSlider.maximum = 1000
self.LandmarkSlider.value = 500
self.LandmarkSlider.singleStep = 10
self.LandmarkSlider.tickInterval = 1
self.LandmarkSlider.decimals = 0
self.LandmarkSlider.connect('valueChanged(double)',
self.onLandmarkSliderChange)
self.ICPFormLayout.addRow(self.label, self.LandmarkSlider)
self.LandmarkNumber = self.LandmarkSlider.value # Set default value
# Slider for Maximum RMS Error for ICP
self.label = qt.QLabel()
self.label.setFont(qt.QFont(self.font_type, self.font_size))
self.label.setText("ICP Maximum RMS Error: ")
self.label.setToolTip(
"Select the maximum root mean square (RMS) error for determining the ICP registration convergence."
)
self.RMS_Slider = ctk.ctkSliderWidget()
self.RMS_Slider.setToolTip(
"Select the maximum root mean square (RMS) error for determining the ICP registration convergence."
)
self.RMS_Slider.minimum = 0.0001
self.RMS_Slider.maximum = 0.05
self.RMS_Slider.value = 0.01
self.RMS_Slider.singleStep = 0.01
self.RMS_Slider.tickInterval = 0.001
self.RMS_Slider.decimals = 3
self.RMS_Slider.connect('valueChanged(double)',
self.onRMS_SliderChange)
self.ICPFormLayout.addRow(self.label, self.RMS_Slider)
self.RMS_Number = self.RMS_Slider.value # Set default value
# Slider for choosing the reference bone
self.label = qt.QLabel()
self.label.setFont(qt.QFont(self.font_type, self.font_size))
self.label.setText("Reference Bone Label: ")
self.label.setToolTip(
"Select the label of the bone to keep static. This bone will be registered among all the volunteers. Note: Please choose the folder with the segmented images first."
)
self.Ref_Bone_Slider = ctk.ctkSliderWidget()
self.Ref_Bone_Slider.setToolTip(
"Select the label of the bone to keep static. This bone will be registered among all the volunteers. Note: Please choose the folder with the segmented images first."
)
self.Ref_Bone_Slider.minimum = 0
self.Ref_Bone_Slider.maximum = 0
self.Ref_Bone_Slider.value = 0
self.Ref_Bone_Slider.singleStep = 1
self.Ref_Bone_Slider.tickInterval = 1
self.Ref_Bone_Slider.decimals = 0
self.Ref_Bone_Slider.connect('valueChanged(double)',
self.onRef_Bone_SliderChange)
self.ICPFormLayout.addRow(self.label, self.Ref_Bone_Slider)
self.ref_label = int(self.Ref_Bone_Slider.value) # Set default value
# Radial buttons for the ICP parameters
self.radial_button_1 = qt.QRadioButton("Similarity")
self.radial_button_1.setFont(qt.QFont(self.font_type, self.font_size))
self.radial_button_1.toggled.connect(self.onICPModeSelect_1)
self.ICPFormLayout.addWidget(self.radial_button_1)
self.radial_button_2 = qt.QRadioButton("Rigid")
self.radial_button_2.setFont(qt.QFont(self.font_type, self.font_size))
self.radial_button_2.setChecked(True)
self.radial_button_2.toggled.connect(self.onICPModeSelect_2)
self.ICPFormLayout.addWidget(self.radial_button_2)
self.radial_button_3 = qt.QRadioButton("Affine")
self.radial_button_3.toggled.connect(self.onICPModeSelect_3)
self.ICPFormLayout.addWidget(self.radial_button_3)
# Text input for choosing which image labels to use
self.label = qt.QLabel()
self.label.setFont(qt.QFont(self.font_type, self.font_size))
self.label.setText("Image Labels: ")
self.label.setToolTip(
"Choose several labels to use for creating the training data. Value of -1 uses the default 1 through 9. Otherwise, input should be similar to '1,2,3' to use labels one, two, and three. "
)
self.lineedit = qt.QLineEdit()
self.lineedit.setFont(qt.QFont(self.font_type, self.font_size))
self.lineedit.setToolTip(
"Choose several labels to use for creating the training data. Value of -1 uses the default 1 through 9. Otherwise, input should be similar to '1,2,3' to use labels one, two, and three. "
)
self.ICPFormLayout.addRow(self.label, self.lineedit)
self.lineedit.setText("-1")
# Bone Smoothing Parameters Collapse Button
self.SmoothCollapsibleButton = ctk.ctkCollapsibleButton()
self.SmoothCollapsibleButton.setFont(
qt.QFont(self.font_type, self.font_size))
self.SmoothCollapsibleButton.text = "Smoothing Options"
self.SmoothCollapsibleButton.collapsed = True # Default is to not show
frameLayout.addWidget(self.SmoothCollapsibleButton)
# Layout within the smoothing options collapsible button
self.SmoothFormLayout = qt.QFormLayout(self.SmoothCollapsibleButton)
# Slider for choosing the number of iterations for bone smoothing
self.label = qt.QLabel()
self.label.setFont(qt.QFont(self.font_type, self.font_size))
self.label.setText("Smoothing Iterations: ")
self.label.setToolTip(
"Select the number of iterations for smoothing the bone surface. Higher iterations will smooth more. Lower iterations will have less smoothing."
)
self.Bone_Smoothing_Its_Slider = ctk.ctkSliderWidget()
self.Bone_Smoothing_Its_Slider.setToolTip(
"Select the number of iterations for smoothing the bone surface. Higher iterations will smooth more. Lower iterations will have less smoothing."
)
self.Bone_Smoothing_Its_Slider.minimum = 0
self.Bone_Smoothing_Its_Slider.maximum = 30
self.Bone_Smoothing_Its_Slider.value = 10
self.Bone_Smoothing_Its_Slider.singleStep = 1
self.Bone_Smoothing_Its_Slider.tickInterval = 1
self.Bone_Smoothing_Its_Slider.decimals = 0
self.Bone_Smoothing_Its_Slider.connect(
'valueChanged(double)', self.onBone_Smoothing_Its_SliderChange)
self.SmoothFormLayout.addRow(self.label,
self.Bone_Smoothing_Its_Slider)
self.smoothing_iterations = self.Bone_Smoothing_Its_Slider.value # Set default value
# Slider for choosing the smoothing relaxation factor
self.label = qt.QLabel()
self.label.setFont(qt.QFont(self.font_type, self.font_size))
self.label.setText("Relaxation Factor: ")
self.label.setToolTip(
"Select the relaxation factor for smoothing the bone surfaces. Higher relaxation will smooth the surface more while a lower factor will have less smoothing."
)
self.Bone_Smoothing_Relaxation_Slider = ctk.ctkSliderWidget()
self.Bone_Smoothing_Relaxation_Slider.setToolTip(
"Select the relaxation factor for smoothing the bone surfaces. Higher relaxation will smooth the surface more while a lower factor will have less smoothing."
)
self.Bone_Smoothing_Relaxation_Slider.minimum = 0
self.Bone_Smoothing_Relaxation_Slider.maximum = 1
self.Bone_Smoothing_Relaxation_Slider.value = 0.4
self.Bone_Smoothing_Relaxation_Slider.singleStep = 0.1
self.Bone_Smoothing_Relaxation_Slider.tickInterval = 0.1
self.Bone_Smoothing_Relaxation_Slider.decimals = 2
self.Bone_Smoothing_Relaxation_Slider.connect(
'valueChanged(double)',
self.onBone_Smoothing_Relaxation_SliderChange)
self.SmoothFormLayout.addRow(self.label,
self.Bone_Smoothing_Relaxation_Slider)
self.relaxation_factor = self.Bone_Smoothing_Relaxation_Slider.value # Set default value
# Slider for choosing the percentage of bone surface decimation
self.label = qt.QLabel()
self.label.setFont(qt.QFont(self.font_type, self.font_size))
self.label.setText("Surface Decimation: ")
self.label.setToolTip(
"Select the ratio of verticies to remove from the bone surface. This results in a smoother surface and less points for faster computation. Too much could cause surface artifacts. For example, 0.1 removes 10 percent while 0.9 removes 90 percent of points."
)
self.Bone_Decimate_Slider = ctk.ctkSliderWidget()
self.Bone_Decimate_Slider.setToolTip(
"Select the ratio of verticies to remove from the bone surface. This results in a smoother surface and less points for faster computation. Too much could cause surface artifacts. For example, 0.1 removes 10 percent while 0.9 removes 90 percent of points."
)
self.Bone_Decimate_Slider.minimum = 0
self.Bone_Decimate_Slider.maximum = 0.9
self.Bone_Decimate_Slider.value = 0
self.Bone_Decimate_Slider.singleStep = 0.05
self.Bone_Decimate_Slider.tickInterval = 0.05
self.Bone_Decimate_Slider.decimals = 2
self.Bone_Decimate_Slider.connect('valueChanged(double)',
self.onBone_Decimate_SliderChange)
self.SmoothFormLayout.addRow(self.label, self.Bone_Decimate_Slider)
self.decimate_surface = self.Bone_Decimate_Slider.value # Set default value
# Debugging Collapse button
self.RenderingCollapsibleButton = ctk.ctkCollapsibleButton()
self.RenderingCollapsibleButton.setFont(
qt.QFont(self.font_type, self.font_size))
self.RenderingCollapsibleButton.text = "Visualization"
self.RenderingCollapsibleButton.collapsed = True # Default is to not show
frameLayout.addWidget(self.RenderingCollapsibleButton)
# Layout within the debug collapsible button
self.CollapseFormLayout = qt.QFormLayout(
self.RenderingCollapsibleButton)
# Show the registered shapes toggle button
self.show_registered_shapes = qt.QCheckBox("Show Registered Shapes")
self.show_registered_shapes.setFont(
qt.QFont(self.font_type, self.font_size))
self.show_registered_shapes.toolTip = "When checked, show each registered bone. Useful for debugging any ICP registration based errors."
self.show_registered_shapes.checked = False
self.CollapseFormLayout.addWidget(self.show_registered_shapes)
# Show the registered shapes toggle button
self.show_extracted_shapes = qt.QCheckBox("Show Extracted Shapes")
self.show_extracted_shapes.setFont(
qt.QFont(self.font_type, self.font_size))
self.show_extracted_shapes.toolTip = "When checked, show the initial surfaces from the images. Useful for debugging errors based on deriving surfaces from the MR images."
self.show_extracted_shapes.checked = False
self.CollapseFormLayout.addWidget(self.show_extracted_shapes)
# Show the loaded images toggle button
self.debug_show_images = qt.QCheckBox("Show Loaded Images")
self.debug_show_images.setFont(qt.QFont(self.font_type,
self.font_size))
self.debug_show_images.toolTip = "When checked, show the loaded images. Useful for debugging if the images are flipped or loading incorrectly."
self.debug_show_images.checked = False
self.CollapseFormLayout.addWidget(self.debug_show_images)
# Debugging Collapse button
self.DebugCollapsibleButton = ctk.ctkCollapsibleButton()
self.DebugCollapsibleButton.setFont(
qt.QFont(self.font_type, self.font_size))
self.DebugCollapsibleButton.text = "Debugging"
self.DebugCollapsibleButton.collapsed = True # Default is to not show
frameLayout.addWidget(self.DebugCollapsibleButton)
# Layout within the debug collapsible button
self.CollapseFormLayout = qt.QFormLayout(self.DebugCollapsibleButton)
# Show the flip image vertically toggle button
self.flip_image_vertically = qt.QCheckBox("Flip Vertically")
self.flip_image_vertically.setFont(
qt.QFont(self.font_type, self.font_size))
self.flip_image_vertically.toolTip = "When checked, flip the images vertically after loading them."
self.flip_image_vertically.checked = False
self.CollapseFormLayout.addWidget(self.flip_image_vertically)
# Show the flip image horizontally toggle button
self.flip_image_horizontally = qt.QCheckBox("Flip Horizontally")
self.flip_image_horizontally.setFont(
qt.QFont(self.font_type, self.font_size))
self.flip_image_horizontally.toolTip = "When checked, flip the images horizontally after loading them."
self.flip_image_horizontally.checked = False
self.CollapseFormLayout.addWidget(self.flip_image_horizontally)
# Show the save bones separately toggle button
self.Save_Extracted_Bones_Separately = qt.QCheckBox(
"Save Extracted Bones Separately")
self.Save_Extracted_Bones_Separately.setFont(
qt.QFont(self.font_type, self.font_size))
self.Save_Extracted_Bones_Separately.toolTip = "When checked, save each bone surface separately after smoothing and before any registration."
self.Save_Extracted_Bones_Separately.checked = False
self.CollapseFormLayout.addWidget(self.Save_Extracted_Bones_Separately)
# Show the save bones separately toggle button
self.Save_Registered_Bones_Separately = qt.QCheckBox(
"Save Registered Bones Separately")
self.Save_Registered_Bones_Separately.setFont(
qt.QFont(self.font_type, self.font_size))
self.Save_Registered_Bones_Separately.toolTip = "When checked, save each bone surface separately after smoothing and registration (instead of combining all the bones for each volunteer/position together)."
self.Save_Registered_Bones_Separately.checked = False
self.CollapseFormLayout.addWidget(
self.Save_Registered_Bones_Separately)
# Skip the registration
self.Skip_Registration = qt.QCheckBox("Skip Registration Steps")
self.Skip_Registration.setFont(qt.QFont(self.font_type,
self.font_size))
self.Skip_Registration.toolTip = "When checked, extract each bone surface from the image and smooth the surface (this is useful if the user only wishes to extract the bones from the images and smooth them.) Consider using along with the save extracted bones setting."
self.Skip_Registration.checked = False
self.CollapseFormLayout.addWidget(self.Skip_Registration)
# Don't save the reference bone toggle button
self.Remove_Ref_Bone = qt.QCheckBox("Remove the reference bone")
self.Remove_Ref_Bone.setFont(qt.QFont(self.font_type, self.font_size))
self.Remove_Ref_Bone.toolTip = "When checked, don't save the refernce bone when saving the PLY file. For example, this is useful if using the radius as a reference bone, but if you don't want it to appear in the final model."
self.Remove_Ref_Bone.checked = False
self.CollapseFormLayout.addWidget(self.Remove_Ref_Bone)
# Choose the number of files to load from the given folder
self.label = qt.QLabel()
self.label.setFont(qt.QFont(self.font_type, self.font_size))
self.label.setText("Number of images: ")
self.label.setToolTip(
"Select how many images to use from the given folder. (Select the folder first). This is useful if want want to use just the first few images to make sure everything runs correctly."
)
self.NumFileSlider = ctk.ctkSliderWidget()
self.NumFileSlider.setToolTip(
"Select how many images to use from the given folder. (Select the folder first). This is useful if want want to use just the first few images to make sure everything runs correctly."
)
self.NumFileSlider.minimum = -1
self.NumFileSlider.maximum = 1
self.NumFileSlider.value = -1
self.NumFileSlider.singleStep = 1
self.NumFileSlider.tickInterval = 1
self.NumFileSlider.decimals = 0
self.NumFileSlider.connect('valueChanged(double)',
self.onNumSliderChange)
self.CollapseFormLayout.addRow(self.label, self.NumFileSlider)
self.num_files = self.NumFileSlider.value # Set default value
# Compute button
self.computeButton = qt.QPushButton("Create The Training Data")
self.computeButton.setFont(qt.QFont(self.font_type, self.font_size))
self.computeButton.toolTip = "Run the module and create the training data for the PCA bone displacement model."
frameLayout.addWidget(self.computeButton)
self.computeButton.connect('clicked()', self.onCompute)
self.computeButton.enabled = False
# Progress Bar (so the user knows how much longer it will take)
self.progressBar = qt.QProgressBar()
self.progressBar.setFont(qt.QFont(self.font_type, self.font_size))
self.progressBar.setValue(0)
frameLayout.addWidget(self.progressBar)
self.progressBar.hide()
def setup(self):
# TODO: The following line is strictly for debug purposes, should be removed when this module is done
slicer.tvwidget = self
# Collapsible buttons
self.parametersCollapsibleButton = ctk.ctkCollapsibleButton()
self.parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(self.parametersCollapsibleButton)
# Layout within the collapsible button
self.parametersFormLayout = qt.QFormLayout(self.parametersCollapsibleButton)
# Transform combobox
self.transformLabel = qt.QLabel()
self.transformLabel.setText("toolCameraToToolTransform: ")
self.transformSelector = slicer.qMRMLNodeComboBox()
self.transformSelector.nodeTypes = ( ("vtkMRMLLinearTransformNode"), "" )
self.transformSelector.noneEnabled = False
self.transformSelector.addEnabled = False
self.transformSelector.removeEnabled = False
self.transformSelector.setMRMLScene( slicer.mrmlScene )
self.transformSelector.setToolTip("Pick the transform that the camera should follow, e.g. 'cauteryCameraToCauteryTransform'")
self.parametersFormLayout.addRow(self.transformLabel, self.transformSelector)
# Camera combobox
self.cameraLabel = qt.QLabel()
self.cameraLabel.setText("Scene Camera: ")
self.cameraSelector = slicer.qMRMLNodeComboBox()
self.cameraSelector.nodeTypes = ( ("vtkMRMLCameraNode"), "" )
self.cameraSelector.noneEnabled = False
self.cameraSelector.addEnabled = False
self.cameraSelector.removeEnabled = False
self.cameraSelector.setMRMLScene( slicer.mrmlScene )
self.cameraSelector.setToolTip("Pick the camera which should be moved, e.g. 'Default Scene Camera'")
self.parametersFormLayout.addRow(self.cameraLabel, self.cameraSelector)
# "Camera Control" Collapsible
self.cameraControlCollapsibleButton = ctk.ctkCollapsibleButton()
self.cameraControlCollapsibleButton.text = "Camera Control"
self.layout.addWidget(self.cameraControlCollapsibleButton)
# Layout within the collapsible button
self.cameraControlFormLayout = qt.QFormLayout(self.cameraControlCollapsibleButton)
# "Degrees of Freedom" Collapsible button
self.degreesOfFreedomCollapsibleButton = ctk.ctkCollapsibleGroupBox()
self.degreesOfFreedomCollapsibleButton.title = "Degrees of Freedom"
self.cameraControlFormLayout.addRow(self.degreesOfFreedomCollapsibleButton)
# Layout within the collapsible button
self.degreesOfFreedomFormLayout = qt.QFormLayout(self.degreesOfFreedomCollapsibleButton)
# A series of radio buttons for changing the degrees of freedom
self.degreesOfFreedom3Label = qt.QLabel(qt.Qt.Horizontal,None)
self.degreesOfFreedom3Label.setText("3DOF: ")
self.degreesOfFreedom3RadioButton = qt.QRadioButton()
self.degreesOfFreedom3RadioButton.setToolTip("The camera will always look at the target model (or if unselected will act like 5DOF)")
self.degreesOfFreedomFormLayout.addRow(self.degreesOfFreedom3Label,self.degreesOfFreedom3RadioButton)
self.degreesOfFreedom5Label = qt.QLabel(qt.Qt.Horizontal,None)
self.degreesOfFreedom5Label.setText("5DOF: ")
self.degreesOfFreedom5RadioButton = qt.QRadioButton()
self.degreesOfFreedom5RadioButton.setToolTip("The camera will always be oriented with the selected 'up direction'")
self.degreesOfFreedomFormLayout.addRow(self.degreesOfFreedom5Label,self.degreesOfFreedom5RadioButton)
self.degreesOfFreedom6Label = qt.QLabel(qt.Qt.Horizontal,None)
self.degreesOfFreedom6Label.setText("6DOF: ")
self.degreesOfFreedom6RadioButton = qt.QRadioButton()
self.degreesOfFreedom6RadioButton.setToolTip("The camera will be virtually attached to the tool, and rotate together with it")
self.degreesOfFreedom6RadioButton.setChecked(True)
self.degreesOfFreedomFormLayout.addRow(self.degreesOfFreedom6Label,self.degreesOfFreedom6RadioButton)
# "Up Direction" Collapsible button
self.upDirectionCollapsibleButton = ctk.ctkCollapsibleGroupBox()
self.upDirectionCollapsibleButton.title = "Up Direction"
self.upDirectionCollapsibleButton.setVisible(False)
self.cameraControlFormLayout.addRow(self.upDirectionCollapsibleButton)
# Layout within the collapsible button
self.upDirectionFormLayout = qt.QFormLayout(self.upDirectionCollapsibleButton)
# Radio buttons for each of the anatomical directions
self.upDirectionAnteriorLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.upDirectionAnteriorLabel.setText("Anterior: ")
self.upDirectionAnteriorRadioButton = qt.QRadioButton()
self.upDirectionAnteriorRadioButton.setChecked(True)
self.upDirectionFormLayout.addRow(self.upDirectionAnteriorLabel,self.upDirectionAnteriorRadioButton)
self.upDirectionPosteriorLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.upDirectionPosteriorLabel.setText("Posterior: ")
self.upDirectionPosteriorRadioButton = qt.QRadioButton()
self.upDirectionFormLayout.addRow(self.upDirectionPosteriorLabel,self.upDirectionPosteriorRadioButton)
self.upDirectionRightLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.upDirectionRightLabel.setText("Right: ")
self.upDirectionRightRadioButton = qt.QRadioButton()
self.upDirectionFormLayout.addRow(self.upDirectionRightLabel,self.upDirectionRightRadioButton)
self.upDirectionLeftLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.upDirectionLeftLabel.setText("Left: ")
self.upDirectionLeftRadioButton = qt.QRadioButton()
self.upDirectionFormLayout.addRow(self.upDirectionLeftLabel,self.upDirectionLeftRadioButton)
self.upDirectionSuperiorLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.upDirectionSuperiorLabel.setText("Superior: ")
self.upDirectionSuperiorRadioButton = qt.QRadioButton()
self.upDirectionFormLayout.addRow(self.upDirectionSuperiorLabel,self.upDirectionSuperiorRadioButton)
self.upDirectionInferiorLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.upDirectionInferiorLabel.setText("Inferior: ")
self.upDirectionInferiorRadioButton = qt.QRadioButton()
self.upDirectionFormLayout.addRow(self.upDirectionInferiorLabel,self.upDirectionInferiorRadioButton)
# "Target Model" Collapsible button
self.targetModelCollapsibleButton = ctk.ctkCollapsibleGroupBox()
self.targetModelCollapsibleButton.title = "Target Model"
self.targetModelCollapsibleButton.setVisible(False)
self.cameraControlFormLayout.addRow(self.targetModelCollapsibleButton)
# Layout within the collapsible button
self.targetModelFormLayout = qt.QFormLayout(self.targetModelCollapsibleButton)
# Selection of the target model
self.targetModelLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.targetModelLabel.text = "Target model: "
self.targetModelSelector = slicer.qMRMLNodeComboBox()
self.targetModelSelector.nodeTypes = ( ("vtkMRMLModelNode"), "" )
self.targetModelSelector.noneEnabled = False
self.targetModelSelector.addEnabled = False
self.targetModelSelector.removeEnabled = False
self.targetModelSelector.setMRMLScene( slicer.mrmlScene )
self.targetModelSelector.setToolTip("This model be the center of rotation using 3DOF Viewpoint (e.g. tumour)")
self.targetModelFormLayout.addRow(self.targetModelLabel,self.targetModelSelector)
# "Zoom" Collapsible button
self.zoomCollapsibleButton = ctk.ctkCollapsibleGroupBox()
self.zoomCollapsibleButton.title = "Zoom"
self.cameraControlFormLayout.addRow(self.zoomCollapsibleButton)
# Layout within the collapsible button
self.zoomFormLayout = qt.QFormLayout(self.zoomCollapsibleButton)
# Camera viewing angle (perspective projection only)
self.cameraViewAngleLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.cameraViewAngleLabel.setText("View angle (degrees): ")
self.cameraViewAngleSlider = slicer.qMRMLSliderWidget()
self.cameraViewAngleSlider.minimum = self.cameraViewAngleMinDeg
self.cameraViewAngleSlider.maximum = self.cameraViewAngleMaxDeg
self.cameraViewAngleSlider.value = self.sliderViewAngleDefaultDeg
self.cameraViewAngleSlider.singleStep = self.sliderSingleStepValue
self.cameraViewAngleSlider.pageStep = self.sliderPageStepValue
self.cameraViewAngleSlider.setToolTip("Make the current viewing target look larger/smaller.")
self.zoomFormLayout.addRow(self.cameraViewAngleLabel,self.cameraViewAngleSlider)
# Camera parallel scale (parallel projection only)
self.cameraParallelScaleLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.cameraParallelScaleLabel.setText("View scale: ")
self.cameraParallelScaleLabel.setVisible(False)
self.cameraParallelScaleSlider = slicer.qMRMLSliderWidget()
self.cameraParallelScaleSlider.minimum = self.cameraParallelScaleMinDeg
self.cameraParallelScaleSlider.maximum = self.cameraParallelScaleMaxDeg
self.cameraParallelScaleSlider.value = self.sliderParallelScaleDefaultDeg
self.cameraParallelScaleSlider.singleStep = self.sliderSingleStepValue
self.cameraParallelScaleSlider.pageStep = self.sliderPageStepValue
self.cameraParallelScaleSlider.setToolTip("Make the current viewing target look larger/smaller.")
self.cameraParallelScaleSlider.setVisible(False)
self.zoomFormLayout.addRow(self.cameraParallelScaleLabel,self.cameraParallelScaleSlider)
# "Translation" Collapsible
self.translationCollapsibleButton = ctk.ctkCollapsibleGroupBox()
self.translationCollapsibleButton.title = "Translation"
self.cameraControlFormLayout.addRow(self.translationCollapsibleButton)
# Layout within the collapsible button
self.translationFormLayout = qt.QFormLayout(self.translationCollapsibleButton)
self.cameraXPosLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.cameraXPosLabel.text = "Left/Right (mm): "
self.cameraXPosSlider = slicer.qMRMLSliderWidget()
self.cameraXPosSlider.minimum = self.sliderTranslationMinMm
self.cameraXPosSlider.maximum = self.sliderTranslationMaxMm
self.cameraXPosSlider.value = self.sliderTranslationDefaultMm
self.cameraXPosSlider.singleStep = self.sliderSingleStepValue
self.cameraXPosSlider.pageStep = self.sliderPageStepValue
self.translationFormLayout.addRow(self.cameraXPosLabel,self.cameraXPosSlider)
self.cameraYPosLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.cameraYPosLabel.setText("Down/Up (mm): ")
self.cameraYPosSlider = slicer.qMRMLSliderWidget()
self.cameraYPosSlider.minimum = self.sliderTranslationMinMm
self.cameraYPosSlider.maximum = self.sliderTranslationMaxMm
self.cameraYPosSlider.value = self.sliderTranslationDefaultMm
self.cameraYPosSlider.singleStep = self.sliderSingleStepValue
self.cameraYPosSlider.pageStep = self.sliderPageStepValue
self.translationFormLayout.addRow(self.cameraYPosLabel,self.cameraYPosSlider)
self.cameraZPosLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.cameraZPosLabel.setText("Front/Back (mm): ")
self.cameraZPosSlider = slicer.qMRMLSliderWidget()
self.cameraZPosSlider.minimum = self.sliderTranslationMinMm
self.cameraZPosSlider.maximum = self.sliderTranslationMaxMm
self.cameraZPosSlider.value = self.sliderTranslationDefaultMm
self.cameraZPosSlider.singleStep = self.sliderSingleStepValue
self.cameraZPosSlider.pageStep = self.sliderPageStepValue
self.translationFormLayout.addRow(self.cameraZPosLabel,self.cameraZPosSlider)
# "Model Visibility" Collapsible
self.modelVisibilityCollapsibleButton = ctk.ctkCollapsibleGroupBox()
self.modelVisibilityCollapsibleButton.title = "Model Visibility"
self.cameraControlFormLayout.addRow(self.modelVisibilityCollapsibleButton)
# Layout within the collapsible button
self.modelVisibilityFormLayout = qt.QFormLayout(self.modelVisibilityCollapsibleButton)
self.modelOnlyViewpointOnLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.modelOnlyViewpointOnLabel.text = "Model visible only for Viewpoint on: "
self.modelOnlyViewpointOnSelector = slicer.qMRMLNodeComboBox()
self.modelOnlyViewpointOnSelector.nodeTypes = ( ("vtkMRMLModelNode"), "" )
self.modelOnlyViewpointOnSelector.noneEnabled = True
self.modelOnlyViewpointOnSelector.addEnabled = False
self.modelOnlyViewpointOnSelector.removeEnabled = False
self.modelOnlyViewpointOnSelector.setMRMLScene( slicer.mrmlScene )
self.modelOnlyViewpointOnSelector.setToolTip("This model be visible if Viewpoint mode is enabled, and invisible otherwise")
self.modelVisibilityFormLayout.addRow(self.modelOnlyViewpointOnLabel,self.modelOnlyViewpointOnSelector)
self.modelOnlyViewpointOffLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.modelOnlyViewpointOffLabel.text = "Model visible only for Viewpoint off: "
self.modelOnlyViewpointOffSelector = slicer.qMRMLNodeComboBox()
self.modelOnlyViewpointOffSelector.nodeTypes = ( ("vtkMRMLModelNode"), "" )
self.modelOnlyViewpointOffSelector.noneEnabled = True
self.modelOnlyViewpointOffSelector.addEnabled = False
self.modelOnlyViewpointOffSelector.removeEnabled = False
self.modelOnlyViewpointOffSelector.setMRMLScene( slicer.mrmlScene )
self.modelOnlyViewpointOffSelector.setToolTip("This model be visible if Viewpoint Mode is disabled, and invisible otherwise")
self.modelVisibilityFormLayout.addRow(self.modelOnlyViewpointOffLabel,self.modelOnlyViewpointOffSelector)
# Camera parallel projection checkbox
self.cameraParallelProjectionLabel = qt.QLabel()
self.cameraParallelProjectionLabel.setText("Parallel Projection")
self.cameraParallelProjectionCheckbox = qt.QCheckBox()
self.cameraParallelProjectionCheckbox.setCheckState(0)
self.cameraParallelProjectionCheckbox.setToolTip("If checked, render with parallel projection (box-shaped view). Otherwise render with perspective projection (cone-shaped view).")
self.cameraControlFormLayout.addRow(self.cameraParallelProjectionLabel,self.cameraParallelProjectionCheckbox)
# "Toggle Tool Point of View" button
self.enableViewpointButton = qt.QPushButton()
self.enableViewpointButton.setToolTip("The camera will continuously update its position so that it follows the tool.")
self.enableViewpointButton.setText(self.enableViewpointButtonTextState0)
self.cameraControlFormLayout.addRow(self.enableViewpointButton)
#Connections
self.enableViewpointButton.connect('clicked()', self.enableViewpointButtonPressed)
self.cameraParallelProjectionCheckbox.connect('stateChanged(int)', self.toggleCameraParallelProjectionCheckboxPressed)
self.cameraViewAngleSlider.connect('valueChanged(double)', self.logic.SetCameraViewAngleDeg)
self.cameraParallelScaleSlider.connect('valueChanged(double)', self.logic.SetCameraParallelScale)
self.cameraXPosSlider.connect('valueChanged(double)', self.logic.SetCameraXPosMm)
self.cameraYPosSlider.connect('valueChanged(double)', self.logic.SetCameraYPosMm)
self.cameraZPosSlider.connect('valueChanged(double)', self.logic.SetCameraZPosMm)
self.upDirectionAnteriorRadioButton.connect('clicked()', self.changeUpToAnterior)
self.upDirectionPosteriorRadioButton.connect('clicked()', self.changeUpToPosterior)
self.upDirectionLeftRadioButton.connect('clicked()', self.changeUpToLeft)
self.upDirectionRightRadioButton.connect('clicked()', self.changeUpToRight)
self.upDirectionSuperiorRadioButton.connect('clicked()', self.changeUpToSuperior)
self.upDirectionInferiorRadioButton.connect('clicked()', self.changeUpToInferior)
self.degreesOfFreedom3RadioButton.connect('clicked()', self.changeInterfaceTo3DOFMode)
self.degreesOfFreedom5RadioButton.connect('clicked()', self.changeInterfaceTo5DOFMode)
self.degreesOfFreedom6RadioButton.connect('clicked()', self.changeInterfaceTo6DOFMode)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
self.PathRecorderModuleDirectoryPath = slicer.modules.pathrecorder.path.replace(
"PathRecorder.py", "")
# Instantiate and connect widgets ...
#
# Reload and Test area
#
reloadCollapsibleButton = ctk.ctkCollapsibleButton()
reloadCollapsibleButton.text = "Reload && Test"
self.layout.addWidget(reloadCollapsibleButton)
reloadFormLayout = qt.QFormLayout(reloadCollapsibleButton)
# reload button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "PathRecorder Reload"
reloadFormLayout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
# reload and test button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadAndTestButton = qt.QPushButton("Reload and Test")
self.reloadAndTestButton.toolTip = "Reload this module and then run the self tests."
reloadFormLayout.addWidget(self.reloadAndTestButton)
self.reloadAndTestButton.connect('clicked()', self.onReloadAndTest)
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# Input fiducial node selector
#
self.inputFiducialsNodeSelector = slicer.qMRMLNodeComboBox()
self.inputFiducialsNodeSelector.nodeTypes = [
'vtkMRMLMarkupsFiducialNode'
]
self.inputFiducialsNodeSelector.selectNodeUponCreation = True
self.inputFiducialsNodeSelector.addEnabled = True
self.inputFiducialsNodeSelector.removeEnabled = False
self.inputFiducialsNodeSelector.noneEnabled = True
self.inputFiducialsNodeSelector.showHidden = False
self.inputFiducialsNodeSelector.showChildNodeTypes = False
self.inputFiducialsNodeSelector.setMRMLScene(slicer.mrmlScene)
self.inputFiducialsNodeSelector.objectName = 'inputFiducialsNodeSelector'
self.inputFiducialsNodeSelector.toolTip = "Select storage node for the recorded points (Markup-Fiducial-Node)."
#inputFiducialsNodeSelector.connect('currentNodeChanged(bool)', self.enableOrDisableCreateButton)
parametersFormLayout.addRow("Storage Node:",
self.inputFiducialsNodeSelector)
#self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)', inputFiducialsNodeSelector, 'setMRMLScene(vtkMRMLScene*)')
# Input Tracker node selector
#
self.inputTrackerNodeSelector = slicer.qMRMLNodeComboBox()
self.inputTrackerNodeSelector.nodeTypes = [
'vtkMRMLLinearTransformNode'
]
self.inputTrackerNodeSelector.selectNodeUponCreation = True
self.inputTrackerNodeSelector.addEnabled = False
self.inputTrackerNodeSelector.removeEnabled = False
self.inputTrackerNodeSelector.noneEnabled = True
self.inputTrackerNodeSelector.showHidden = False
self.inputTrackerNodeSelector.showChildNodeTypes = False
self.inputTrackerNodeSelector.setMRMLScene(slicer.mrmlScene)
self.inputTrackerNodeSelector.objectName = 'inputTrackerNodeSelector'
self.inputTrackerNodeSelector.toolTip = "Select the tracker linear transform node."
#inputTrackerNodeSelector.connect('currentNodeChanged(bool)', self.enableOrDisableCreateButton)
parametersFormLayout.addRow("Tracker Transform:",
self.inputTrackerNodeSelector)
#self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)', inputTrackerNodeSelector, 'setMRMLScene(vtkMRMLScene*)')
#
# Status Area
#
statusCollapsibleButton = ctk.ctkCollapsibleButton()
statusCollapsibleButton.text = "Tracker Status"
self.layout.addWidget(statusCollapsibleButton)
# Layout within the status collapsible button
statusFormLayout = qt.QFormLayout(statusCollapsibleButton)
#
# Status Button
#
self.statusRedIcon = qt.QIcon(self.PathRecorderModuleDirectoryPath +
'/Resources/Icons/icon_DotRed.png')
self.statusGreenIcon = qt.QIcon(self.PathRecorderModuleDirectoryPath +
'/Resources/Icons/icon_DotGreen.png')
self.statusButton = qt.QPushButton("")
#self.statusButton.toolTip = "Tracker Status"
self.statusButton.enabled = False
self.statusButton.setIcon(self.statusRedIcon)
self.statusButton.setMaximumWidth(25)
# Bold and large font for needle label
largeFont = qt.QFont()
largeFont.setPixelSize(14)
#
# Label for showing the tracker position
#
self.currentCoordinatesLabel = qt.QLabel('[ NaN , NaN , NaN ]')
self.currentCoordinatesLabel.setToolTip("Tracker Position")
statusFormLayout.addRow(self.statusButton,
self.currentCoordinatesLabel)
#
# Collect Area
#
collectCollapsibleButton = ctk.ctkCollapsibleButton()
collectCollapsibleButton.text = "Acquire Points"
self.layout.addWidget(collectCollapsibleButton)
# Layout within the collect collapsible button
collectFormLayout = qt.QFormLayout(collectCollapsibleButton)
#
# Name base line-edit
#
self.nameBaseLineEdit = qt.QLineEdit()
self.nameBaseLineEdit.setToolTip("Fiducials Name Base")
collectFormLayout.addRow("Fiducials Name Base:", self.nameBaseLineEdit)
#
# Single Acquire Button
#
self.singleAcquireButton = qt.QPushButton("Single Point")
self.singleAcquireButton.toolTip = "Acquire a single point at the current position."
self.singleAcquireButton.enabled = True
collectFormLayout.addRow(self.singleAcquireButton)
#
# Continuous Acquire Button
#
self.recordButtonIcon = qt.QIcon(self.PathRecorderModuleDirectoryPath +
'/Resources/Icons/icon_Record.png')
self.stopButtonIcon = qt.QIcon(self.PathRecorderModuleDirectoryPath +
'/Resources/Icons/icon_Stop.png')
self.acquireButton = qt.QPushButton("Continuous")
self.acquireButton.toolTip = "Start acquiring points continiously."
self.acquireButton.enabled = True
self.acquireButton.checkable = True
self.acquireButton.setIcon(self.recordButtonIcon)
#self.acquireButton.setMinimumWidth(80)
#self.acquireButton.setMaximumWidth(80)
collectFormLayout.addRow(self.acquireButton)
#
# Distance-based Radio Button
#
self.distanceBasedButton = qt.QRadioButton("Minimum Distance:")
self.distanceBasedButton.setChecked(1)
#collectFormLayout.addRow()
# Distance slider
distanceSlider = ctk.ctkSliderWidget()
#distanceSlider.decimals = 0
distanceSlider.minimum = 0.1
distanceSlider.maximum = 100
distanceSlider.suffix = " mm"
distanceSlider.value = 1
distanceSlider.toolTip = "Set minimum distance between recorded points"
self.distanceSlider = distanceSlider
collectFormLayout.addRow("Minimum Distance:", distanceSlider)
#
# Delete Button
#
self.deleteButton = qt.QPushButton("Delete")
self.deleteButton.toolTip = "Delete all the points."
self.deleteButton.enabled = True
collectFormLayout.addRow(self.deleteButton)
#
# Export Area
#
exportCollapsibleButton = ctk.ctkCollapsibleButton()
exportCollapsibleButton.text = "Export Points"
self.layout.addWidget(exportCollapsibleButton)
# Layout within the dummy collapsible button
exportFormLayout = qt.QFormLayout(exportCollapsibleButton)
#
# Load Button
#
self.exportDirectoryButton = ctk.ctkDirectoryButton()
exportFormLayout.addRow(self.exportDirectoryButton)
#
# Name base line-edit
#
self.fileNameBaseLineEdit = qt.QLineEdit()
self.fileNameBaseLineEdit.setToolTip("File name base")
self.fileNameBaseLineEdit.text = 'PathRecorder'
exportFormLayout.addRow("File Name Base:", self.fileNameBaseLineEdit)
#
# Save Button
#
saveButtonIcon = qt.QIcon(self.PathRecorderModuleDirectoryPath +
'/Resources/Icons/icon_Save.png')
self.exportButton = qt.QPushButton()
self.exportButton.setIcon(saveButtonIcon)
self.exportButton.toolTip = "Save points."
self.exportButton.enabled = True
exportFormLayout.addRow(self.exportButton)
# connections
self.inputFiducialsNodeSelector.connect(
'currentNodeChanged(vtkMRMLNode*)',
self.setAnnotationHierarchyNode)
self.inputTrackerNodeSelector.connect(
'currentNodeChanged(vtkMRMLNode*)', self.setTransformNode)
self.distanceBasedButton.connect('toggled(bool)',
self.distanceBasedSelected)
self.acquireButton.connect('toggled(bool)',
self.onAcquireButtonToggled)
self.singleAcquireButton.connect('clicked()',
self.onSingleAcButtonClicked)
self.deleteButton.connect('clicked()', self.onDeleteButtonClicked)
self.exportButton.connect('clicked()', self.onExportButtonClicked)
#self.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
#self.outputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
# Instantiate and connect widgets ...
if self.developerMode:
#
# Reload and Test area
#
reloadCollapsibleButton = ctk.ctkCollapsibleButton()
reloadCollapsibleButton.text = "Reload && Test"
self.layout.addWidget(reloadCollapsibleButton)
reloadFormLayout = qt.QFormLayout(reloadCollapsibleButton)
# reload button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "CompareVolumes Reload"
reloadFormLayout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
# reload and test button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadAndTestButton = qt.QPushButton("Reload and Test All")
self.reloadAndTestButton.toolTip = "Reload this module and then run the self tests."
reloadFormLayout.addWidget(self.reloadAndTestButton)
self.reloadAndTestButton.connect('clicked()', self.onReloadAndTest)
# reload and run specific tests
scenarios = (
"Three Volume",
"View Watcher",
"LayerReveal",
)
for scenario in scenarios:
button = qt.QPushButton("Reload and Test %s" % scenario)
self.reloadAndTestButton.toolTip = "Reload this module and then run the %s self test." % scenario
reloadFormLayout.addWidget(button)
button.connect(
'clicked()',
lambda s=scenario: self.onReloadAndTest(scenario=s))
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# orientation
#
self.orientationBox = qt.QGroupBox("Orientation")
self.orientationBox.setLayout(qt.QFormLayout())
self.orientationButtons = {}
self.orientations = ("Axial", "Sagittal", "Coronal")
for orientation in self.orientations:
self.orientationButtons[orientation] = qt.QRadioButton()
self.orientationButtons[orientation].text = orientation
self.orientationButtons[orientation].connect(
"clicked()", lambda o=orientation: self.setOrientation(o))
self.orientationBox.layout().addWidget(
self.orientationButtons[orientation])
parametersFormLayout.addWidget(self.orientationBox)
self.setOrientation(self.orientations[0])
#
# target volume selector
#
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = (("vtkMRMLVolumeNode"), "")
self.inputSelector.selectNodeUponCreation = True
self.inputSelector.addEnabled = False
self.inputSelector.removeEnabled = False
self.inputSelector.noneEnabled = False
self.inputSelector.showHidden = False
self.inputSelector.showChildNodeTypes = True
self.inputSelector.setMRMLScene(slicer.mrmlScene)
self.inputSelector.setToolTip("Pick the input to the algorithm.")
parametersFormLayout.addRow("Target Volume: ", self.inputSelector)
#
# lightbox
#
self.lightboxVolumeButton = qt.QPushButton("Lightbox Target Volume")
self.lightboxVolumeButton.setToolTip(
"Make a set of slice views that span the extent of this study at equally spaced locations in the selected orientation."
)
parametersFormLayout.addRow(self.lightboxVolumeButton)
self.lightboxVolumeButton.connect("clicked()", self.onLightboxVolume)
#
# background volume selector
#
self.backgroundSelector = slicer.qMRMLNodeComboBox()
self.backgroundSelector.nodeTypes = (("vtkMRMLVolumeNode"), "")
self.backgroundSelector.selectNodeUponCreation = True
self.backgroundSelector.addEnabled = False
self.backgroundSelector.removeEnabled = False
self.backgroundSelector.noneEnabled = True
self.backgroundSelector.showHidden = False
self.backgroundSelector.showChildNodeTypes = True
self.backgroundSelector.setMRMLScene(slicer.mrmlScene)
self.backgroundSelector.setToolTip(
"Common background - all lightbox panes will have this background and a different volume in each foreground."
)
parametersFormLayout.addRow("Common Background Volume: ",
self.backgroundSelector)
#
# label volume selector
#
self.labelSelector = slicer.qMRMLNodeComboBox()
self.labelSelector.nodeTypes = (("vtkMRMLLabelMapVolumeNode"), "")
self.labelSelector.selectNodeUponCreation = True
self.labelSelector.addEnabled = False
self.labelSelector.removeEnabled = False
self.labelSelector.noneEnabled = True
self.labelSelector.showHidden = False
self.labelSelector.showChildNodeTypes = True
self.labelSelector.setMRMLScene(slicer.mrmlScene)
self.labelSelector.setToolTip(
"Common label - all lightbox panes will have this label on top.")
parametersFormLayout.addRow("Common Label Volume: ",
self.labelSelector)
self.lightboxVolumesButton = qt.QPushButton("Lightbox All Volumes")
self.lightboxVolumesButton.setToolTip(
"Make a set of slice views that show each of the currently loaded volumes, with optional companion volumes, in the selected orientation."
)
parametersFormLayout.addRow(self.lightboxVolumesButton)
self.lightboxVolumesButton.connect("clicked()", self.onLightboxVolumes)
#
# Add layer reveal area
#
layerRevealCollapsibleButton = ctk.ctkCollapsibleButton()
layerRevealCollapsibleButton.text = "Layer Reveal Cursor"
self.layout.addWidget(layerRevealCollapsibleButton)
layerRevealFormLayout = qt.QFormLayout(layerRevealCollapsibleButton)
self.layerRevealCheck = qt.QCheckBox()
layerRevealFormLayout.addRow("Layer Reveal Cursor",
self.layerRevealCheck)
self.layerRevealCheck.connect("toggled(bool)",
self.onLayerRevealToggled)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# TODO: The following lines are strictly for debug purposes, should be removed when this module is done
self.developerMode = True
slicer.igwidget = self
self.logic = InsertionGridPlannerLogic()
# Collapsible buttons
self.parametersCollapsibleButton = ctk.ctkCollapsibleButton()
self.parametersCollapsibleButton.text = "InsertionGridPlanner"
self.layout.addWidget(self.parametersCollapsibleButton)
# Layout within the collapsible button
self.parametersFormLayout = qt.QFormLayout(
self.parametersCollapsibleButton)
# Transform Tool Tip To Reference combobox
self.transformNodeGridToTargetLabel = qt.QLabel()
self.transformNodeGridToTargetLabel.setText(
"Grid to Target Transform: ")
self.transformNodeGridToTargetSelector = slicer.qMRMLNodeComboBox()
self.transformNodeGridToTargetSelector.nodeTypes = ((
"vtkMRMLLinearTransformNode"), "")
self.transformNodeGridToTargetSelector.noneEnabled = False
self.transformNodeGridToTargetSelector.addEnabled = False
self.transformNodeGridToTargetSelector.removeEnabled = False
self.transformNodeGridToTargetSelector.setMRMLScene(slicer.mrmlScene)
self.transformNodeGridToTargetSelector.setToolTip(
"Pick the transform for going from the grid's coordinate system to the target (reference) coordinate system"
)
self.parametersFormLayout.addRow(
self.transformNodeGridToTargetLabel,
self.transformNodeGridToTargetSelector)
# Grid type
self.gridPatternRectangularLabel = qt.QLabel(qt.Qt.Horizontal, None)
self.gridPatternRectangularLabel.setText("Rectangular Grid")
self.gridPatternRectangularRadioButton = qt.QRadioButton()
self.gridPatternRectangularRadioButton.setToolTip(
"Make the grid rectangular")
self.gridPatternRectangularRadioButton.setChecked(True)
self.parametersFormLayout.addRow(
self.gridPatternRectangularLabel,
self.gridPatternRectangularRadioButton)
self.gridPatternTriangularLabel = qt.QLabel(qt.Qt.Horizontal, None)
self.gridPatternTriangularLabel.setText("Triangular Grid")
self.gridPatternTriangularRadioButton = qt.QRadioButton()
self.gridPatternTriangularRadioButton.setToolTip(
"Make the grid triangular")
self.parametersFormLayout.addRow(self.gridPatternTriangularLabel,
self.gridPatternTriangularRadioButton)
# Grid size
self.gridSizeLeftLabel = qt.QLabel()
self.gridSizeLeftLabel.setText("Extent left (mm): ")
self.gridSizeLeftSlider = slicer.qMRMLSliderWidget()
self.gridSizeLeftSlider.minimum = 0 # mm
self.gridSizeLeftSlider.maximum = 150 # mm
self.gridSizeLeftSlider.value = 0 # mm
self.gridSizeLeftSlider.setToolTip("Adjust the size of the grid")
self.parametersFormLayout.addRow(self.gridSizeLeftLabel,
self.gridSizeLeftSlider)
self.gridSizeRightLabel = qt.QLabel()
self.gridSizeRightLabel.setText("Extent right (mm): ")
self.gridSizeRightSlider = slicer.qMRMLSliderWidget()
self.gridSizeRightSlider.minimum = 0 # mm
self.gridSizeRightSlider.maximum = 150 # mm
self.gridSizeRightSlider.value = 0 # mm
self.gridSizeRightSlider.setToolTip("Adjust the size of the grid")
self.parametersFormLayout.addRow(self.gridSizeRightLabel,
self.gridSizeRightSlider)
self.gridSizeUpLabel = qt.QLabel()
self.gridSizeUpLabel.setText("Extent up (mm): ")
self.gridSizeUpSlider = slicer.qMRMLSliderWidget()
self.gridSizeUpSlider.minimum = 0 # mm
self.gridSizeUpSlider.maximum = 150 # mm
self.gridSizeUpSlider.value = 0 # mm
self.gridSizeUpSlider.setToolTip("Adjust the size of the grid")
self.parametersFormLayout.addRow(self.gridSizeUpLabel,
self.gridSizeUpSlider)
self.gridSizeDownLabel = qt.QLabel()
self.gridSizeDownLabel.setText("Extent down (mm): ")
self.gridSizeDownSlider = slicer.qMRMLSliderWidget()
self.gridSizeDownSlider.minimum = 0 # mm
self.gridSizeDownSlider.maximum = 150 # mm
self.gridSizeDownSlider.value = 0 # mm
self.gridSizeDownSlider.setToolTip("Adjust the size of the grid")
self.parametersFormLayout.addRow(self.gridSizeDownLabel,
self.gridSizeDownSlider)
# Grid spacing
self.gridSpacingHorizontalLabel = qt.QLabel(qt.Qt.Horizontal, None)
self.gridSpacingHorizontalLabel.text = "Horizontal Spacing (mm): "
self.gridSpacingHorizontalSlider = slicer.qMRMLSliderWidget()
self.gridSpacingHorizontalSlider.minimum = 1 # mm
self.gridSpacingHorizontalSlider.maximum = 50 # mm
self.gridSpacingHorizontalSlider.value = 10 # mm
self.parametersFormLayout.addRow(self.gridSpacingHorizontalLabel,
self.gridSpacingHorizontalSlider)
self.gridSpacingVerticalLabel = qt.QLabel(qt.Qt.Horizontal, None)
self.gridSpacingVerticalLabel.text = "Vertical Spacing (mm): "
self.gridSpacingVerticalSlider = slicer.qMRMLSliderWidget()
self.gridSpacingVerticalSlider.minimum = 1 # mm
self.gridSpacingVerticalSlider.maximum = 50 # mm
self.gridSpacingVerticalSlider.value = 10 # mm
self.parametersFormLayout.addRow(self.gridSpacingVerticalLabel,
self.gridSpacingVerticalSlider)
# Grid creation
self.createGridButton = qt.QPushButton()
self.createGridButton.text = "Create Grid"
self.createGridButton.setToolTip("Create the virtual grid guide.")
self.parametersFormLayout.addRow(self.createGridButton)
self.deleteGridButton = qt.QPushButton()
self.deleteGridButton.text = "Delete Grid"
self.deleteGridButton.setToolTip("Delete the virtual grid guide.")
self.parametersFormLayout.addRow(self.deleteGridButton)
# Add vertical spacer
self.layout.addStretch(1)
#Connections
self.createGridButton.connect('clicked()',
self.createGridButtonPressed)
self.deleteGridButton.connect('clicked()', self.logic.deleteGrid)
def createUserInterface(self):
""" This method uses qt to create a user interface of radio buttons to select
a registration method. Note that BSpline registration is so slow and memory-consuming
as to at one point break Slicer. There is an option to run it with limited memory,
but this may take prohibitively long. <- NOTE this last comment was based on
expert automated registration - not sure about other modules.
"""
self.__layout = self.__parent.createUserInterface()
step_label = qt.QLabel(
"""Select your preferred method of registration. If you have already registered your images, or no registration is required, check the option "No Registration." The moving image will be registered to the fixed image, and then resampled at the dimensions of the fixed image. Be aware that many other modules in Slicer have more complex and/or customizable registration methods, should you require more thorough registration.
""")
step_label.setWordWrap(True)
self.__primaryGroupBox = qt.QGroupBox()
self.__primaryGroupBox.setTitle('Information')
self.__primaryGroupBoxLayout = qt.QFormLayout(self.__primaryGroupBox)
self.__primaryGroupBoxLayout.addRow(step_label)
self.__layout.addRow(self.__primaryGroupBox)
# Moving/Fixed Image Registration Order Options
OrderGroupBox = qt.QGroupBox()
OrderGroupBox.setTitle('Registration Order')
self.__layout.addRow(OrderGroupBox)
OrderGroupBoxLayout = qt.QFormLayout(OrderGroupBox)
self.__OrderRadio1 = qt.QRadioButton(
"Register pre-contrast to post-contrast.")
self.__OrderRadio1.toolTip = "Your pre-contrast image will be transformed."
OrderGroupBoxLayout.addRow(self.__OrderRadio1)
self.__OrderRadio1.setChecked(True)
self.__OrderRadio2 = qt.QRadioButton(
"Register post-contrast to pre-contrast.")
self.__OrderRadio2.toolTip = "Your post-contrast image will be transformed."
OrderGroupBoxLayout.addRow(self.__OrderRadio2)
# Registration Method Options
RegistrationGroupBox = qt.QGroupBox()
RegistrationGroupBox.setTitle('Registration Method')
self.__layout.addRow(RegistrationGroupBox)
RegistrationGroupBoxLayout = qt.QFormLayout(RegistrationGroupBox)
self.__RegistrationRadio1 = qt.QRadioButton("No Registration")
self.__RegistrationRadio1.toolTip = "Performs no registration."
RegistrationGroupBoxLayout.addRow(self.__RegistrationRadio1)
self.__RegistrationRadio2 = qt.QRadioButton("Rigid Registration")
self.__RegistrationRadio2.toolTip = """Computes a rigid registration on the pre-contrast image with respect to the post-contrast image. This will likely be the fastest registration method"""
RegistrationGroupBoxLayout.addRow(self.__RegistrationRadio2)
self.__RegistrationRadio3 = qt.QRadioButton("Affine Registration")
self.__RegistrationRadio3.toolTip = "Computes a rigid and affine registration on the pre-contrast image with respect to the post-contrast image. This method may take longer than rigid registration, but has the ability to stretch or compress images in addition to rotation and translation."
RegistrationGroupBoxLayout.addRow(self.__RegistrationRadio3)
self.__RegistrationRadio3.setChecked(True)
self.__RegistrationRadio4 = qt.QRadioButton("Deformable Registration")
self.__RegistrationRadio4.toolTip = """Computes a BSpline Registration on the pre-contrast image with respect to the post-contrast image. This method is slowest and may be necessary for only severly distorted images."""
RegistrationGroupBoxLayout.addRow(self.__RegistrationRadio4)
# Output Volume Preference
OutputGroupBox = qt.QGroupBox()
OutputGroupBox.setTitle('Registration Output')
self.__layout.addRow(OutputGroupBox)
OutputGroupBoxLayout = qt.QFormLayout(OutputGroupBox)
self.__OutputRadio1 = qt.QRadioButton("Create new volume.")
self.__OutputRadio1.toolTip = "A new volume will be created with the naming convention \"[pre]_reg_[post]\"."
OutputGroupBoxLayout.addRow(self.__OutputRadio1)
self.__OutputRadio1.setChecked(True)
self.__OutputRadio2 = qt.QRadioButton("Replace existing volume.")
self.__OutputRadio2.toolTip = "Your registered volume will be overwritten at the end of this step."
OutputGroupBoxLayout.addRow(self.__OutputRadio2)
# Registration Button and Progress Indicator
RunGroupBox = qt.QGroupBox()
RunGroupBox.setTitle('Run Registration')
self.__layout.addRow(RunGroupBox)
RunGroupBoxLayout = qt.QFormLayout(RunGroupBox)
self.__registrationButton = qt.QPushButton('Run registration')
self.__registrationStatus = qt.QLabel('Register scans')
self.__registrationStatus.alignment = 4 # This codes for centered alignment, although I'm not sure why.
RunGroupBoxLayout.addRow(self.__registrationStatus)
RunGroupBoxLayout.addRow(self.__registrationButton)
self.__registrationButton.connect('clicked()',
self.onRegistrationRequest)
def setup(self):
self.FilteringFrame = qt.QFrame()
self.FilteringFrame.setLayout(qt.QVBoxLayout())
self.FilteringFrame.enabled = False
self.FilteringFrame.setObjectName('FilteringFrame')
self.FilteringFrame.setStyleSheet(
'#FilteringFrame {border: 1px solid lightGray; color: black; }')
self.layout.addWidget(self.FilteringFrame)
filterLabel = qt.QLabel()
filterLabel.setText('Filtering')
self.FilteringFrame.layout().addWidget(filterLabel)
radioButtonsGroup = qt.QGroupBox()
radioButtonsGroup.setLayout(qt.QHBoxLayout())
radioButtonsGroup.setFixedWidth(120)
radioButtonsGroup.setObjectName('radioButtonsGroup')
radioButtonsGroup.setStyleSheet(
'#radioButtonsGroup {border: 1px solid white; color: black; }')
self.filterOnRadioButton = qt.QRadioButton()
self.filterOnRadioButton.setText('On')
self.filterOnRadioButton.setChecked(0)
radioButtonsGroup.layout().addWidget(self.filterOnRadioButton)
self.filterOffRadioButton = qt.QRadioButton()
self.filterOffRadioButton.setText('Off')
self.filterOffRadioButton.setChecked(1)
radioButtonsGroup.layout().addWidget(self.filterOffRadioButton)
self.FilteringFrame.layout().addWidget(radioButtonsGroup)
self.filterOptionsFrame = qt.QFrame()
self.filterOptionsFrame.setLayout(qt.QVBoxLayout())
self.filterOptionsFrame.setObjectName('filterOptionsFrame')
self.filterOptionsFrame.setStyleSheet(
'#filterOptionsFrame {border: 0.5px solid lightGray; color: black; }'
)
self.filterOptionsFrame.hide()
self.FilteringFrame.layout().addWidget(self.filterOptionsFrame)
self.filterApplication = qt.QCheckBox()
self.filterApplication.setText('Filter for Phenotype Analysis')
self.filterApplication.setChecked(0)
self.filterOptionsFrame.layout().addWidget(self.filterApplication)
filterOptionsGroup = qt.QGroupBox()
filterOptionsGroup.setLayout(qt.QHBoxLayout())
filterOptionsGroup.setFixedWidth(220)
filterOptionsGroup.setObjectName('filterOptionsGroup')
filterOptionsGroup.setStyleSheet(
'#filterOptionsGroup {border: 1px solid white; color: black; }')
self.NLMFilterRadioButton = qt.QRadioButton()
self.NLMFilterRadioButton.setText('NLM')
self.NLMFilterRadioButton.setChecked(1)
filterOptionsGroup.layout().addWidget(self.NLMFilterRadioButton)
self.MedianFilterRadioButton = qt.QRadioButton()
self.MedianFilterRadioButton.setText('Median')
self.MedianFilterRadioButton.setChecked(0)
filterOptionsGroup.layout().addWidget(self.MedianFilterRadioButton)
self.GaussianFilterRadioButton = qt.QRadioButton()
self.GaussianFilterRadioButton.setText('Gaussian')
self.GaussianFilterRadioButton.setChecked(0)
filterOptionsGroup.layout().addWidget(self.GaussianFilterRadioButton)
self.filterOptionsFrame.layout().addWidget(filterOptionsGroup)
# Filter Params
FilterParams = qt.QFrame()
FilterParams.setLayout(qt.QVBoxLayout())
self.filterOptionsFrame.layout().addWidget(FilterParams)
DimGroupBox = qt.QGroupBox()
DimGroupBox.setLayout(qt.QHBoxLayout())
DimGroupBox.setFixedWidth(180)
DimGroupBox.setObjectName('DimGroupBox')
DimGroupBox.setStyleSheet(
'#DimGroupBox {border: 1px solid white; color: black; }')
FilterParams.layout().addWidget(DimGroupBox)
FilterDimensionLabel = qt.QLabel()
FilterDimensionLabel.setText('Dimensions: ')
FilterDimensionLabel.setToolTip(
'Choose if the filter has to operate in 2D or 3D.')
DimGroupBox.layout().addWidget(FilterDimensionLabel)
self.Filt2DOption = qt.QPushButton()
self.Filt2DOption.setText('2D')
self.Filt2DOption.setCheckable(1)
self.Filt2DOption.setChecked(1)
self.Filt2DOption.setAutoExclusive(1)
self.Filt2DOption.setFixedWidth(45)
DimGroupBox.layout().addWidget(self.Filt2DOption)
self.Filt3DOption = qt.QPushButton()
self.Filt3DOption.setText('3D')
self.Filt3DOption.setCheckable(1)
self.Filt3DOption.setChecked(0)
self.Filt3DOption.setFixedWidth(45)
self.Filt3DOption.setAutoExclusive(1)
DimGroupBox.layout().addWidget(self.Filt3DOption)
StrengthGroupBox = qt.QGroupBox()
StrengthGroupBox.setLayout(qt.QHBoxLayout())
StrengthGroupBox.setFixedWidth(270)
StrengthGroupBox.setObjectName('StrengthGroupBox')
StrengthGroupBox.setStyleSheet(
'#StrengthGroupBox {border: 1px solid white; color: black; }')
FilterParams.layout().addWidget(StrengthGroupBox)
FilterStrengthLabel = qt.QLabel()
FilterStrengthLabel.setText('Strength: ')
FilterStrengthLabel.setToolTip(
'Choose strength of the filtering process.')
StrengthGroupBox.layout().addWidget(FilterStrengthLabel)
self.SmoothOption = qt.QPushButton()
self.SmoothOption.setText('Smooth')
self.SmoothOption.setCheckable(1)
self.SmoothOption.setChecked(1)
self.SmoothOption.setAutoExclusive(1)
self.SmoothOption.setFixedWidth(60)
StrengthGroupBox.layout().addWidget(self.SmoothOption)
self.MediumOption = qt.QPushButton()
self.MediumOption.setText('Medium')
self.MediumOption.setCheckable(1)
self.MediumOption.setChecked(0)
self.MediumOption.setFixedWidth(60)
self.MediumOption.setAutoExclusive(1)
StrengthGroupBox.layout().addWidget(self.MediumOption)
self.HeavyOption = qt.QPushButton()
self.HeavyOption.setText('Heavy')
self.HeavyOption.setCheckable(1)
self.HeavyOption.setChecked(0)
self.HeavyOption.setFixedWidth(60)
self.HeavyOption.setAutoExclusive(1)
StrengthGroupBox.layout().addWidget(self.HeavyOption)
# Downsampling option for label map creation
self.LMCreationFrame = qt.QFrame()
self.LMCreationFrame.setLayout(qt.QVBoxLayout())
self.LMCreationFrame.enabled = False
self.LMCreationFrame.setObjectName('LMCreationFrame')
self.LMCreationFrame.setStyleSheet(
'#LMCreationFrame {border: 1px solid lightGray; color: black; }')
self.parent.layout().addWidget(self.LMCreationFrame)
LMCreationLabel = qt.QLabel()
LMCreationLabel.setText('Label Map Creation:')
self.LMCreationFrame.layout().addWidget(LMCreationLabel)
self.DownSamplingGroupBox = qt.QGroupBox()
self.DownSamplingGroupBox.setLayout(qt.QHBoxLayout())
self.DownSamplingGroupBox.setFixedWidth(130)
self.DownSamplingGroupBox.setObjectName('DownSamplingGroupBox')
self.DownSamplingGroupBox.setStyleSheet(
'#DownSamplingGroupBox {border: 1px solid white; color: black; }')
self.DownSamplingGroupBox.setToolTip(
'Choose between fast and slow label map creation.')
self.LMCreationFrame.layout().addWidget(self.DownSamplingGroupBox)
self.FastOption = qt.QRadioButton()
self.FastOption.setText('Fast')
self.FastOption.setCheckable(1)
self.FastOption.setChecked(0)
self.DownSamplingGroupBox.layout().addWidget(self.FastOption)
self.SlowOption = qt.QRadioButton()
self.SlowOption.setText('Slow')
self.SlowOption.setCheckable(1)
self.SlowOption.setChecked(1)
self.DownSamplingGroupBox.layout().addWidget(self.SlowOption)
self.filterOnRadioButton.connect('toggled(bool)',
self.showFilterParams)
self.filterOffRadioButton.connect('toggled(bool)',
self.hideFilterParams)
def initMainPanel(self):
# Create main collapsible Button
self.mainCollapsibleBtn = ctk.ctkCollapsibleButton()
self.mainCollapsibleBtn.setStyleSheet(
"ctkCollapsibleButton { background-color: DarkSeaGreen }")
self.mainCollapsibleBtn.text = "Remeshing Tools Selection"
#self.mainCollapsibleBtn.collapsible = True
self.layout.addWidget(self.mainCollapsibleBtn)
self.mainFormLayout = qt.QFormLayout(self.mainCollapsibleBtn)
# Create input Segmentation Selector
self.inputSelectorCoBx = slicer.qMRMLNodeComboBox()
self.inputSelectorCoBx.nodeTypes = ["vtkMRMLModelNode"]
self.inputSelectorCoBx.setFixedWidth(200)
self.inputSelectorCoBx.selectNodeUponCreation = True
self.inputSelectorCoBx.addEnabled = False
self.inputSelectorCoBx.removeEnabled = False
self.inputSelectorCoBx.noneEnabled = False
self.inputSelectorCoBx.showHidden = False
self.inputSelectorCoBx.showChildNodeTypes = False
self.inputSelectorCoBx.setMRMLScene(slicer.mrmlScene)
self.inputSelectorCoBx.setToolTip(
"select an .stl file as the input segmentation")
self.mainFormLayout.addRow("Input segmentation: ",
self.inputSelectorCoBx)
# Create button to show mesh of InputNode
self.showMeshBtn = qt.QPushButton("Show Mesh")
self.showMeshBtn.setFixedHeight(20)
self.showMeshBtn.setFixedWidth(100)
self.showMeshBtn.setStyleSheet(
"QPushButton{ background-color: DarkSeaGreen }")
self.showMeshBtn.toolTip = (
'How to use:'
' Click the Show Mesh Button to show mesh of Input Segmentation ')
self.showMeshBtn.connect('clicked(bool)', self.onShowBtnClick)
self.mainFormLayout.addRow("Input Segmentation: ", self.showMeshBtn)
# Create button to set visibility to 1 of inputNode
self.showBtn = qt.QPushButton("Show Input")
self.showBtn.setFixedHeight(20)
self.showBtn.setFixedWidth(100)
self.showBtn.setStyleSheet(
"QPushButton{ background-color: DarkSeaGreen }")
self.showBtn.toolTip = (
'How to use:'
' Click the Show Mesh Button to show Input Segmentation ')
self.showBtn.connect('clicked(bool)', self.onInputBtnClick)
self.mainFormLayout.addRow("Input Segmentation: ", self.showBtn)
# ---------------------------------------INSTANT MESHING--------------------------------------------
# Create collapsible Button for Instant-Meshing options
self.instantCollapsibleBtn = ctk.ctkCollapsibleButton()
self.instantCollapsibleBtn.text = "Instant-Meshing"
self.layout.addWidget(self.instantCollapsibleBtn)
self.instantFormLayout = qt.QFormLayout(self.instantCollapsibleBtn)
self.instantCollapsibleBtn.connect('clicked(bool)',
self.onInstantClick)
# Create button to run the Instant-Meshing tool
self.imBtn = qt.QPushButton("Run")
self.imBtn.setFixedHeight(40)
self.imBtn.setFixedWidth(100)
self.imBtn.setStyleSheet(
"QPushButton{ background-color: DarkSeaGreen }")
self.imBtn.toolTip = (
'How to use:'
' Click the Run Button to start instant-meshing ')
self.imBtn.connect('clicked(bool)', self.onImBtnClick)
self.instantFormLayout.addRow(self.imBtn, self.imtimeLbl)
# Create check box to display normals
self.checkshowNormals = qt.QCheckBox()
self.checkshowNormals.checked = False
self.checkshowNormals.toolTip = ('If activated:' ' shows normals ')
self.checkshowNormals.stateChanged.connect(
self.onCheckShowNormalsChkBx)
self.instantFormLayout.addRow(
" Show normals: ",
self.checkshowNormals)
# ---------------------------------------ADVANCED USER OPTIONS--------------------------------------------
# Create group box for advanced user options
self.instantCollapsiblegroupBtn = ctk.ctkCollapsibleGroupBox()
self.instantCollapsiblegroupBtn.title = "Advanced Options"
self.layout.addWidget(self.instantCollapsiblegroupBtn)
self.instantCollapsiblegroupBtn.collapsed = True
self.instantFormLayout.addRow(self.instantCollapsiblegroupBtn)
self.instantCGBFormLayout = qt.QFormLayout(
self.instantCollapsiblegroupBtn)
# Create radio buttons for triangle or quad meshing
self.checkTR = qt.QRadioButton()
self.checkTR.text = "Triangles (6/6)"
self.checkTR.checked = True # use triangle meshing by default
self.instantCGBFormLayout.addRow(
"Orientation and Position Symmetry Type: ", self.checkTR)
self.checkQD1 = qt.QRadioButton()
self.checkQD1.text = "Quads (2/4)"
self.instantCGBFormLayout.addRow(
" ", self.checkQD1)
self.checkQD2 = qt.QRadioButton()
self.checkQD2.text = "Quads (4/4)"
self.instantCGBFormLayout.addRow(
" ", self.checkQD2)
# Create check boxes for boolean values
self.checkintrinsic = qt.QCheckBox()
self.checkintrinsic.checked = False # use extrinsic by default
self.checkintrinsic.toolTip = (
'If activated:'
' Measures smoothness directly on the surface instead of natural alignment to surface features '
)
self.checkintrinsic.stateChanged.connect(self.oncheckint)
self.instantCGBFormLayout.addRow("Intrinsic: ", self.checkintrinsic)
self.checkdominant = qt.QCheckBox()
self.checkdominant.checked = False
self.checkdominant.toolTip = (
'If activated:'
' Generates a tri/quad dominant mesh instead of a pure tri/quad mesh '
)
self.checkdominant.stateChanged.connect(self.oncheckdom)
self.instantCGBFormLayout.addRow("Dominant: ", self.checkdominant)
self.checkdetermin = qt.QCheckBox()
self.checkdetermin.checked = False
self.checkdetermin.toolTip = (
'If activated:'
' Prefers (slower) deterministic algorithms ')
self.checkdetermin.stateChanged.connect(self.oncheckdet)
self.instantCGBFormLayout.addRow("Deterministic: ", self.checkdetermin)
# Create slider widget to adjust face count (triangle), prior vertex count (to change back, change -f in cmd to -v)
self.vertSlider = ctk.ctkSliderWidget()
self.vertSlider.minimum = 1000
self.vertSlider.maximum = 10000
self.vertSlider.setFixedWidth(400)
self.vertSlider.value = 2800
self.vertSlider.toolTip = ('What it changes:'
' Desired face count of the output mesh ')
self.instantCGBFormLayout.addRow("Triangle count: ", self.vertSlider)
# Create slider widget to adjust smoothing & ray tracing reprojection steps
self.smoothraySlider = ctk.ctkSliderWidget()
self.smoothraySlider.minimum = 0
self.smoothraySlider.maximum = 10
self.smoothraySlider.setFixedWidth(400)
self.smoothraySlider.value = 2
self.smoothraySlider.toolTip = (
'What it changes:'
' Number of smoothing & ray tracing reprojection steps (default: 2) '
)
self.instantCGBFormLayout.addRow("Smoothing Steps: ",
self.smoothraySlider)
# Create slider widget to adjust Point cloud mode
self.knnSlider = ctk.ctkSliderWidget()
self.knnSlider.minimum = 5
self.knnSlider.maximum = 20
self.knnSlider.setFixedWidth(400)
self.knnSlider.value = 10
self.knnSlider.toolTip = (
'Point cloud mode:'
' Number of adjacent points to consider (default: 10) ')
self.instantCGBFormLayout.addRow("Adjacent Points: ", self.knnSlider)
# Create slider widget to adjust Dihedral angle threshold
self.angleSlider = ctk.ctkSliderWidget()
self.angleSlider.minimum = -1
self.angleSlider.maximum = 90
self.angleSlider.setFixedWidth(400)
self.angleSlider.value = -1
self.angleSlider.toolTip = (
'What it changes:'
' Dihedral angle threshold for creases, -1 means sharp creases ')
self.instantCGBFormLayout.addRow("Crease Angle: ", self.angleSlider)
# ---------------------------------------ROBUST QUAD/HEX-DOMINANT MESHING--------------------------------------------
# Create collapsible Button for robust quad/hex-dominant meshing options
self.quadhexCollapsibleBtn = ctk.ctkCollapsibleButton()
self.quadhexCollapsibleBtn.text = "Robust Quad/Hex-dominant Meshing"
self.layout.addWidget(self.quadhexCollapsibleBtn)
self.quadhexCollapsibleBtn.collapsed = True
self.quadhexFormLayout = qt.QFormLayout(self.quadhexCollapsibleBtn)
self.quadhexCollapsibleBtn.connect('clicked(bool)',
self.onQuadHexClick)
# Create button to run the tool
self.rmBtn = qt.QPushButton("Run")
self.rmBtn.setFixedHeight(40)
self.rmBtn.setFixedWidth(100)
self.rmBtn.setStyleSheet(
"QPushButton{ background-color: DarkSeaGreen }")
self.rmBtn.toolTip = (
'How to use:'
' Click the Run Button to start robust quad/hex-dominant meshing ')
self.rmBtn.connect('clicked(bool)', self.onRmBtnClick)
self.quadhexFormLayout.addRow(self.rmBtn, self.qhtimeLbl)
# ---------------------------------------ADVANCED USER OPTIONS--------------------------------------------
# Create group box for advanced user options
self.robustCollapsiblegroupBtn = ctk.ctkCollapsibleGroupBox()
self.robustCollapsiblegroupBtn.title = "Advanced Options"
self.layout.addWidget(self.robustCollapsiblegroupBtn)
self.robustCollapsiblegroupBtn.collapsed = True
self.quadhexFormLayout.addRow(self.robustCollapsiblegroupBtn)
self.robustCGBFormLayout = qt.QFormLayout(
self.robustCollapsiblegroupBtn)
# Create radio buttons to adjust dimension
self.checkdim2 = qt.QRadioButton()
self.checkdim2.checked = True # use dimension 2 by default
self.checkdim2.text = "2"
self.robustCGBFormLayout.addRow("Dimension: ", self.checkdim2)
# Create slider widget to adjust scale
self.scaleSlider = ctk.ctkSliderWidget()
self.scaleSlider.minimum = 2
self.scaleSlider.maximum = 10
self.scaleSlider.setFixedWidth(400)
self.scaleSlider.value = 3
self.robustCGBFormLayout.addRow("Scale: ", self.scaleSlider)
# Create slider widget to adjust smooth iterator
self.smoothSlider = ctk.ctkSliderWidget()
self.smoothSlider.minimum = 5
self.smoothSlider.maximum = 20
self.smoothSlider.setFixedWidth(400)
self.smoothSlider.value = 10
self.robustCGBFormLayout.addRow("Smoothing iteration count: ",
self.smoothSlider)
def open(self):
# main dialog
self.dialog = qt.QDialog(slicer.util.mainWindow())
self.dialog.setWindowTitle('Export to DICOM Study')
self.dialog.setWindowModality(1)
layout = qt.QVBoxLayout()
self.dialog.setLayout(layout)
self.studyLabel = qt.QLabel('Attach Data to Study: %s' % self.studyUID)
layout.addWidget(self.studyLabel)
# scene or volume option
self.selectFrame = qt.QFrame(self.dialog)
layout.addWidget(self.selectFrame)
self.selectLayout = qt.QGridLayout()
self.selectFrame.setLayout(self.selectLayout)
self.exportScene = qt.QRadioButton("Export Entire Scene",
self.selectFrame)
self.exportScene.setToolTip(
"Create a Slicer Data Bundle in a DICOM Private Creator\n(Only compatible with Slicer)"
)
self.exportVolume = qt.QRadioButton("Export Selected Volume",
self.selectFrame)
self.exportVolume.setToolTip(
"Create a compatible DICOM series of slice images")
self.exportVolume.checked = True
self.selectLayout.addWidget(self.exportScene, 0, 0)
self.selectLayout.addWidget(self.exportVolume, 1, 0)
self.exportScene.connect('toggled(bool)', self.onExportRadio)
self.exportVolume.connect('toggled(bool)', self.onExportRadio)
# select volume
self.volumeSelector = slicer.qMRMLNodeComboBox(self.dialog)
self.volumeSelector.nodeTypes = ("vtkMRMLScalarVolumeNode", "")
self.volumeSelector.selectNodeUponCreation = False
self.volumeSelector.addEnabled = False
self.volumeSelector.noneEnabled = False
self.volumeSelector.removeEnabled = False
self.volumeSelector.showHidden = False
self.volumeSelector.showChildNodeTypes = False
self.volumeSelector.setMRMLScene(slicer.mrmlScene)
self.volumeSelector.setToolTip("Pick the label map to edit")
self.selectLayout.addWidget(self.volumeSelector, 1, 1)
# DICOM Parameters
self.dicomFrame = qt.QFrame(self.dialog)
self.dicomFormLayout = qt.QFormLayout()
self.dicomFrame.setLayout(self.dicomFormLayout)
self.dicomEntries = {}
exporter = DICOMLib.DICOMExporter(self.studyUID)
self.dicomParameters = exporter.parametersFromStudy()
self.dicomParameters['Series Description'] = '3D Slicer Export'
for label in self.dicomParameters.keys():
self.dicomEntries[label] = qt.QLineEdit()
self.dicomEntries[label].text = self.dicomParameters[label]
self.dicomFormLayout.addRow(label + ": ", self.dicomEntries[label])
layout.addWidget(self.dicomFrame)
# button box
bbox = qt.QDialogButtonBox(self.dialog)
bbox.addButton(bbox.Ok)
bbox.addButton(bbox.Cancel)
bbox.connect('accepted()', self.onOk)
bbox.connect('rejected()', self.onCancel)
layout.addWidget(bbox)
self.dialog.open()
def setup(self):
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.onVCMRMLSceneChanged)
w = qt.QWidget()
layout = qt.QGridLayout()
w.setLayout(layout)
self.layout.addWidget(w)
w.show()
self.layout = layout
# create frames
self.inputFrame = ctk.ctkCollapsibleButton()
self.inputFrame.text = "Input"
self.inputFrame.collapsed = 0
inputFrameLayout = qt.QFormLayout(self.inputFrame)
self.layout.addWidget(self.inputFrame)
self.ctrlFrame = ctk.ctkCollapsibleButton()
self.ctrlFrame.text = "Frame control"
self.ctrlFrame.collapsed = 0
ctrlFrameLayout = qt.QGridLayout(self.ctrlFrame)
self.layout.addWidget(self.ctrlFrame)
self.plotFrame = ctk.ctkCollapsibleButton()
self.plotFrame.text = "Plotting"
self.plotFrame.collapsed = 0
plotFrameLayout = qt.QGridLayout(self.plotFrame)
self.layout.addWidget(self.plotFrame)
self.plotSettingsFrame = ctk.ctkCollapsibleButton()
self.plotSettingsFrame.text = "Settings"
self.plotSettingsFrame.collapsed = 1
plotSettingsFrameLayout = qt.QGridLayout(self.plotSettingsFrame)
plotFrameLayout.addWidget(self.plotSettingsFrame, 0, 1)
label = qt.QLabel('Input multivolume')
self.__mvSelector = slicer.qMRMLNodeComboBox()
self.__mvSelector.nodeTypes = ['vtkMRMLMultiVolumeNode']
self.__mvSelector.setMRMLScene(slicer.mrmlScene)
self.__mvSelector.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.onVCMRMLSceneChanged)
self.__mvSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onInputChanged)
self.__mvSelector.addEnabled = 0
inputFrameLayout.addRow(label, self.__mvSelector)
label = qt.QLabel('Input secondary multivolume')
self.fgSelector = slicer.qMRMLNodeComboBox()
self.fgSelector.nodeTypes = ['vtkMRMLMultiVolumeNode']
self.fgSelector.setMRMLScene(slicer.mrmlScene)
self.fgSelector.addEnabled = 0
self.fgSelector.noneEnabled = 1
self.fgSelector.toolTip = "Secondary multivolume will be used for the secondary \
plot in interactive charting. As an example, this can be used to overlay the \
curve obtained by fitting a model to the data"
inputFrameLayout.addRow(label, self.fgSelector)
# TODO: initialize the slider based on the contents of the labels array
# slider to scroll over metadata stored in the vector container being explored
self.__mdSlider = ctk.ctkSliderWidget()
label = qt.QLabel('Current frame number')
# "play" control
self.playButton = qt.QPushButton('Play')
self.playButton.toolTip = 'Iterate over multivolume frames'
self.playButton.checkable = True
ctrlFrameLayout.addWidget(label, 0, 0)
ctrlFrameLayout.addWidget(self.__mdSlider, 0, 1)
ctrlFrameLayout.addWidget(self.playButton, 0, 2)
self.playButton.connect('toggled(bool)', self.onPlayButtonToggled)
self.__mdSlider.connect('valueChanged(double)', self.onSliderChanged)
label = qt.QLabel('Current frame copy')
self.__vfSelector = slicer.qMRMLNodeComboBox()
self.__vfSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__vfSelector.setMRMLScene(slicer.mrmlScene)
self.__vfSelector.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.onVFMRMLSceneChanged)
self.__vfSelector.addEnabled = 1
self.__vfSelector.enabled = 0
# do not show "children" of vtkMRMLScalarVolumeNode
self.__vfSelector.hideChildNodeTypes = ["vtkMRMLDiffusionWeightedVolumeNode", \
"vtkMRMLDiffusionTensorVolumeNode", "vtkMRMLVectorVolumeNode"]
self.extractFrame = False
self.extractButton = qt.QPushButton('Enable current frame copying')
self.extractButton.checkable = True
self.extractButton.connect('toggled(bool)', self.onExtractFrameToggled)
ctrlFrameLayout.addWidget(label, 1, 0)
ctrlFrameLayout.addWidget(self.__vfSelector, 1, 1, 1, 2)
ctrlFrameLayout.addWidget(self.extractButton, 2, 0, 1, 3)
# initialize slice observers (from DataProbe.py)
# keep list of pairs: [observee,tag] so they can be removed easily
self.styleObserverTags = []
# keep a map of interactor styles to sliceWidgets so we can easily get sliceLogic
self.sliceWidgetsPerStyle = {}
self.refreshObservers()
# label map for probing
label = qt.QLabel('Probed label volume')
self.__fSelector = slicer.qMRMLNodeComboBox()
self.__fSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__fSelector.addAttribute('vtkMRMLScalarVolumeNode', 'LabelMap',
'1')
self.__fSelector.toolTip = 'Label map to be probed'
self.__fSelector.setMRMLScene(slicer.mrmlScene)
self.__fSelector.addEnabled = 0
self.chartButton = qt.QPushButton('Chart')
self.chartButton.checkable = False
self.chartButton.connect('clicked()', self.onChartRequested)
plotSettingsFrameLayout.addWidget(label, 0, 0)
plotSettingsFrameLayout.addWidget(self.__fSelector, 0, 1)
plotSettingsFrameLayout.addWidget(self.chartButton, 0, 2)
self.iCharting = qt.QPushButton()
self.iCharting.text = 'Enable interactive charting'
self.iCharting.checkable = True
plotSettingsFrameLayout.addWidget(self.iCharting, 1, 0, 1, 3)
self.iCharting.setChecked(True)
self.iCharting.connect('toggled(bool)',
self.onInteractiveChartingChanged)
groupLabel = qt.QLabel('Interactive plotting mode:')
self.iChartingMode = qt.QButtonGroup()
self.iChartingIntensity = qt.QRadioButton('Signal intensity')
#self.iChartingIntensity.tooltip = 'Plot range adjusted dynamically to the range over the time course for the selected pixel'
self.iChartingIntensityFixedAxes = qt.QRadioButton(
'Fixed range intensity')
#self.iChartingIntensityFixedAxes.tooltip = "If checked, the extent of the vertical axis of the plot will be fixed to the range of the intensities in the input MultiVolume"
self.iChartingPercent = qt.QRadioButton('Percent change')
#self.iChartingPercent.tooltip = 'Percent change relative to the average of the first N frames (parameter set below)'
self.iChartingIntensity.setChecked(1)
self.groupWidget = qt.QWidget()
self.groupLayout = qt.QFormLayout(self.groupWidget)
self.groupLayout.addRow(groupLabel)
self.groupLayout.addRow(self.iChartingIntensity)
self.groupLayout.addRow(self.iChartingIntensityFixedAxes)
self.groupLayout.addRow(self.iChartingPercent)
self.baselineFrames = qt.QSpinBox()
self.baselineFrames.minimum = 1
label = qt.QLabel('Number of frames for baseline calculation')
self.groupLayout.addRow(label, self.baselineFrames)
self.xLogScaleCheckBox = qt.QCheckBox()
self.xLogScaleCheckBox.setChecked(0)
label = qt.QLabel('Use log scale for X axis')
self.groupLayout.addRow(self.xLogScaleCheckBox, label)
self.xLogScaleCheckBox.connect('stateChanged(int)',
self.onXLogScaleRequested)
self.yLogScaleCheckBox = qt.QCheckBox()
self.yLogScaleCheckBox.setChecked(0)
label = qt.QLabel('Use log scale for Y axis')
self.groupLayout.addRow(self.yLogScaleCheckBox, label)
self.yLogScaleCheckBox.connect('stateChanged(int)',
self.onYLogScaleRequested)
plotSettingsFrameLayout.addWidget(self.groupWidget, 2, 0)
# add chart container widget
self.__chartView = ctk.ctkVTKChartView(w)
plotFrameLayout.addWidget(self.__chartView, 3, 0, 1, 3)
self.__chart = self.__chartView.chart()
self.__chartTable = vtk.vtkTable()
self.__xArray = vtk.vtkFloatArray()
self.__yArray = vtk.vtkFloatArray()
# will crash if there is no name
self.__xArray.SetName('')
self.__yArray.SetName('signal intensity')
self.__chartTable.AddColumn(self.__xArray)
self.__chartTable.AddColumn(self.__yArray)
def setup(self):
"""This is called one time when the module GUI is initialized
"""
ScriptedLoadableModuleWidget.setup(self)
# Create objects that can be used anywhere in the module. Example: in most cases there should be just one
# object of the logic class
self.logic = CIP_PAARatioLogic()
#
# Create all the widgets. Example Area
mainAreaCollapsibleButton = ctk.ctkCollapsibleButton()
mainAreaCollapsibleButton.text = "Main parameters"
self.layout.addWidget(mainAreaCollapsibleButton)
self.mainAreaLayout = qt.QGridLayout(mainAreaCollapsibleButton)
self.label = qt.QLabel("Select the volume")
self.label.setStyleSheet("margin:10px 0 20px 7px")
self.mainAreaLayout.addWidget(self.label, 0, 0)
self.volumeSelector = slicer.qMRMLNodeComboBox()
self.volumeSelector.nodeTypes = ("vtkMRMLScalarVolumeNode", "")
# DEPRECATED. Now there is a new vtkMRMLLabelMapNode
#self.volumeSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", "0" ) # No labelmaps
self.volumeSelector.selectNodeUponCreation = True
self.volumeSelector.autoFillBackground = True
self.volumeSelector.addEnabled = True
self.volumeSelector.noneEnabled = False
self.volumeSelector.removeEnabled = False
self.volumeSelector.showHidden = False
self.volumeSelector.showChildNodeTypes = False
self.volumeSelector.setMRMLScene(slicer.mrmlScene)
self.volumeSelector.setStyleSheet(
"margin:0px 0 0px 0; padding:2px 0 2px 5px")
self.mainAreaLayout.addWidget(self.volumeSelector, 0, 1)
# self.label2 = qt.QLabel("Select the slice")
# self.label2.setStyleSheet("margin:0px 0 20px 7px; padding-top:20px")
# self.mainAreaLayout.addWidget(self.label2, 1, 0)
self.placeDefaultRulersButton = ctk.ctkPushButton()
self.placeDefaultRulersButton.text = "Place default rulers"
# self.placeDefaultRulersSliceButton.toolTip = "Navigate to the best estimated slice to place the rulers"
self.placeDefaultRulersButton.setIcon(
qt.QIcon("{0}/next.png".format(SlicerUtil.CIP_ICON_DIR)))
self.placeDefaultRulersButton.setIconSize(qt.QSize(20, 20))
self.placeDefaultRulersButton.setStyleSheet("font-weight: bold;")
# self.placeDefaultRulersButton.setFixedWidth(140)
self.mainAreaLayout.addWidget(self.placeDefaultRulersButton, 1, 1)
### Structure Selector
self.structuresGroupbox = qt.QGroupBox("Select the structure")
self.groupboxLayout = qt.QVBoxLayout()
self.structuresGroupbox.setLayout(self.groupboxLayout)
self.mainAreaLayout.addWidget(self.structuresGroupbox, 2, 0)
self.structuresButtonGroup = qt.QButtonGroup()
# btn = qt.QRadioButton("None")
# btn.visible = False
# self.structuresButtonGroup.addButton(btn)
# self.groupboxLayout.addWidget(btn)
btn = qt.QRadioButton("Both")
btn.checked = True
self.structuresButtonGroup.addButton(btn, 0)
self.groupboxLayout.addWidget(btn)
btn = qt.QRadioButton("Pulmonary Arterial")
self.structuresButtonGroup.addButton(btn, 1)
self.groupboxLayout.addWidget(btn)
btn = qt.QRadioButton("Aorta")
self.structuresButtonGroup.addButton(btn, 2)
self.groupboxLayout.addWidget(btn)
### Buttons toolbox
self.buttonsToolboxFrame = qt.QFrame()
self.buttonsToolboxLayout = qt.QGridLayout()
self.buttonsToolboxFrame.setLayout(self.buttonsToolboxLayout)
self.mainAreaLayout.addWidget(self.buttonsToolboxFrame, 2, 1)
self.placeRulersButton = ctk.ctkPushButton()
self.placeRulersButton.text = "Place ruler/s"
self.placeRulersButton.toolTip = "Place the ruler/s for the selected structure/s in the current slice"
self.placeRulersButton.setIcon(
qt.QIcon("{0}/ruler.png".format(SlicerUtil.CIP_ICON_DIR)))
self.placeRulersButton.setIconSize(qt.QSize(20, 20))
self.placeRulersButton.setFixedWidth(105)
self.placeRulersButton.setStyleSheet("font-weight:bold")
self.buttonsToolboxLayout.addWidget(self.placeRulersButton, 0, 0)
self.moveUpButton = ctk.ctkPushButton()
self.moveUpButton.text = "Move up"
self.moveUpButton.toolTip = "Move the selected ruler/s one slice up"
self.moveUpButton.setIcon(
qt.QIcon("{0}/move_up.png".format(SlicerUtil.CIP_ICON_DIR)))
self.moveUpButton.setIconSize(qt.QSize(20, 20))
self.moveUpButton.setFixedWidth(95)
self.buttonsToolboxLayout.addWidget(self.moveUpButton, 0, 1)
self.moveDownButton = ctk.ctkPushButton()
self.moveDownButton.text = "Move down"
self.moveDownButton.toolTip = "Move the selected ruler/s one slice down"
self.moveDownButton.setIcon(
qt.QIcon("{0}/move_down.png".format(SlicerUtil.CIP_ICON_DIR)))
self.moveDownButton.setIconSize(qt.QSize(20, 20))
self.moveDownButton.setFixedWidth(95)
self.buttonsToolboxLayout.addWidget(self.moveDownButton, 0, 2)
self.removeButton = ctk.ctkPushButton()
self.removeButton.text = "Remove ALL rulers"
self.removeButton.toolTip = "Remove all the rulers for this volume"
self.removeButton.setIcon(
qt.QIcon("{0}/delete.png".format(SlicerUtil.CIP_ICON_DIR)))
self.removeButton.setIconSize(qt.QSize(20, 20))
self.buttonsToolboxLayout.addWidget(self.removeButton, 1, 1, 1, 2, 2)
### Textboxes
self.textboxesFrame = qt.QFrame()
self.textboxesLayout = qt.QFormLayout()
self.textboxesFrame.setLayout(self.textboxesLayout)
self.textboxesFrame.setFixedWidth(190)
self.mainAreaLayout.addWidget(self.textboxesFrame, 3, 0)
self.paTextBox = qt.QLineEdit()
self.paTextBox.setReadOnly(True)
self.textboxesLayout.addRow("PA (mm): ", self.paTextBox)
self.aortaTextBox = qt.QLineEdit()
self.aortaTextBox.setReadOnly(True)
self.textboxesLayout.addRow("Aorta (mm): ", self.aortaTextBox)
self.ratioTextBox = qt.QLineEdit()
self.ratioTextBox.setReadOnly(True)
self.textboxesLayout.addRow("Ratio PA/A: ", self.ratioTextBox)
# Save case data
self.reportsCollapsibleButton = ctk.ctkCollapsibleButton()
self.reportsCollapsibleButton.text = "Reporting"
self.layout.addWidget(self.reportsCollapsibleButton)
self.reportsLayout = qt.QHBoxLayout(self.reportsCollapsibleButton)
self.storedColumnNames = [
"caseId", "paDiameter_mm", "aortaDiameter_mm", "pa1r", "pa1a",
"pa1s", "pa2r", "pa2a", "pa2s", "a1r", "a1a", "a1s", "a2r", "a2a",
"a2s"
]
self.reportsWidget = CaseReportsWidget(
"CIP_PAARatio",
columnNames=self.storedColumnNames,
parentWidget=self.reportsCollapsibleButton)
self.reportsWidget.setup()
self.switchToRedView()
#####
# Case navigator
if SlicerUtil.isSlicerACILLoaded():
caseNavigatorAreaCollapsibleButton = ctk.ctkCollapsibleButton()
caseNavigatorAreaCollapsibleButton.text = "Case navigator"
self.layout.addWidget(caseNavigatorAreaCollapsibleButton, 0x0020)
# caseNavigatorLayout = qt.QVBoxLayout(caseNavigatorAreaCollapsibleButton)
# Add a case list navigator
from ACIL.ui import CaseNavigatorWidget
self.caseNavigatorWidget = CaseNavigatorWidget(
self.moduleName, caseNavigatorAreaCollapsibleButton)
self.caseNavigatorWidget.setup()
self.layout.addStretch()
# Connections
self.observers = []
self.__addSceneObservables__()
self.volumeSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onVolumeSelectorChanged)
self.placeDefaultRulersButton.connect('clicked()',
self.oPlaceDefaultRulersClicked)
self.placeRulersButton.connect('clicked()', self.onPlaceRulersClicked)
self.moveUpButton.connect('clicked()', self.onMoveUpRulerClicked)
self.moveDownButton.connect('clicked()', self.onMoveDownRulerClicked)
self.removeButton.connect('clicked()', self.onRemoveRulerClicked)
self.reportsWidget.addObservable(
self.reportsWidget.EVENT_SAVE_BUTTON_CLICKED, self.onSaveReport)
def setup(self, wName, parent):
if self.ctrlWidget:
return
self.LinkViewers()
self.numFrames = len(self.nodeImgList[0][0])
if parent:
self.ctrlWidget = parent
else:
# Create seperate window
self.ctrlWidget = slicer.qMRMLWidget()
self.ctrlWidget.setMRMLScene(slicer.mrmlScene)
self.ctrlWidget.setLayout(qt.QFormLayout())
self.ctrlWidget.setWindowTitle(wName)
ctrlLayout = self.ctrlWidget.layout()
# Create Slider Panel
self.sliderPanel = qt.QWidget()
self.sliderPanel.setLayout(qt.QGridLayout())
ctrlLayout.addWidget(self.sliderPanel)
sliderLayout = self.sliderPanel.layout()
if self.numFrames > 1:
self.ctrlFrameLabel = qt.QLabel('Frame')
self.ctrlFrameSlider = ctk.ctkSliderWidget()
self.ctrlFrameSlider.connect('valueChanged(double)',
self.onSliderFrameChanged)
sliderLayout.addWidget(self.ctrlFrameLabel, 0, 0)
sliderLayout.addWidget(self.ctrlFrameSlider, 0, 1)
self.ctrlLevelLabel = qt.QLabel('Level')
self.ctrlLevelSlider = ctk.ctkSliderWidget()
self.ctrlLevelSlider.connect('valueChanged(double)',
self.onSliderLevelChanged)
sliderLayout.addWidget(self.ctrlLevelLabel, 1, 0)
sliderLayout.addWidget(self.ctrlLevelSlider, 1, 1)
self.ctrlWindowLabel = qt.QLabel('Window')
self.ctrlWindowSlider = ctk.ctkSliderWidget()
self.ctrlWindowSlider.connect('valueChanged(double)',
self.onSliderWindowChanged)
sliderLayout.addWidget(self.ctrlWindowLabel, 2, 0)
sliderLayout.addWidget(self.ctrlWindowSlider, 2, 1)
self.setSliderRangesAndValues()
if self.sliceNodeList:
self.orientPanel = qt.QWidget()
self.orientPanel.setLayout(qt.QGridLayout())
ctrlLayout.addWidget(self.orientPanel)
self.orientationButtons = {}
index = 0
for orientation in self.orientations:
self.orientationButtons[orientation] = qt.QRadioButton()
self.orientationButtons[orientation].text = orientation
# self.orientationBox.layout().addWidget(self.orientationButtons[orientation])
self.orientPanel.layout().addWidget(
self.orientationButtons[orientation], 0, index)
self.orientationButtons[orientation].connect(
"clicked()", lambda o=orientation: self.setOrientation(o))
index += 1
self.setOrientation(self.selectedOrientation)
if False:
#self.plotFrame = ctk.ctkCollapsibleButton()
#self.plotFrame.text = "Plotting"
#self.plotFrame.collapsed = 0
self.plotFrame = qt.QWidget()
plotFrameLayout = qt.QGridLayout(self.plotFrame)
ctrlLayout.addWidget(self.plotFrame)
self.plotSettingsFrame = ctk.ctkCollapsibleButton()
self.plotSettingsFrame.text = "Settings"
self.plotSettingsFrame.collapsed = 1
plotSettingsFrameLayout = qt.QGridLayout(self.plotSettingsFrame)
#plotFrameLayout.addWidget(self.plotSettingsFrame,0,1)
self.xLogScaleCheckBox = qt.QCheckBox()
self.xLogScaleCheckBox.setChecked(0)
self.yLogScaleCheckBox = qt.QCheckBox()
self.yLogScaleCheckBox.setChecked(0)
# taken from https://github.com/fedorov/MultiVolumeExplorer
self.__chartView = ctk.ctkVTKChartView(self.ctrlWidget)
# self.plotFrame)
# self.ctrlWidget
plotFrameLayout.addWidget(self.__chartView, 0, 0)
self.__chart = self.__chartView.chart()
self.__chartTable = vtk.vtkTable()
self.__xArray = vtk.vtkFloatArray()
self.__yArray = vtk.vtkFloatArray()
# will crash if there is no name
self.__xArray.SetName('')
self.__yArray.SetName('signal intensity')
self.__chartTable.AddColumn(self.__xArray)
self.__chartTable.AddColumn(self.__yArray)
self.onInputChanged()
self.refreshObservers()
self.buttonPanel = qt.QWidget()
self.buttonPanel.setLayout(qt.QGridLayout())
ctrlLayout.addWidget(self.buttonPanel)
self.exitButton = qt.QPushButton("Exit")
self.exitButton.toolTip = "Close down slicer."
self.exitButton.name = "sviewer exit"
self.buttonPanel.layout().addWidget(self.exitButton, 0, 0)
self.exitButton.connect('clicked()', exit)
# do not do ctrlWin.show() here - for some reason window does not pop up then
return self.ctrlWidget
def createUserInterface(self):
""" As of now, this user interface is fairly simple. If there are other methods of
normalization, they could be added here.
"""
self.__layout = self.__parent.createUserInterface()
step_label = qt.QLabel(
"""Normalize intensities between your two images before subtracting them."""
)
step_label.setWordWrap(True)
self.__primaryGroupBox = qt.QGroupBox()
self.__primaryGroupBox.setTitle('Information')
self.__primaryGroupBoxLayout = qt.QFormLayout(self.__primaryGroupBox)
self.__primaryGroupBoxLayout.addRow(step_label)
self.__layout.addRow(self.__primaryGroupBox)
# Normalization methods - there aren't many now, but there may be in the future.
NormGroupBox = qt.QGroupBox()
NormGroupBox.setTitle('Normalization Methods')
self.__layout.addRow(NormGroupBox)
NormGroupBoxLayout = qt.QFormLayout(NormGroupBox)
self.__normalizationButton = qt.QPushButton(
'Run Gaussian Normalization')
NormGroupBoxLayout.addRow(self.__normalizationButton)
self.__normalizationButton.connect('clicked()',
self.onGaussianNormalizationRequest)
self.__normalizationButton.setEnabled(1)
# Create new volumes options.
self.__OutputRadio1 = qt.QRadioButton("Create new volumes.")
self.__OutputRadio1.toolTip = "New volumes will be created with the naming convention \"[vol]_normalized\"."
NormGroupBoxLayout.addRow(self.__OutputRadio1)
self.__OutputRadio1.setChecked(True)
self.__OutputRadio2 = qt.QRadioButton("Replace existing volumes.")
self.__OutputRadio2.toolTip = "Original volumes will be overwritten at the end of this step."
NormGroupBoxLayout.addRow(self.__OutputRadio2)
# Normalization order options. May not be relevant in every case.
OrderGroupBox = qt.QGroupBox()
OrderGroupBox.setTitle('Normalization Order')
self.__layout.addRow(OrderGroupBox)
OrderGroupBoxLayout = qt.QFormLayout(OrderGroupBox)
self.__OrderRadio1 = qt.QRadioButton(
"Normalize pre-contrast to post-contrast.")
self.__OrderRadio1.toolTip = "Your pre-contrast image will be normalized."
OrderGroupBoxLayout.addRow(self.__OrderRadio1)
self.__OrderRadio1.setChecked(True)
self.__OrderRadio2 = qt.QRadioButton(
"Normalize post-contrast to pre-contrast.")
self.__OrderRadio2.toolTip = "Your post-contrast image will be normalized."
OrderGroupBoxLayout.addRow(self.__OrderRadio2)
# Subtraction methods. Likely only one method, in practice.
SubtractGroupBox = qt.QGroupBox()
SubtractGroupBox.setTitle('Calculate Subtraction Map')
self.__layout.addRow(SubtractGroupBox)
SubtractGroupBoxLayout = qt.QFormLayout(SubtractGroupBox)
self.__subtractionButton = qt.QPushButton('Run Subtraction Algorithm')
SubtractGroupBoxLayout.addRow(self.__subtractionButton)
self.__subtractionButton.connect('clicked()',
self.onSubtractionRequest)
self.__subtractionButton.setEnabled(1)
def setup(self):
# intialize variables
# Data of current loaded patient
self.IDcurrPatient = {}
self.imageNodes = {} # List of currently loaded image nodes
self.labelNodes = {} # List of currently loaded label nodes
self.ModelNodes = {}
# Data of database
self.mainPatientdir = self.outputDir = self.datafile = {}
#---------------------------------------------------------
# 2D Slice Snapshots
self.IMGSliceExtractCollapsibleButton = ctk.ctkCollapsibleButton()
self.IMGSliceExtractCollapsibleButton.text = "2D Slice and Model Image Capture"
self.layout.addWidget(self.IMGSliceExtractCollapsibleButton)
self.IMGSliceExtractCollapsibleButton.collapsed = False
self.IMGSliceExtractFormLayout = qt.QFormLayout(
self.IMGSliceExtractCollapsibleButton)
# Input 1: Input Directory selector
self.input6Frame = qt.QFrame(self.IMGSliceExtractCollapsibleButton)
self.input6Frame.setLayout(qt.QHBoxLayout())
self.IMGSliceExtractFormLayout.addWidget(self.input6Frame)
self.input6Selector = qt.QLabel("Input Directory (DICOM): ",
self.input6Frame)
self.input6Frame.layout().addWidget(self.input6Selector)
self.input6Button = qt.QPushButton("Select main directory DICOM files")
self.input6Button.toolTip = "Select main directory with DICOM files (folder names are patient names)"
self.input6Button.enabled = True
self.input6Frame.layout().addWidget(self.input6Button)
# Input 2: Output Directory selector
self.input7Frame = qt.QFrame(self.IMGSliceExtractCollapsibleButton)
self.input7Frame.setLayout(qt.QHBoxLayout())
self.IMGSliceExtractFormLayout.addWidget(self.input7Frame)
self.input7Selector = qt.QLabel("Output Directory: ",
self.input7Frame)
self.input7Frame.layout().addWidget(self.input7Selector)
self.input7Button = qt.QPushButton(
"Select main directory output NRRD or NFITI files")
self.input7Button.toolTip = "Select main directory for output NRRD or NIFTI files (folder names are patient names)"
self.input7Button.enabled = True
self.input7Frame.layout().addWidget(self.input7Button)
# Keywords Collapsible Button
self.KeywordsCollapsibleButton = ctk.ctkCollapsibleButton(
self.IMGSliceExtractCollapsibleButton)
self.KeywordsCollapsibleButton.text = "Keyword Matching"
self.KeywordsCollapsibleButtonLayout = qt.QHBoxLayout()
self.KeywordsCollapsibleButton.setLayout(
self.KeywordsCollapsibleButtonLayout)
self.IMGSliceExtractFormLayout.addWidget(
self.KeywordsCollapsibleButton)
self.KeywordsCollapsibleButton.collapsed = False
self.keywordsFrame = qt.QFrame(self.KeywordsCollapsibleButton)
self.keywordsFrame.setLayout(qt.QFormLayout())
self.KeywordsCollapsibleButtonLayout.addWidget(self.keywordsFrame)
# Radio Buttons Frame
self.radioButtonFrame = qt.QFrame(self.keywordsFrame)
self.radioButtonFrame.setLayout(qt.QFormLayout())
self.fileFormatGroup = qt.QButtonGroup(self.radioButtonFrame)
self.nrrdButton = qt.QRadioButton("NRRD")
self.nrrdButton.checked = True
self.niftiButton = qt.QRadioButton("NIFTI")
self.fileFormatGroup.addButton(self.nrrdButton)
self.fileFormatGroup.addButton(self.niftiButton)
self.radioButtonFrame.layout().addRow(self.nrrdButton,
self.niftiButton)
self.keywordsHeader = qt.QLabel("Keyword Matching:",
self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.keywordsHeader)
# Keywords Frame
self.inputMaskHeader = qt.QLabel("Input Image File Type:",
self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.inputMaskHeader,
self.radioButtonFrame)
self.inputImageKeywords = qt.QLabel("Input Image Keywords:",
self.keywordsFrame)
self.inputImageKeywordsField = qt.QLineEdit("", self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.inputImageKeywords,
self.inputImageKeywordsField)
self.inputImageExclusionKeywords = qt.QLabel(
"Input Image Exclusion Keywords:", self.keywordsFrame)
self.inputImageExclusionKeywordsField = qt.QLineEdit(
"", self.keywordsFrame)
self.keywordsFrame.layout().addRow(
self.inputImageExclusionKeywords,
self.inputImageExclusionKeywordsField)
self.inputLabelKeywords = qt.QLabel("Input Label Keywords:",
self.keywordsFrame)
self.inputLabelKeywordsField = qt.QLineEdit("", self.keywordsFrame)
self.keywordsFrame.layout().addRow(self.inputLabelKeywords,
self.inputLabelKeywordsField)
self.inputLabelExclusionKeywords = qt.QLabel(
"Input Label Exclusion Keywords:", self.keywordsFrame)
self.inputLabelExclusionKeywordsField = qt.QLineEdit(
"", self.keywordsFrame)
self.keywordsFrame.layout().addRow(
self.inputLabelExclusionKeywords,
self.inputLabelExclusionKeywordsField)
# IMG Slice Extract Button
self.IMGSliceExtractButton = qt.QPushButton("Extract Images")
self.IMGSliceExtractFormLayout.addWidget(self.IMGSliceExtractButton)
#---------------------------------------------------------
# Connections
self.input6Button.connect('clicked(bool)', self.onInput6Button)
self.input7Button.connect('clicked(bool)', self.onInput7Button)
self.IMGSliceExtractButton.connect('clicked(bool)',
self.onIMGSliceExtract)
def create(self):
super(PETTumorSegmentationEffectOptions, self).create()
#Save space in the GUI
self.frame.layout().setSpacing(0)
self.frame.layout().setMargin(0)
# refinementBoxesFrame contains the options for how clicks are handled
self.refinementBoxesFrame = qt.QFrame(self.frame)
self.refinementBoxesFrame.setLayout(qt.QHBoxLayout())
self.refinementBoxesFrame.layout().setSpacing(0)
self.refinementBoxesFrame.layout().setMargin(0)
self.frame.layout().addWidget(self.refinementBoxesFrame)
#default is global refinement (threshold refinement)
self.noRefinementRadioButton = qt.QRadioButton(
"Create new", self.refinementBoxesFrame)
self.noRefinementRadioButton.setToolTip(
"On click, always segment a new object.")
self.globalRefinementRadioButton = qt.QRadioButton(
"Global refinement", self.refinementBoxesFrame)
self.globalRefinementRadioButton.setToolTip(
"On click, refine globally (adjusting then entire boundary) if no center point for the label, otherwise segment a new object."
)
self.localRefinementRadioButton = qt.QRadioButton(
"Local refinement", self.refinementBoxesFrame)
self.localRefinementRadioButton.setToolTip(
"On click, refine locally (adjusting part of the boundary) if no center point for the label, otherwise segment a new object."
)
self.globalRefinementRadioButton.setChecked(True)
#radio button so only one can be applied
self.refinementBoxesFrame.layout().addWidget(
qt.QLabel("Interaction style: ", self.refinementBoxesFrame))
self.refinementBoxesFrame.layout().addWidget(
self.noRefinementRadioButton)
self.refinementBoxesFrame.layout().addWidget(
self.globalRefinementRadioButton)
self.refinementBoxesFrame.layout().addWidget(
self.localRefinementRadioButton)
self.refinementBoxesFrame.layout().addStretch(1)
self.widgets.append(self.noRefinementRadioButton)
self.widgets.append(self.globalRefinementRadioButton)
self.widgets.append(self.localRefinementRadioButton)
self.noRefinementRadioButton.connect('clicked()',
self.onRefinementTypeChanged)
self.localRefinementRadioButton.connect('clicked()',
self.onRefinementTypeChanged)
self.globalRefinementRadioButton.connect('clicked()',
self.onRefinementTypeChanged)
#options are hidden (collapsed) until requested
self.optFrame = ctk.ctkCollapsibleButton(self.frame)
self.optFrame.setText("Options")
self.optFrame.setLayout(qt.QVBoxLayout())
self.optFrame.layout().setSpacing(0)
self.optFrame.layout().setMargin(0)
self.optFrame.visible = True
self.optFrame.collapsed = True
self.optFrame.collapsedHeight = 0
self.optFrame.setToolTip("Displays algorithm options.")
#most useful options are kept on top: Splitting, Sealing, Assist Centering, Allow
# Overwriting
#to save vertical space, put 2 ina row, so subframes here with horizontal layout are used
#first row
self.commonCheckBoxesFrame1 = qt.QFrame(self.optFrame)
self.commonCheckBoxesFrame1.setLayout(qt.QHBoxLayout())
self.commonCheckBoxesFrame1.layout().setSpacing(0)
self.commonCheckBoxesFrame1.layout().setMargin(0)
self.optFrame.layout().addWidget(self.commonCheckBoxesFrame1)
#top left
self.splittingCheckBox = qt.QCheckBox("Splitting",
self.commonCheckBoxesFrame1)
self.splittingCheckBox.setToolTip(
"Cut off adjacent objects to the target via watershed or local minimum. Useful for lymph node chains."
)
self.splittingCheckBox.checked = False
self.commonCheckBoxesFrame1.layout().addWidget(self.splittingCheckBox)
self.widgets.append(self.splittingCheckBox)
#top right
self.sealingCheckBox = qt.QCheckBox("Sealing",
self.commonCheckBoxesFrame1)
self.sealingCheckBox.setToolTip(
"Close single-voxel gaps in the object or between the object and other objects, if above the threshold. Useful for lymph node chains."
)
self.sealingCheckBox.checked = False
self.commonCheckBoxesFrame1.layout().addWidget(self.sealingCheckBox)
self.widgets.append(self.sealingCheckBox)
#second row
self.commonCheckBoxesFrame2 = qt.QFrame(self.optFrame)
self.commonCheckBoxesFrame2.setLayout(qt.QHBoxLayout())
self.commonCheckBoxesFrame2.layout().setSpacing(0)
self.commonCheckBoxesFrame2.layout().setMargin(0)
self.optFrame.layout().addWidget(self.commonCheckBoxesFrame2)
#bottom left
self.assistCenteringCheckBox = qt.QCheckBox(
"Assist Centering", self.commonCheckBoxesFrame2)
self.assistCenteringCheckBox.setToolTip(
"Move the center to the highest voxel within 7 physical units, without being on or next to other object labels. Improves consistency."
)
self.assistCenteringCheckBox.checked = True
self.commonCheckBoxesFrame2.layout().addWidget(
self.assistCenteringCheckBox)
self.widgets.append(self.assistCenteringCheckBox)
#bottom right
self.allowOverwritingCheckBox = qt.QCheckBox(
"Allow Overwriting", self.commonCheckBoxesFrame2)
self.allowOverwritingCheckBox.setToolTip("Ignore other object labels.")
self.allowOverwritingCheckBox.checked = False
self.commonCheckBoxesFrame2.layout().addWidget(
self.allowOverwritingCheckBox)
self.widgets.append(self.allowOverwritingCheckBox)
#advanced options, for abnormal cases such as massive necrotic objects or
#low-transition scans like phantoms
#infrequently used, just keep vertical
self.advFrame = ctk.ctkCollapsibleButton(self.optFrame)
self.advFrame.setText("Advanced")
self.advFrame.setLayout(qt.QVBoxLayout())
self.advFrame.layout().setSpacing(0)
self.advFrame.layout().setMargin(0)
self.advFrame.visible = True
self.advFrame.collapsed = True
self.advFrame.collapsedHeight = 0
self.advFrame.setToolTip(
"Displays more advanced algorithm options. Do not use if you don't know what they mean."
)
#top
self.necroticRegionCheckBox = qt.QCheckBox("Necrotic Region",
self.advFrame)
self.necroticRegionCheckBox.setToolTip(
"Prevents cutoff from low uptake. Use if placing a center inside a necrotic region."
)
self.necroticRegionCheckBox.checked = False
self.advFrame.layout().addWidget(self.necroticRegionCheckBox)
self.widgets.append(self.necroticRegionCheckBox)
#middle
self.denoiseThresholdCheckBox = qt.QCheckBox("Denoise Threshold",
self.advFrame)
self.denoiseThresholdCheckBox.setToolTip(
"Calculates threshold based on median-filtered image. Use only if scan is very noisey."
)
self.denoiseThresholdCheckBox.checked = False
self.advFrame.layout().addWidget(self.denoiseThresholdCheckBox)
self.widgets.append(self.denoiseThresholdCheckBox)
#bottom
self.linearCostCheckBox = qt.QCheckBox("Linear Cost", self.advFrame)
self.linearCostCheckBox.setToolTip(
"Cost function below threshold is linear rather than based on region. Use only if little/no transition region in uptake."
)
self.linearCostCheckBox.checked = False
self.advFrame.layout().addWidget(self.linearCostCheckBox)
self.widgets.append(self.linearCostCheckBox)
self.optFrame.layout().addWidget(self.advFrame)
#apply button kept at bottom of all options
self.applyButton = qt.QPushButton("Apply", self.optFrame)
self.optFrame.layout().addWidget(self.applyButton)
self.applyButton.connect('clicked()', self.onApply)
self.widgets.append(self.applyButton)
self.applyButton.setToolTip(
"Redo last segmentation with the same center and refinement points with any changes in options."
)
#When changing settings, update the MRML with it
self.assistCenteringCheckBox.connect('toggled(bool)',
self.updateMRMLFromGUI)
self.allowOverwritingCheckBox.connect('toggled(bool)',
self.updateMRMLFromGUI)
self.splittingCheckBox.connect('toggled(bool)', self.updateMRMLFromGUI)
self.sealingCheckBox.connect('toggled(bool)', self.updateMRMLFromGUI)
self.necroticRegionCheckBox.connect('toggled(bool)',
self.updateMRMLFromGUI)
self.denoiseThresholdCheckBox.connect('toggled(bool)',
self.updateMRMLFromGUI)
self.linearCostCheckBox.connect('toggled(bool)',
self.updateMRMLFromGUI)
self.frame.layout().addWidget(self.optFrame)
EditorLib.HelpButton(
self.frame,
"Click on a lesion in a PET scan to segment it. Depending on refinement settings, click again to refine globally and/or locally. Options may help deal with cases such as segmenting individual lesions in a chain. For more information: http://www.slicer.org/slicerWiki/index.php/Documentation/4.4/Modules/PETTumorSegmentationEffect"
)
# Add vertical spacer
self.frame.layout().addStretch(1)
# Clear any existing data and undo/redo queue; working directly with other tools is
# beyond the scope of this
self.logic.reset()
self.updateGUIFromMRML(self, 0)
def setup(self):
"""Init the widget """
self.modulePath = SlicerUtil.getModuleFolder("CIP_GetImage")
self.resourcesPath = os.path.join(self.modulePath,
"CIP_GetImage_Resources")
self.StudyId = ""
self.logic = CIP_GetImageLogic(self.modulePath)
# Widget to load cases faster
self.loadSaveDatabuttonsWidget = CIPUI.LoadSaveDataWidget(
parentWidget=self.parent)
self.loadSaveDatabuttonsWidget.setup(moduleName="CIP_GetImage")
#
# Obligatory parameters area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Image data"
self.layout.addWidget(parametersCollapsibleButton)
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
# Study radio buttons
label = qt.QLabel()
label.text = "Select the study:"
parametersFormLayout.addRow(label)
self.rbgStudy = qt.QButtonGroup()
for key in self.studyIds:
rbStudyid = qt.QRadioButton(key)
self.rbgStudy.addButton(rbStudyid)
parametersFormLayout.addWidget(rbStudyid)
self.txtOtherStudy = qt.QLineEdit()
self.txtOtherStudy.hide()
parametersFormLayout.addWidget(self.txtOtherStudy)
# Case id
self.txtCaseId = qt.QLineEdit()
parametersFormLayout.addRow("Case ID ", self.txtCaseId)
# Image types
label = qt.QLabel()
label.text = "Select the images that you want to load:"
parametersFormLayout.addRow(label)
self.cbsImageTypes = []
for key in self.imageTypes:
check = qt.QCheckBox()
check.checked = True
check.setText(key)
parametersFormLayout.addWidget(check)
self.cbsImageTypes.append(check)
# Label maps
label = qt.QLabel()
label.text = "Select the label maps that you want to load:"
parametersFormLayout.addRow(label)
# Labelmap types checkboxes
self.cbsLabelMapTypes = []
for key in self.labelMapTypes:
check = qt.QCheckBox()
check.setText(key)
check.checked = self.labelMapTypes[key][0]
parametersFormLayout.addWidget(check)
self.cbsLabelMapTypes.append(check)
# Load image Button
self.downloadButton = qt.QPushButton("Download")
self.downloadButton.toolTip = "Load the image"
#self.downloadButton.enabled = False
self.downloadButton.setStyleSheet(
"background-color: green; font-weight:bold; color:white")
parametersFormLayout.addRow(self.downloadButton)
self.downloadButton.connect('clicked (bool)', self.onDownloadButton)
# Information message
self.lblDownloading = qt.QLabel()
self.lblDownloading.text = "Downloading images. Please wait..."
self.lblDownloading.hide()
parametersFormLayout.addRow(self.lblDownloading)
#
# Optional Parameters
#
optionalParametersCollapsibleButton = ctk.ctkCollapsibleButton()
optionalParametersCollapsibleButton.text = "Optional parameters"
self.layout.addWidget(optionalParametersCollapsibleButton)
optionalParametersFormLayout = qt.QFormLayout(
optionalParametersCollapsibleButton)
# Local storage (Slicer temporary path)
self.localStoragePath = "{0}/CIP".format(slicer.app.temporaryPath)
if not os.path.exists(self.localStoragePath):
os.makedirs(self.localStoragePath)
# Make sure that everybody has write permissions (sometimes there are problems because of umask)
os.chmod(self.localStoragePath, 0o777)
self.storagePathButton = ctk.ctkDirectoryButton()
self.storagePathButton.directory = self.localStoragePath
optionalParametersFormLayout.addRow("Local directory: ",
self.storagePathButton)
# Connection type (SSH, "normal")
label = qt.QLabel()
label.text = "Connection type:"
optionalParametersFormLayout.addRow(label)
self.rbgConnectionType = qt.QButtonGroup()
self.rbSSH = qt.QRadioButton("SSH (secure connection)")
self.rbSSH.setChecked(True)
self.rbgConnectionType.addButton(self.rbSSH)
optionalParametersFormLayout.addWidget(self.rbSSH)
self.rbCP = qt.QRadioButton("Common")
self.rbgConnectionType.addButton(self.rbCP)
optionalParametersFormLayout.addWidget(self.rbCP)
# SSH Server login
self.txtServer = qt.QLineEdit()
s = SlicerUtil.settingGetOrSetDefault(
"CIP_GetImage", "server",
"This is your ssh user and server. Example: [email protected]")
self.txtServer.text = s # This is your ssh user and server. Example: [email protected]"
optionalParametersFormLayout.addRow("Server:", self.txtServer)
# Server root path
self.txtServerpath = qt.QLineEdit()
s = SlicerUtil.settingGetOrSetDefault(
"CIP_GetImage", "serverRootPath",
"This is your root path to search for files. Ex: /Cases/Processed")
self.txtServerpath.text = s # This is your root path to search for files. Ex: /Cases/Processed
optionalParametersFormLayout.addRow("Server root path:",
self.txtServerpath)
# SSH Private key
self.txtPrivateKeySSH = qt.QLineEdit()
s = SlicerUtil.settingGetOrSetDefault("CIP_GetImage", "sshKey", "")
self.txtPrivateKeySSH.text = s # this is the full path to your ssh key if you need it. Be aware of Unix/Windows comaptibility (hint: use os.path.join)
# Please notice that you won't need a SSH key if your computer already has one locally installed"
optionalParametersFormLayout.addRow(
"SSH private key (leave blank for computer's default): ",
self.txtPrivateKeySSH)
# Cache mode
self.cbCacheMode = qt.QCheckBox("Cache mode activated")
self.cbCacheMode.setChecked(True) # Cache mode is activated by default
optionalParametersFormLayout.addRow("", self.cbCacheMode)
# Clean cache Button
self.cleanCacheButton = qt.QPushButton("Clean cache")
self.cleanCacheButton.toolTip = "Remove all the local cached files"
optionalParametersFormLayout.addRow(self.cleanCacheButton)
optionalParametersCollapsibleButton.collapsed = True
if SlicerUtil.IsDevelopment:
# reload button
self.reloadButton = qt.QPushButton("Reload (just development)")
self.reloadButton.toolTip = "Reload this module (for development purposes)."
self.reloadButton.name = "Reload"
self.layout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
# Add vertical spacer
self.layout.addStretch(1)
# Connections
self.rbgStudy.connect("buttonClicked (QAbstractButton*)",
self.onRbStudyClicked)
self.txtOtherStudy.connect("textEdited (QString)",
self.onTxtOtherStudyEdited)
self.rbgConnectionType.connect("buttonClicked (QAbstractButton*)",
self.onRbgConnectionType)
self.storagePathButton.connect("directorySelected(QString)",
self.onTmpDirChanged)
self.cleanCacheButton.connect('clicked (bool)',
self.onCleanCacheButtonClicked)
def setup(self):
"""Instantiate and connect widgets ..."""
self.scene = slicer.mrmlScene
self.icp = vtk.vtkIterativeClosestPointTransform()
#
# Reload and Test area
#
reloadCollapsibleButton = ctk.ctkCollapsibleButton()
reloadCollapsibleButton.text = "Reload && Test"
self.layout.addWidget(reloadCollapsibleButton)
reloadFormLayout = qt.QFormLayout(reloadCollapsibleButton)
# reload button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "SurfaceICPRegistration Reload"
reloadFormLayout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
# reload and test button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadAndTestButton = qt.QPushButton("Reload and Test")
self.reloadAndTestButton.toolTip = "Reload this module and then run the self tests."
reloadFormLayout.addWidget(self.reloadAndTestButton)
self.reloadAndTestButton.connect('clicked()', self.onReloadAndTest)
#
# Input Surface Volume Collapsible Button
#
inputSurfaceCollapsibleButton = ctk.ctkCollapsibleButton()
inputSurfaceCollapsibleButton.text = "Input Surface Volumes"
self.layout.addWidget(inputSurfaceCollapsibleButton)
inputSurfaceFormLayout = qt.QFormLayout(inputSurfaceCollapsibleButton)
#
# Input Surface Volume Options
#
self.modelSelectors = {}
self.viewNames = ("Fixed Surface Volume", "Moving Surface Volume")
for viewName in self.viewNames:
self.modelSelectors[viewName] = slicer.qMRMLNodeComboBox()
self.modelSelectors[viewName].nodeTypes = (("vtkMRMLModelNode"),
"")
self.modelSelectors[viewName].selectNodeUponCreation = False
self.modelSelectors[viewName].addEnabled = False
self.modelSelectors[viewName].removeEnabled = True
self.modelSelectors[viewName].noneEnabled = True
self.modelSelectors[viewName].showHidden = False
self.modelSelectors[viewName].showChildNodeTypes = True
self.modelSelectors[viewName].setMRMLScene(slicer.mrmlScene)
self.modelSelectors[viewName].setToolTip(
"Pick the %s surface volume." % viewName.lower())
inputSurfaceFormLayout.addRow("%s" % viewName,
self.modelSelectors[viewName])
#
# Input Inicial Transform Options
#
self.volumeInitialTransformSelectors = {}
self.volumeInitialTransformSelectors[
"Initial Transform"] = slicer.qMRMLNodeComboBox()
self.volumeInitialTransformSelectors["Initial Transform"].nodeTypes = (
("vtkMRMLLinearTransformNode"), "")
self.volumeInitialTransformSelectors[
"Initial Transform"].selectNodeUponCreation = False
self.volumeInitialTransformSelectors[
"Initial Transform"].addEnabled = False
self.volumeInitialTransformSelectors[
"Initial Transform"].removeEnabled = True
self.volumeInitialTransformSelectors[
"Initial Transform"].noneEnabled = True
self.volumeInitialTransformSelectors[
"Initial Transform"].showHidden = False
self.volumeInitialTransformSelectors[
"Initial Transform"].showChildNodeTypes = True
self.volumeInitialTransformSelectors["Initial Transform"].setMRMLScene(
slicer.mrmlScene)
self.volumeInitialTransformSelectors["Initial Transform"].setToolTip(
"Pick the initial Transform file")
inputSurfaceFormLayout.addRow(
"(Optional) Initial Transform",
self.volumeInitialTransformSelectors["Initial Transform"])
#
# Input Registration Parameters Collapsible Button
#
inputRegistrationParametersCollapsibleButton = ctk.ctkCollapsibleButton(
)
inputRegistrationParametersCollapsibleButton.text = "Input Registration Parameters"
self.layout.addWidget(inputRegistrationParametersCollapsibleButton)
inputRegistrationParametersFormLayout = qt.QFormLayout(
inputRegistrationParametersCollapsibleButton)
#
# Landmark Transform Mode TYPE SELECTION
# - allows selection of the active registration type to display
#
self.landmarkTransformTypeBox = qt.QGroupBox("Landmark Transform Mode")
self.landmarkTransformTypeBox.setLayout(qt.QFormLayout())
self.landmarkTransformTypeButtons = {}
self.landmarkTransformTypes = ("RigidBody", "Similarity", "Affine")
for landmarkTransformType in self.landmarkTransformTypes:
self.landmarkTransformTypeButtons[
landmarkTransformType] = qt.QRadioButton()
self.landmarkTransformTypeButtons[
landmarkTransformType].text = landmarkTransformType
self.landmarkTransformTypeButtons[
landmarkTransformType].setToolTip(
"Pick the type of registration")
self.landmarkTransformTypeButtons[landmarkTransformType].connect(
"clicked()",
lambda t=landmarkTransformType: self.onLandmarkTrandformType(t
))
self.landmarkTransformTypeBox.layout().addWidget(
self.landmarkTransformTypeButtons[landmarkTransformType])
inputRegistrationParametersFormLayout.addWidget(
self.landmarkTransformTypeBox)
#
# Mean Distance Mode TYPE SELECTION
#
self.meanDistanceTypeBox = qt.QGroupBox("Mean Distance Mode")
self.meanDistanceTypeBox.setLayout(qt.QFormLayout())
self.meanDistanceTypeButtons = {}
self.meanDistanceTypes = ("RMS", "Absolute Value")
inputRegistrationParametersFormLayout.addWidget(
self.landmarkTransformTypeBox)
for meanDistanceType in self.meanDistanceTypes:
self.meanDistanceTypeButtons[meanDistanceType] = qt.QRadioButton()
self.meanDistanceTypeButtons[
meanDistanceType].text = meanDistanceType
self.meanDistanceTypeButtons[meanDistanceType].setToolTip(
"Pick the type of registration")
self.meanDistanceTypeButtons[meanDistanceType].connect(
"clicked()",
lambda t=meanDistanceType: self.onMeanDistanceType(t))
self.meanDistanceTypeBox.layout().addWidget(
self.meanDistanceTypeButtons[meanDistanceType])
inputRegistrationParametersFormLayout.addWidget(
self.meanDistanceTypeBox)
#
# Start by Matching Centroids Options
#
self.startMatchingCentroids = qt.QCheckBox()
self.startMatchingCentroids.checked = True
self.startMatchingCentroids.connect("toggled(bool)",
self.onMatchCentroidsLinearActive)
inputRegistrationParametersFormLayout.addRow(
"Start by matching centroids ", self.startMatchingCentroids)
#
# Check Mean Distance Options
#
self.checkMeanDistance = qt.QCheckBox()
self.checkMeanDistance.checked = True
self.checkMeanDistance.connect("toggled(bool)",
self.onCheckMeanDistanceActive)
inputRegistrationParametersFormLayout.addRow("Check Mean Distance ",
self.checkMeanDistance)
# Number of Iterations
numberOfIterations = ctk.ctkSliderWidget()
numberOfIterations.connect('valueChanged(double)',
self.numberOfIterationsValueChanged)
numberOfIterations.decimals = 0
numberOfIterations.minimum = 50
numberOfIterations.maximum = 80000
numberOfIterations.value = 50
inputRegistrationParametersFormLayout.addRow("Number of Iterations:",
numberOfIterations)
# Number of Landmarks
numberOfLandmarks = ctk.ctkSliderWidget()
numberOfLandmarks.connect('valueChanged(double)',
self.numberOfLandmarksValueChanged)
numberOfLandmarks.decimals = 0
numberOfLandmarks.minimum = 0
numberOfLandmarks.maximum = 10000
numberOfLandmarks.value = 200
inputRegistrationParametersFormLayout.addRow("Number of Landmarks:",
numberOfLandmarks)
# Maximum Distance
maxDistance = ctk.ctkSliderWidget()
maxDistance.connect('valueChanged(double)',
self.maxDistanceValueChanged)
maxDistance.decimals = 4
maxDistance.minimum = 0.0001
maxDistance.maximum = 10
maxDistance.value = 0.01
inputRegistrationParametersFormLayout.addRow("Maximum Distance:",
maxDistance)
#
# Output Surface Collapsible Button
#
outputSurfaceCollapsibleButton = ctk.ctkCollapsibleButton()
outputSurfaceCollapsibleButton.text = "Output Files"
self.layout.addWidget(outputSurfaceCollapsibleButton)
outputSurfaceFormLayout = qt.QFormLayout(
outputSurfaceCollapsibleButton)
#
# Output Surface Volume Options
#
self.modelOutputSurfaceSelectors = {}
self.modelOutputSurfaceSelectors[
"Output Surface Volume"] = slicer.qMRMLNodeComboBox()
self.modelOutputSurfaceSelectors["Output Surface Volume"].nodeTypes = (
("vtkMRMLModelNode"), "")
self.modelOutputSurfaceSelectors[
"Output Surface Volume"].addEnabled = True
self.modelOutputSurfaceSelectors[
"Output Surface Volume"].selectNodeUponCreation = True
self.modelOutputSurfaceSelectors[
"Output Surface Volume"].removeEnabled = True
self.modelOutputSurfaceSelectors[
"Output Surface Volume"].noneEnabled = True
self.modelOutputSurfaceSelectors[
"Output Surface Volume"].showHidden = False
self.modelOutputSurfaceSelectors[
"Output Surface Volume"].showChildNodeTypes = True
self.modelOutputSurfaceSelectors["Output Surface Volume"].setMRMLScene(
slicer.mrmlScene)
self.modelOutputSurfaceSelectors["Output Surface Volume"].setToolTip(
"Pick the Output Surface Volume")
outputSurfaceFormLayout.addRow(
"Output Surface Volume",
self.modelOutputSurfaceSelectors["Output Surface Volume"])
#
# Output Transform Options
#
self.volumeOutputTransformSelectors = {}
self.volumeOutputTransformSelectors[
"Output Transform"] = slicer.qMRMLNodeComboBox()
self.volumeOutputTransformSelectors["Output Transform"].nodeTypes = ((
"vtkMRMLLinearTransformNode"), "")
self.volumeOutputTransformSelectors[
"Output Transform"].selectNodeUponCreation = True
self.volumeOutputTransformSelectors[
"Output Transform"].addEnabled = True
self.volumeOutputTransformSelectors[
"Output Transform"].removeEnabled = True
self.volumeOutputTransformSelectors[
"Output Transform"].noneEnabled = True
self.volumeOutputTransformSelectors[
"Output Transform"].showHidden = False
self.volumeOutputTransformSelectors[
"Output Transform"].showChildNodeTypes = True
self.volumeOutputTransformSelectors["Output Transform"].setMRMLScene(
slicer.mrmlScene)
self.volumeOutputTransformSelectors["Output Transform"].setToolTip(
"Pick the Output Transform file")
outputSurfaceFormLayout.addRow(
"Output Transform",
self.volumeOutputTransformSelectors["Output Transform"])
#
# Apply Button
#
self.applyButton = qt.QPushButton("Run Registration")
self.applyButton.toolTip = "Run the registration algorithm."
self.applyButton.enabled = True
outputSurfaceFormLayout.addRow(self.applyButton)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
#for selector in self.volumeSelectors.values():
# selector.connect("currentNodeChanged(vtkMRMLNode*)", self.onApplyButton)
#self.volumeInitialTransformSelectors.values().connect('currentNodeChanged(vtkMRMLNode*)', self.onVolumeInitialTransformSelect)
# listen to the scene
#self.addObservers()
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
self.logic = NeedleTrackingLogic(None)
self.logic.setWidget(self)
#--------------------------------------------------
# For debugging
#
# Reload and Test area
reloadCollapsibleButton = ctk.ctkCollapsibleButton()
reloadCollapsibleButton.text = "Reload && Test"
self.layout.addWidget(reloadCollapsibleButton)
reloadFormLayout = qt.QFormLayout(reloadCollapsibleButton)
reloadCollapsibleButton.collapsed = True
# reload button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "Reload"
reloadFormLayout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
#
#--------------------------------------------------
self.nCath = 1 # Number of catheters
#--------------------------------------------------
# GUI components
#
# Connection Area
#
connectionCollapsibleButton = ctk.ctkCollapsibleButton()
connectionCollapsibleButton.text = "Connection (OpenIGTLink)"
self.layout.addWidget(connectionCollapsibleButton)
# Layout within the dummy collapsible button
connectionFormLayout = qt.QFormLayout(connectionCollapsibleButton)
#--------------------------------------------------
# Connector Selector
#--------------------------------------------------
self.igtlConnector1 = NeedleTrackingIGTLConnector("Connector 1")
self.igtlConnector1.port = 18944
self.igtlConnector1.buildGUI(connectionFormLayout)
#--------------------------------------------------
# Catheter
#--------------------------------------------------
catheterCollapsibleButton = ctk.ctkCollapsibleButton()
catheterCollapsibleButton.text = "Tracking Node"
self.layout.addWidget(catheterCollapsibleButton)
catheterFormLayout = qt.QFormLayout(catheterCollapsibleButton)
#--------------------------------------------------
# Tracking node selector
trackingNodeGroupBox = ctk.ctkCollapsibleGroupBox()
trackingNodeGroupBox.title = "Tracking Node"
catheterFormLayout.addWidget(trackingNodeGroupBox)
trackingNodeFormLayout = qt.QFormLayout(trackingNodeGroupBox)
self.trackingDataSelector = slicer.qMRMLNodeComboBox()
self.trackingDataSelector.nodeTypes = ((
"vtkMRMLIGTLTrackingDataBundleNode"), "")
self.trackingDataSelector.selectNodeUponCreation = True
self.trackingDataSelector.addEnabled = True
self.trackingDataSelector.removeEnabled = False
self.trackingDataSelector.noneEnabled = False
self.trackingDataSelector.showHidden = True
self.trackingDataSelector.showChildNodeTypes = False
self.trackingDataSelector.setMRMLScene(slicer.mrmlScene)
self.trackingDataSelector.setToolTip("Incoming tracking data")
trackingNodeFormLayout.addRow("TrackingData: ",
self.trackingDataSelector)
#
# check box to trigger transform conversion
#
self.activeTrackingCheckBox = qt.QCheckBox()
self.activeTrackingCheckBox.checked = 0
self.activeTrackingCheckBox.enabled = 1
self.activeTrackingCheckBox.setToolTip("Activate Tracking")
trackingNodeFormLayout.addRow("Active: ", self.activeTrackingCheckBox)
#--------------------------------------------------
# Catheter Configuration
configGroupBox = ctk.ctkCollapsibleGroupBox()
configGroupBox.title = "Catheter Configuration"
configGroupBox.collapsed = True
catheterFormLayout.addWidget(configGroupBox)
configFormLayout = qt.QFormLayout(configGroupBox)
self.tipLengthSliderWidget = [None] * self.nCath
self.catheterDiameterSliderWidget = [None] * self.nCath
self.catheterOpacitySliderWidget = [None] * self.nCath
for cath in range(self.nCath):
#
# Tip Length (legnth between the catheter tip and the first coil)
#
self.tipLengthSliderWidget[cath] = ctk.ctkSliderWidget()
self.tipLengthSliderWidget[cath].singleStep = 0.5
self.tipLengthSliderWidget[cath].minimum = 0.0
self.tipLengthSliderWidget[cath].maximum = 100.0
self.tipLengthSliderWidget[cath].value = 10.0
self.tipLengthSliderWidget[cath].setToolTip(
"Set the length of the catheter tip.")
configFormLayout.addRow("Cath %d Tip Length (mm): " % cath,
self.tipLengthSliderWidget[cath])
#
# Catheter #1 Catheter diameter
#
self.catheterDiameterSliderWidget[cath] = ctk.ctkSliderWidget()
self.catheterDiameterSliderWidget[cath].singleStep = 0.1
self.catheterDiameterSliderWidget[cath].minimum = 0.1
self.catheterDiameterSliderWidget[cath].maximum = 10.0
self.catheterDiameterSliderWidget[cath].value = 1.0
self.catheterDiameterSliderWidget[cath].setToolTip(
"Set the diameter of the catheter")
configFormLayout.addRow("Cath %d Diameter (mm): " % cath,
self.catheterDiameterSliderWidget[cath])
#
# Catheter #1 Catheter opacity
#
self.catheterOpacitySliderWidget[cath] = ctk.ctkSliderWidget()
self.catheterOpacitySliderWidget[cath].singleStep = 0.1
self.catheterOpacitySliderWidget[cath].minimum = 0.0
self.catheterOpacitySliderWidget[cath].maximum = 1.0
self.catheterOpacitySliderWidget[cath].value = 1.0
self.catheterOpacitySliderWidget[cath].setToolTip(
"Set the opacity of the catheter")
configFormLayout.addRow("Cath %d Opacity: " % cath,
self.catheterOpacitySliderWidget[cath])
#
# Check box to show/hide coil labels
#
self.showCoilLabelCheckBox = qt.QCheckBox()
self.showCoilLabelCheckBox.checked = 0
self.showCoilLabelCheckBox.setToolTip("Show/hide coil labels")
configFormLayout.addRow("Show Coil Labels: ",
self.showCoilLabelCheckBox)
#--------------------------------------------------
# Coordinate System
#
coordinateGroupBox = ctk.ctkCollapsibleGroupBox()
coordinateGroupBox.title = "Coordinate System"
coordinateGroupBox.collapsed = True
catheterFormLayout.addWidget(coordinateGroupBox)
coordinateLayout = qt.QFormLayout(coordinateGroupBox)
self.coordinateRPlusRadioButton = qt.QRadioButton("+X")
self.coordinateRMinusRadioButton = qt.QRadioButton("-X")
self.coordinateRPlusRadioButton.checked = 1
self.coordinateRBoxLayout = qt.QHBoxLayout()
self.coordinateRBoxLayout.addWidget(self.coordinateRPlusRadioButton)
self.coordinateRBoxLayout.addWidget(self.coordinateRMinusRadioButton)
self.coordinateRGroup = qt.QButtonGroup()
self.coordinateRGroup.addButton(self.coordinateRPlusRadioButton)
self.coordinateRGroup.addButton(self.coordinateRMinusRadioButton)
coordinateLayout.addRow("Right:", self.coordinateRBoxLayout)
self.coordinateAPlusRadioButton = qt.QRadioButton("+Y")
self.coordinateAMinusRadioButton = qt.QRadioButton("-Y")
self.coordinateAPlusRadioButton.checked = 1
self.coordinateABoxLayout = qt.QHBoxLayout()
self.coordinateABoxLayout.addWidget(self.coordinateAPlusRadioButton)
self.coordinateABoxLayout.addWidget(self.coordinateAMinusRadioButton)
self.coordinateAGroup = qt.QButtonGroup()
self.coordinateAGroup.addButton(self.coordinateAPlusRadioButton)
self.coordinateAGroup.addButton(self.coordinateAMinusRadioButton)
coordinateLayout.addRow("Anterior:", self.coordinateABoxLayout)
self.coordinateSPlusRadioButton = qt.QRadioButton("+Z")
self.coordinateSMinusRadioButton = qt.QRadioButton("-Z")
self.coordinateSPlusRadioButton.checked = 1
self.coordinateSBoxLayout = qt.QHBoxLayout()
self.coordinateSBoxLayout.addWidget(self.coordinateSPlusRadioButton)
self.coordinateSBoxLayout.addWidget(self.coordinateSMinusRadioButton)
self.coordinateSGroup = qt.QButtonGroup()
self.coordinateSGroup.addButton(self.coordinateSPlusRadioButton)
self.coordinateSGroup.addButton(self.coordinateSMinusRadioButton)
coordinateLayout.addRow("Superior:", self.coordinateSBoxLayout)
#--------------------------------------------------
# Reslice
#
resliceCollapsibleButton = ctk.ctkCollapsibleButton()
resliceCollapsibleButton.text = "Image Reslice"
self.layout.addWidget(resliceCollapsibleButton)
#resliceLayout = qt.QFormLayout(resliceCollapsibleButton)
self.reslice = NeedleTrackingReslice("Image Reslice")
self.reslice.nCath = self.nCath
self.reslice.buildGUI(resliceCollapsibleButton)
#--------------------------------------------------
# Connections
#--------------------------------------------------
self.trackingDataSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onTrackingDataSelected)
self.activeTrackingCheckBox.connect('toggled(bool)',
self.onActiveTracking)
for cath in range(self.nCath):
self.tipLengthSliderWidget[cath].connect(
"valueChanged(double)",
functools.partial(self.onTipLengthChanged, cath))
self.catheterDiameterSliderWidget[cath].connect(
"valueChanged(double)",
functools.partial(self.onCatheterDiameterChanged, cath))
self.catheterOpacitySliderWidget[cath].connect(
"valueChanged(double)",
functools.partial(self.onCatheterOpacityChanged, cath))
self.showCoilLabelCheckBox.connect('toggled(bool)',
self.onCoilLabelChecked)
self.coordinateRPlusRadioButton.connect('clicked(bool)',
self.onSelectCoordinate)
self.coordinateRMinusRadioButton.connect('clicked(bool)',
self.onSelectCoordinate)
self.coordinateAPlusRadioButton.connect('clicked(bool)',
self.onSelectCoordinate)
self.coordinateAMinusRadioButton.connect('clicked(bool)',
self.onSelectCoordinate)
self.coordinateSPlusRadioButton.connect('clicked(bool)',
self.onSelectCoordinate)
self.coordinateSMinusRadioButton.connect('clicked(bool)',
self.onSelectCoordinate)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
# Instantiate and connect widgets ...
#
# Reload and Test area
#
if True:
"""Developer interface"""
reloadCollapsibleButton = ctk.ctkCollapsibleButton()
reloadCollapsibleButton.text = "Advanced - Reload && Test"
reloadCollapsibleButton.collapsed = False
self.layout.addWidget(reloadCollapsibleButton)
reloadFormLayout = qt.QFormLayout(reloadCollapsibleButton)
# reload button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "CardiacAgatstonMeasures Reload"
reloadFormLayout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
# reload and test button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadAndTestButton = qt.QPushButton("Reload and Test")
self.reloadAndTestButton.toolTip = "Reload this module and then run the self tests."
reloadFormLayout.addWidget(self.reloadAndTestButton)
self.reloadAndTestButton.connect('clicked()', self.onReloadAndTest)
# Collapsible button for Input Parameters
self.measuresCollapsibleButton = ctk.ctkCollapsibleButton()
self.measuresCollapsibleButton.text = "Input Parameters"
self.layout.addWidget(self.measuresCollapsibleButton)
# Collapsible button for Label Parameters
self.labelsCollapsibleButton = ctk.ctkCollapsibleButton()
self.labelsCollapsibleButton.text = "Label Parameters"
#self.layout.addWidget(self.labelsCollapsibleButton)
# Layout within the sample collapsible button
self.measuresFormLayout = qt.QFormLayout(
self.measuresCollapsibleButton)
self.labelsFormLayout = qt.QFormLayout(self.labelsCollapsibleButton)
# The Input Volume Selector
self.inputFrame = qt.QFrame(self.measuresCollapsibleButton)
self.inputFrame.setLayout(qt.QHBoxLayout())
self.measuresFormLayout.addRow(self.inputFrame)
self.inputSelector = qt.QLabel("Input Volume: ", self.inputFrame)
self.inputFrame.layout().addWidget(self.inputSelector)
self.inputSelector = slicer.qMRMLNodeComboBox(self.inputFrame)
self.inputSelector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.inputSelector.addEnabled = False
self.inputSelector.removeEnabled = False
self.inputSelector.setMRMLScene(slicer.mrmlScene)
self.inputFrame.layout().addWidget(self.inputSelector)
# Radio Buttons for Selecting 80 KEV or 120 KEV
self.RadioButtonsFrame = qt.QFrame(self.measuresCollapsibleButton)
self.RadioButtonsFrame.setLayout(qt.QHBoxLayout())
self.measuresFormLayout.addRow(self.RadioButtonsFrame)
self.KEV80 = qt.QRadioButton("80 KEV", self.RadioButtonsFrame)
self.KEV80.setToolTip("Select 80 KEV.")
self.KEV80.checked = False
self.RadioButtonsFrame.layout().addWidget(self.KEV80)
self.KEV120 = qt.QRadioButton("120 KEV", self.RadioButtonsFrame)
self.KEV120.setToolTip("Select 120 KEV.")
self.KEV120.checked = False
self.RadioButtonsFrame.layout().addWidget(self.KEV120)
# Threshold button
thresholdButton = qt.QPushButton("Threshold Volume")
thresholdButton.toolTip = "Threshold the selected Input Volume"
thresholdButton.setStyleSheet("background-color: rgb(230,241,255)")
self.measuresFormLayout.addRow(thresholdButton)
thresholdButton.connect('clicked(bool)', self.onThresholdButtonClicked)
# Add vertical spacer
self.layout.addStretch(1)
# Set local var as instance attribute
self.thresholdButton = thresholdButton
# sets the layout to Red Slice Only
layoutManager = slicer.app.layoutManager()
layoutManager.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)
def setup(self):
# make an instance of the logic
self.logic = TwoTensorModelVizLogic()
#
# Model Selection Area
#
modelCollapsibleButton = ctk.ctkCollapsibleButton()
modelCollapsibleButton.text = "Basic"
self.layout.addWidget(modelCollapsibleButton)
modelFormLayout = qt.QFormLayout(modelCollapsibleButton)
# ============Fiber model selector===================
self.modelSelector = slicer.qMRMLNodeComboBox()
self.modelSelector.nodeTypes = ( ("vtkMRMLFiberBundleNode"), "" )
self.modelSelector.selectNodeUponCreation = True
self.modelSelector.addEnabled = False
self.modelSelector.removeEnabled = False
self.modelSelector.noneEnabled = False
self.modelSelector.showHidden = False
self.modelSelector.showChildNodeTypes = False
self.modelSelector.setMRMLScene( slicer.mrmlScene )
self.modelSelector.setToolTip( "Pick a bundle of fibers." )
modelFormLayout.addRow("Fiber bundles: ", self.modelSelector)
self.modelSelector.connect('currentNodeChanged(vtkMRMLNode*)', \
self.onModelSelect)
# ============Glyph Space scroller=================
self.sliderGlyphSpace = ctk.ctkSliderWidget()
self.sliderGlyphSpace.decimals = 0
self.sliderGlyphSpace.minimum=1
self.sliderGlyphSpace.maximum=100
self.sliderGlyphSpace.value=10
self.sliderGlyphSpace.enabled = False
modelFormLayout.addRow("Glyph Space:", self.sliderGlyphSpace)
self.sliderGlyphSpace.connect('valueChanged(double)', \
self.onGlyphSpaceChanged)
# ============Glyph Scale scroller=================
self.sliderGlyphScale = ctk.ctkSliderWidget()
self.sliderGlyphScale.decimals = 0
self.sliderGlyphScale.minimum=1
self.sliderGlyphScale.maximum=10000
self.sliderGlyphScale.value=2000
self.sliderGlyphScale.enabled = False
modelFormLayout.addRow("Glyph Scale:", self.sliderGlyphScale)
self.sliderGlyphScale.connect('valueChanged(double)', \
self.onGlyphScaleChanged)
modelGridLayout=qt.QGridLayout()
modelFormLayout.addRow("View Items:",modelGridLayout)
# ============Check Box for showing lines==============
self.checkboxLines=qt.QCheckBox("Lines")
self.checkboxLines.toolTip="When checked, fiber lines are shown."
self.checkboxLines.checked=True
self.checkboxLines.enabled=False
#modelFormLayout.addRow(self.checkboxLines)
modelGridLayout.addWidget(self.checkboxLines,0,0)
# ============Check Box for showing tensor 1==============
self.checkboxTensor1=qt.QCheckBox("Tensor 1")
self.checkboxTensor1.toolTip="When checked, cylinder glyphs are shown for tensor 1."
self.checkboxTensor1.checked=True
self.checkboxTensor1.enabled=False
modelGridLayout.addWidget(self.checkboxTensor1,0,1)
# ============Check Box for showing tensor 2==============
self.checkboxTensor2=qt.QCheckBox("Tensor 2")
self.checkboxTensor2.toolTip="When checked, cylinder glyphs are shown for tensor 2."
self.checkboxTensor2.checked=True
self.checkboxTensor2.enabled=False
modelGridLayout.addWidget(self.checkboxTensor2,0,2)
# ============Check Box for showing tube==============
self.checkboxTubes=qt.QCheckBox("Tubes")
self.checkboxTubes.toolTip="When checked, tubes will be shown."
self.checkboxTubes.checked=True
self.checkboxTubes.enabled=False
modelGridLayout.addWidget(self.checkboxTubes,0,3)
#
# Fiber Filter Area
#
filterCollapsibleButton = ctk.ctkCollapsibleButton()
filterCollapsibleButton.text = "Fiber Filter"
self.layout.addWidget(filterCollapsibleButton)
filterFormLayout = qt.QFormLayout(filterCollapsibleButton)
# ============Line Space scroller=================
self.sliderLineSpace = ctk.ctkSliderWidget()
self.sliderLineSpace.decimals = 0
self.sliderLineSpace.minimum=1
self.sliderLineSpace.maximum=100
self.sliderLineSpace.value=10
self.sliderLineSpace.enabled = False
filterFormLayout.addRow("One of n Fibers:", self.sliderLineSpace)
self.sliderLineSpace.connect('valueChanged(double)', \
self.onLineSpaceChanged)
# ============Line Num scroller=================
self.sliderLineNum = ctk.ctkSliderWidget()
self.sliderLineNum.decimals = 0
self.sliderLineNum.minimum=1
self.sliderLineNum.maximum=100
self.sliderLineNum.value=1
self.sliderLineNum.enabled = False
filterFormLayout.addRow("Specific Fiber No:", self.sliderLineNum)
self.sliderLineNum.connect('valueChanged(double)', \
self.onLineNumChanged)
# ============Check Box for showing one fiber==============
self.checkboxOnlyOneLine=qt.QCheckBox("Only show the specific fiber")
self.checkboxOnlyOneLine.toolTip="When checked, only the specified fiber is shown."
self.checkboxOnlyOneLine.checked=False
self.checkboxOnlyOneLine.enabled=False
filterFormLayout.addWidget(self.checkboxOnlyOneLine)
#
# Cylinder Color Mapping Area
#
cylinderColorCollapsibleButton = ctk.ctkCollapsibleButton()
cylinderColorCollapsibleButton.text = "Cylinder Boby Color"
self.layout.addWidget(cylinderColorCollapsibleButton)
cylinderVBoxLayOut = qt.QVBoxLayout(cylinderColorCollapsibleButton)
# Add a TabWidget
cylinderTabWidget=qt.QTabWidget()
cylinderVBoxLayOut.addWidget(cylinderTabWidget)
# Create four pages and the GridLayOut
redPage=qt.QWidget()
redGrid=qt.QGridLayout(redPage)
cylinderTabWidget.addTab(redPage,'Red')
greenPage=qt.QWidget()
greenGrid=qt.QGridLayout(greenPage)
cylinderTabWidget.addTab(greenPage,'Green')
bluePage=qt.QWidget()
blueGrid=qt.QGridLayout(bluePage)
cylinderTabWidget.addTab(bluePage,'Blue')
alphaPage=qt.QWidget()
alphaGrid=qt.QGridLayout(alphaPage)
cylinderTabWidget.addTab(alphaPage,'Alpha')
#========= Set the Red page ==============
groupBox=qt.QGroupBox()
grid = qt.QGridLayout(groupBox)
redGrid.addWidget(groupBox,0,1)
self.bodRadioR1=qt.QRadioButton("Fixed to:")
self.bodRadioR2=qt.QRadioButton("Mapped to:")
self.bodRadioR1.checked=True
self.bodSliderR = ctk.ctkSliderWidget()
self.bodSliderR.decimals = 0
self.bodSliderR.minimum=0
self.bodSliderR.maximum=255
self.bodSliderR.value=1
self.bodSliderR.enabled = True
self.bodComboR = qt.QComboBox()
self.bodComboR.duplicatesEnabled= False
grid.addWidget(self.bodRadioR1,0,0)
grid.addWidget(self.bodRadioR2,1,0)
grid.addWidget(self.bodSliderR,0,1)
grid.addWidget(self.bodComboR,1,1)
#========= Set the Green page ==============
groupBox=qt.QGroupBox()
grid = qt.QGridLayout(groupBox)
greenGrid.addWidget(groupBox,0,1)
self.bodRadioG1=qt.QRadioButton("Fixed to:")
self.bodRadioG2=qt.QRadioButton("Mapped to:")
self.bodRadioG1.checked=True
self.bodSliderG = ctk.ctkSliderWidget()
self.bodSliderG.decimals = 0
self.bodSliderG.minimum=0
self.bodSliderG.maximum=255
self.bodSliderG.value=1
self.bodSliderG.enabled = True
self.bodComboG = qt.QComboBox()
self.bodComboG.duplicatesEnabled= False
grid.addWidget(self.bodRadioG1,0,0)
grid.addWidget(self.bodRadioG2,1,0)
grid.addWidget(self.bodSliderG,0,1)
grid.addWidget(self.bodComboG,1,1)
#========= Set the Blue page ==============
groupBox=qt.QGroupBox()
grid = qt.QGridLayout(groupBox)
blueGrid.addWidget(groupBox,0,1)
self.bodRadioB1=qt.QRadioButton("Fixed to:")
self.bodRadioB2=qt.QRadioButton("Mapped to:")
self.bodRadioB1.checked=True
self.bodSliderB = ctk.ctkSliderWidget()
self.bodSliderB.decimals = 0
self.bodSliderB.minimum=0
self.bodSliderB.maximum=255
self.bodSliderB.value=1
self.bodSliderB.enabled = True
self.bodComboB = qt.QComboBox()
self.bodComboB.duplicatesEnabled= False
grid.addWidget(self.bodRadioB1,0,0)
grid.addWidget(self.bodRadioB2,1,0)
grid.addWidget(self.bodSliderB,0,1)
grid.addWidget(self.bodComboB,1,1)
#========= Set the Alpha page ==============
groupBox=qt.QGroupBox()
grid = qt.QGridLayout(groupBox)
alphaGrid.addWidget(groupBox,0,1)
self.bodRadioA1=qt.QRadioButton("Fixed to:")
self.bodRadioA2=qt.QRadioButton("Mapped to:")
self.bodRadioA1.checked=True
self.bodSliderA = ctk.ctkSliderWidget()
self.bodSliderA.decimals = 0
self.bodSliderA.minimum=0
self.bodSliderA.maximum=255
self.bodSliderA.value=1
self.bodSliderA.enabled = True
self.bodComboA = qt.QComboBox()
self.bodComboA.duplicatesEnabled= False
grid.addWidget(self.bodRadioA1,0,0)
grid.addWidget(self.bodRadioA2,1,0)
grid.addWidget(self.bodSliderA,0,1)
grid.addWidget(self.bodComboA,1,1)
#
# Tube Mapping Area
#
tubeColorCollapsibleButton = ctk.ctkCollapsibleButton()
tubeColorCollapsibleButton.text = "Tube Mapping"
self.layout.addWidget(tubeColorCollapsibleButton)
tubeVboxLayOut = qt.QVBoxLayout(tubeColorCollapsibleButton)
# Add a TabWidget
tubeTabWidget=qt.QTabWidget()
tubeVboxLayOut.addWidget(tubeTabWidget)
# Create three pages and the GridLayOut
tubeColorPage=qt.QWidget()
tubeColorGrid=qt.QGridLayout(tubeColorPage)
tubeTabWidget.addTab(tubeColorPage,'Color')
tubeSizePage=qt.QWidget()
tubeSizeGrid=qt.QGridLayout(tubeSizePage)
tubeTabWidget.addTab(tubeSizePage,'Size')
#========= Set the color page ==============
groupBox=qt.QGroupBox()
grid = qt.QGridLayout(groupBox)
tubeColorGrid.addWidget(groupBox,0,0)
self.tubeRadioFixedTo=qt.QRadioButton("Fixed to")
self.tubeRadioByOrientation=qt.QRadioButton("Color by orientation")
self.tubeRadioSameAsCylinderBody=qt.QRadioButton("Same as Cylinder Body")
self.tubeRadioByOrientation.checked=True
grid.addWidget(self.tubeRadioFixedTo,0,0)
grid.addWidget(self.tubeRadioByOrientation,1,0)
grid.addWidget(self.tubeRadioSameAsCylinderBody,2,0)
self.tubeColorButton=qt.QPushButton('Specifying Color')
self.tubeColorButton.setAutoFillBackground(True)
grid.addWidget(self.tubeColorButton,0,1)
self.tubeColorButton.connect('clicked()', \
self.onTubeFixedColor)
#========= Set the size page ==============
self.tubeSizeRadio1=qt.QRadioButton("Fixed to:")
self.tubeSizeRadio2=qt.QRadioButton("Mapped to:")
self.tubeSizeRadio1.checked=True
self.tubeSizeSlider = ctk.ctkSliderWidget()
self.tubeSizeSlider.decimals = 2
self.tubeSizeSlider.minimum=0.0
self.tubeSizeSlider.maximum=5.0
self.tubeSizeSlider.value=0.1
self.tubeSizeSlider.enabled = True
self.tubeComboBox = qt.QComboBox()
self.tubeComboBox.duplicatesEnabled= False
tubeSizeGrid.addWidget(self.tubeSizeRadio1,0,0)
tubeSizeGrid.addWidget(self.tubeSizeRadio2,1,0)
tubeSizeGrid.addWidget(self.tubeSizeSlider,0,1)
tubeSizeGrid.addWidget(self.tubeComboBox,1,1)
# ============Scale scroller=================
label=qt.QLabel('Tube Scale:')
self.sliderTubeScale = ctk.ctkSliderWidget()
self.sliderTubeScale.decimals = 0
self.sliderTubeScale.minimum=1
self.sliderTubeScale.maximum=100
self.sliderTubeScale.value=5
self.sliderTubeScale.enabled = False
tubeSizeGrid.addWidget(label,2,0)
tubeSizeGrid.addWidget(self.sliderTubeScale,2,1)
self.sliderTubeScale.connect('valueChanged(double)', \
self.onTubeScaleChanged)
#
# ============Apply button=================
#
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Apply the visualization."
self.applyButton.enabled = False
self.applyButton.setPalette(qt.QPalette(qt.QColor(128,255,128)))
self.parent.layout().addWidget(self.applyButton)
self.applyButton.connect('clicked()', \
self.onApply)
#
# ============Clear button=================
#
self.clearButton = qt.QPushButton("Clear")
self.clearButton.toolTip = "Clear objects rendered in 3D view windows."
self.clearButton.enabled = False
self.clearButton.setPalette(qt.QPalette(qt.QColor(255,128,128)))
self.parent.layout().addWidget(self.clearButton)
self.clearButton.connect('clicked()', \
self.onClear)
# ===========Finally, Add vertical spacer================
self.layout.addStretch(2)
def createUserInterface(self):
""" This method uses qt to create a user interface of radio buttons to select
a registration method. Note that BSpline registration is so slow and memory-consuming
as to at one point break Slicer. There is an option to run it with limited memory,
but this may take prohibitively long. <- NOTE this last comment was based on
expert automated registration - not sure about other modules.
"""
self.__layout = self.__parent.createUserInterface()
step_label = qt.QLabel(
"""This step allows you to pre-process your data as necessary for deep learning segmentation. Your data may already be preprocessed, in which case you can skip this step. Note that for proper deep learning segmentation, your data will need to be A) registered, and B) resampled into isotropic space.
""")
step_label.setWordWrap(True)
self.__informationGroupBox = qt.QGroupBox()
self.__informationGroupBox.setTitle('Information')
self.__informationGroupBoxLayout = qt.QFormLayout(
self.__informationGroupBox)
self.__informationGroupBoxLayout.addRow(step_label)
self.__layout.addRow(self.__informationGroupBox)
self.__registrationCollapsibleButton = ctk.ctkCollapsibleButton()
self.__registrationCollapsibleButton.text = "Registration"
self.__layout.addWidget(self.__registrationCollapsibleButton)
self.__registrationLayout = qt.QFormLayout(
self.__registrationCollapsibleButton)
# Moving/Fixed Image Registration Order Options
OrderGroupBox = qt.QGroupBox()
OrderGroupBox.setTitle('Registration Base Volume')
self.__registrationLayout.addRow(OrderGroupBox)
OrderGroupBoxLayout = qt.QFormLayout(OrderGroupBox)
self.__OrderRadio1 = qt.QRadioButton("Register to T2.")
self.__OrderRadio1.toolTip = "Your images will be registered to T2 space."
OrderGroupBoxLayout.addRow(self.__OrderRadio1)
self.__OrderRadio1.setChecked(True)
self.__OrderRadio2 = qt.QRadioButton("Register to FLAIR")
self.__OrderRadio2.toolTip = "Your images will be registered to FLAIR space."
OrderGroupBoxLayout.addRow(self.__OrderRadio2)
self.__OrderRadio3 = qt.QRadioButton("Register to post-contrast T1")
self.__OrderRadio3.toolTip = "Your images will be registered to post-contrast T1 space."
OrderGroupBoxLayout.addRow(self.__OrderRadio3)
self.__OrderRadio4 = qt.QRadioButton("Register to pre-contrast T1")
self.__OrderRadio4.toolTip = "Your images will be registered to pre-contrast T1 space."
OrderGroupBoxLayout.addRow(self.__OrderRadio4)
self.__orderMapping = dict(
zip(self.volumeLabels, [
self.__OrderRadio1, self.__OrderRadio2, self.__OrderRadio3,
self.__OrderRadio4
]))
# Registration Method Options
RegistrationGroupBox = qt.QGroupBox()
RegistrationGroupBox.setTitle('Registration Method')
self.__registrationLayout.addRow(RegistrationGroupBox)
RegistrationGroupBoxLayout = qt.QFormLayout(RegistrationGroupBox)
self.__RegistrationRadio1 = qt.QRadioButton("Rigid Registration")
self.__RegistrationRadio1.toolTip = """Computes a rigid registration on the pre-contrast image with respect to the post-contrast image. This will likely be the fastest registration method"""
RegistrationGroupBoxLayout.addRow(self.__RegistrationRadio1)
self.__RegistrationRadio2 = qt.QRadioButton("Affine Registration")
self.__RegistrationRadio2.toolTip = "Computes a rigid and affine registration on the pre-contrast image with respect to the post-contrast image. This method may take longer than rigid registration, but has the ability to stretch or compress images in addition to rotation and translation."
RegistrationGroupBoxLayout.addRow(self.__RegistrationRadio2)
self.__RegistrationRadio2.setChecked(True)
self.__RegistrationRadio3 = qt.QRadioButton("Deformable Registration")
self.__RegistrationRadio3.toolTip = """Computes a BSpline Registration on the pre-contrast image with respect to the post-contrast image. This method is slowest and may be necessary for only severly distorted images."""
RegistrationGroupBoxLayout.addRow(self.__RegistrationRadio3)
# Output Volume Preference
OutputGroupBox = qt.QGroupBox()
OutputGroupBox.setTitle('Registration Output')
self.__registrationLayout.addRow(OutputGroupBox)
OutputGroupBoxLayout = qt.QFormLayout(OutputGroupBox)
self.__OutputRadio1 = qt.QRadioButton("Create new volume.")
self.__OutputRadio1.toolTip = "A new volume will be created with the naming convention \"[pre]_reg_[post]\"."
OutputGroupBoxLayout.addRow(self.__OutputRadio1)
self.__OutputRadio1.setChecked(True)
self.__OutputRadio2 = qt.QRadioButton("Replace existing volume.")
self.__OutputRadio2.toolTip = "Your registered volume will be overwritten at the end of this step."
OutputGroupBoxLayout.addRow(self.__OutputRadio2)
# Registration Button and Progress Indicator
RunGroupBox = qt.QGroupBox()
RunGroupBox.setTitle('Run Registration')
self.__registrationLayout.addRow(RunGroupBox)
RunGroupBoxLayout = qt.QFormLayout(RunGroupBox)
self.__registrationButton = qt.QPushButton('Run registration')
self.__registrationStatus = qt.QLabel('Register scans')
self.__registrationStatus.alignment = 4 # This codes for centered alignment, although I'm not sure why.
RunGroupBoxLayout.addRow(self.__registrationStatus)
RunGroupBoxLayout.addRow(self.__registrationButton)
self.__registrationButton.connect('clicked()',
self.onRegistrationRequest)
def setup(self):
# Instantiate and connect widgets ...
w = qt.QWidget()
layout = qt.QGridLayout()
w.setLayout(layout)
self.layout.addWidget(w)
w.show()
#self.layout = layout
#
# Reload and Test area
#
reloadCollapsibleButton = ctk.ctkCollapsibleButton()
reloadCollapsibleButton.text = "Reload && Test"
self.layout.addWidget(reloadCollapsibleButton)
reloadFormLayout = qt.QFormLayout(reloadCollapsibleButton)
# reload button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "SequenceRegistration Reload"
reloadFormLayout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
# reload and test button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadAndTestButton = qt.QPushButton("Reload and Test")
self.reloadAndTestButton.toolTip = "Reload this module and then run the self tests."
reloadFormLayout.addWidget(self.reloadAndTestButton)
self.reloadAndTestButton.connect('clicked()', self.onReloadAndTest)
#
# Input Area
#
parametersCollapsibleButton1 = ctk.ctkCollapsibleButton()
parametersCollapsibleButton1.text = "Inputs"
self.layout.addWidget(parametersCollapsibleButton1)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton1)
#
# Input fixed image
#
self.fixedImageSelector = slicer.qMRMLNodeComboBox()
self.fixedImageSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
self.fixedImageSelector.selectNodeUponCreation = True
self.fixedImageSelector.addEnabled = False
self.fixedImageSelector.removeEnabled = False
self.fixedImageSelector.noneEnabled = False
self.fixedImageSelector.showHidden = False
self.fixedImageSelector.showChildNodeTypes = False
self.fixedImageSelector.setMRMLScene( slicer.mrmlScene )
self.fixedImageSelector.setToolTip( "Please select the fixed image node for tracking." )
parametersFormLayout.addRow("Reference sequence/image node: ", self.fixedImageSelector)
#
# Input moving sequence image
#
self.movingImageSequenceSelector = slicer.qMRMLNodeComboBox()
self.movingImageSequenceSelector.nodeTypes = ( ("vtkMRMLSequenceNode"), "" )
self.movingImageSequenceSelector.selectNodeUponCreation = True
self.movingImageSequenceSelector.addEnabled = False
self.movingImageSequenceSelector.removeEnabled = False
self.movingImageSequenceSelector.noneEnabled = False
self.movingImageSequenceSelector.showHidden = False
self.movingImageSequenceSelector.showChildNodeTypes = False
self.movingImageSequenceSelector.setMRMLScene( slicer.mrmlScene )
self.movingImageSequenceSelector.setToolTip( "Please select the moving sequence image node for tracking." )
parametersFormLayout.addRow("Moving sequence/image node: ", self.movingImageSequenceSelector)
#
# Input rigid transform
#
self.linearTransformSelector = slicer.qMRMLNodeComboBox()
self.linearTransformSelector.nodeTypes = ( ("vtkMRMLLinearTransformNode"), "" )
self.linearTransformSelector.selectNodeUponCreation = True
self.linearTransformSelector.addEnabled = True
self.linearTransformSelector.removeEnabled = True
self.linearTransformSelector.noneEnabled = True
self.linearTransformSelector.showHidden = False
self.linearTransformSelector.showChildNodeTypes = False
self.linearTransformSelector.setMRMLScene( slicer.mrmlScene )
self.linearTransformSelector.setToolTip( "Please select a transform." )
parametersFormLayout.addRow("Initial transform node: ", self.linearTransformSelector)
#
# ROI
#
self.InputROISelector = slicer.qMRMLNodeComboBox()
self.InputROISelector.nodeTypes = ( ("vtkMRMLAnnotationROINode"), "" )
self.InputROISelector.selectNodeUponCreation = True
self.InputROISelector.addEnabled = True
self.InputROISelector.removeEnabled = True
self.InputROISelector.noneEnabled = True
self.InputROISelector.showHidden = False
self.InputROISelector.showChildNodeTypes = False
self.InputROISelector.setMRMLScene( slicer.mrmlScene )
parametersFormLayout.addRow("ROI: ", self.InputROISelector)
self.ROIVisibilityButton = qt.QPushButton("Off")
self.ROIVisibilityButton.checkable = True
self.ROIVisibilityButton.checked = False
self.ROIVisibilityButton.enabled = False
parametersFormLayout.addRow("ROI Visibility: ", self.ROIVisibilityButton)
self.InitializeTransformModeOptions = ("Off","useGeometryAlign","useMomentsAlign")
#
#Initialization
#
self.groupBox = qt.QGroupBox("Initialize Transform Mode")
self.groupBoxLayout = qt.QHBoxLayout(self.groupBox)
parametersFormLayout.addRow(self.groupBox)
#
# layout selection
#
for initializeTransformModeOption in self.InitializeTransformModeOptions:
initializeTransformModeButton = qt.QRadioButton(initializeTransformModeOption)
initializeTransformModeButton.connect('clicked()', lambda itmo=initializeTransformModeOption: self.selectInitializeTransformMode(itmo))
self.groupBoxLayout.addWidget(initializeTransformModeButton)
#self.groupBoxLayout.addRow("Layout", layoutHolder)
#
# Register Button
#
self.registerButton = qt.QPushButton("Register")
self.registerButton.toolTip = "Run the algorithm."
self.registerButton.enabled = False
parametersFormLayout.addRow(self.registerButton)
# Connections
self.fixedImageSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onInputSelect)
self.movingImageSequenceSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onInputSelect)
self.InputROISelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onInputSelect)
self.ROIVisibilityButton.connect('clicked(bool)', self.onROIVisible)
self.registerButton.connect('clicked(bool)', self.onApply)
#
# Output Area
#
outputsCollapsibleButton1 = ctk.ctkCollapsibleButton()
outputsCollapsibleButton1.text = "Outputs (at least one output must be specified)"
self.layout.addWidget(outputsCollapsibleButton1)
# Layout within the dummy collapsible button
outputsFormLayout = qt.QFormLayout(outputsCollapsibleButton1)
#
# Output rigid transform
#
self.outputTransformSequenceSelector = slicer.qMRMLNodeComboBox()
self.outputTransformSequenceSelector.nodeTypes = ( ("vtkMRMLSequenceNode"), "" )
self.outputTransformSequenceSelector.selectNodeUponCreation = True
self.outputTransformSequenceSelector.addEnabled = True
self.outputTransformSequenceSelector.removeEnabled = True
self.outputTransformSequenceSelector.noneEnabled = True
self.outputTransformSequenceSelector.showHidden = False
self.outputTransformSequenceSelector.showChildNodeTypes = False
self.outputTransformSequenceSelector.setMRMLScene( slicer.mrmlScene )
self.outputTransformSequenceSelector.setToolTip( "Please select a sequence transform node." )
outputsFormLayout.addRow("Output sequence transform node: ", self.outputTransformSequenceSelector)
#
# Output images
#
self.outputImageSequenceSelector = slicer.qMRMLNodeComboBox()
self.outputImageSequenceSelector.nodeTypes = ( ("vtkMRMLSequenceNode"), "" )
self.outputImageSequenceSelector.selectNodeUponCreation = True
self.outputImageSequenceSelector.addEnabled = True
self.outputImageSequenceSelector.removeEnabled = True
self.outputImageSequenceSelector.noneEnabled = True
self.outputImageSequenceSelector.showHidden = False
self.outputImageSequenceSelector.showChildNodeTypes = False
self.outputImageSequenceSelector.setMRMLScene( slicer.mrmlScene )
self.outputImageSequenceSelector.setToolTip( "Please select a sequence image node." )
outputsFormLayout.addRow("Output sequence image node: ", self.outputImageSequenceSelector)
# Comment out the following code as this functionality is not moved to Sequence Browser module
# plottingCollapsibleButton = ctk.ctkCollapsibleButton()
# plottingCollapsibleButton.text = "Plotting"
# plottingCollapsibleButton.collapsed = 0
# self.layout.addWidget(plottingCollapsibleButton)
# plottingFrameLayout = qt.QGridLayout(plottingCollapsibleButton)
# self.ChartingDisplayOptions = ("LR","AP","SI")
# self.chartingDisplayOption = 'LR'
# #
# #Initialization
# #
# self.chartGroupBox = qt.QGroupBox("Display options:")
# self.chartGroupBoxLayout = qt.QHBoxLayout(self.chartGroupBox)
# plottingFrameLayout.addWidget(self.chartGroupBox,0,0,1,3)
# #
# # layout selection
# #
# for chartingDisplayOption in self.ChartingDisplayOptions:
# chartingDisplayOptionButton = qt.QRadioButton(chartingDisplayOption)
# chartingDisplayOptionButton.connect('clicked()', lambda cdo=chartingDisplayOption: self.selectChartingDisplayOption(cdo))
# self.chartGroupBoxLayout.addWidget(chartingDisplayOptionButton)
# #self.groupBoxLayout.addRow("Layout", layoutHolder)
# # add chart container widget
# self.__chartView = ctk.ctkVTKChartView(w)
# plottingFrameLayout.addWidget(self.__chartView,1,0,1,3)
# self.__chart = self.__chartView.chart()
# self.__chartTable = vtk.vtkTable()
# self.__xArray = vtk.vtkFloatArray()
# self.__yArray = vtk.vtkFloatArray()
# self.__zArray = vtk.vtkFloatArray()
# self.__mArray = vtk.vtkFloatArray()
# # will crash if there is no name
# self.__xArray.SetName('')
# self.__yArray.SetName('signal intensity')
# self.__zArray.SetName('')
# self.__mArray.SetName('signal intensity')
# self.__chartTable.AddColumn(self.__xArray)
# self.__chartTable.AddColumn(self.__yArray)
# self.__chartTable.AddColumn(self.__zArray)
# self.__chartTable.AddColumn(self.__mArray)
self.outputTransformSequenceSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onOutputSelect)
self.outputImageSequenceSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onOutputSelect)
# Add vertical spacer
self.layout.addStretch(1)