def createUserInterface(self):
""" This step is mostly empty. A volume rendering threshold is added to be useful.
"""
self.__layout = self.__parent.createUserInterface()
self.__threshRange = slicer.qMRMLRangeWidget()
self.__threshRange.decimals = 0
self.__threshRange.singleStep = 1
self.__threshRange.connect('valuesChanged(double,double)',
self.onThresholdChanged)
qt.QTimer.singleShot(0, self.killButton)
ThreshGroupBox = qt.QGroupBox()
ThreshGroupBox.setTitle('3D Visualization Intensity Threshold')
ThreshGroupBoxLayout = qt.QFormLayout(ThreshGroupBox)
ThreshGroupBoxLayout.addRow(self.__threshRange)
self.__layout.addRow(ThreshGroupBox)
editorWidgetParent = slicer.qMRMLWidget()
editorWidgetParent.setLayout(qt.QVBoxLayout())
editorWidgetParent.setMRMLScene(slicer.mrmlScene)
self.__editorWidget = EditorWidget(parent=editorWidgetParent)
self.__editorWidget.setup()
self.__layout.addRow(editorWidgetParent)
self.hideUnwantedEditorUIElements()
RestartGroupBox = qt.QGroupBox()
RestartGroupBox.setTitle('Restart')
RestartGroupBoxLayout = qt.QFormLayout(RestartGroupBox)
self.__RestartButton = qt.QPushButton('Return to Step 1')
RestartGroupBoxLayout.addRow(self.__RestartButton)
self.__RemoveCroppedSubtractionMap = qt.QCheckBox()
self.__RemoveCroppedSubtractionMap.checked = True
self.__RemoveCroppedSubtractionMap.setToolTip(
"Delete the cropped version of your subtaction map.")
RestartGroupBoxLayout.addRow("Delete cropped subtraction map: ",
self.__RemoveCroppedSubtractionMap)
self.__RemoveFullSubtracitonMap = qt.QCheckBox()
self.__RemoveFullSubtracitonMap.checked = True
self.__RemoveFullSubtracitonMap.setToolTip(
"Delete the full version of your subtaction map.")
RestartGroupBoxLayout.addRow("Delete full subtraction map: ",
self.__RemoveFullSubtracitonMap)
self.__RemoveROI = qt.QCheckBox()
self.__RemoveROI.checked = False
self.__RemoveROI.setToolTip(
"Delete the ROI resulting from your subtaction map.")
RestartGroupBoxLayout.addRow("Delete ROI: ", self.__RemoveROI)
# self.__RestartButton.setEnabled(0)
self.__RestartButton.connect('clicked()', self.Restart)
self.__RestartActivated = True
self.__layout.addRow(RestartGroupBox)
def createUserInterface(self):
""" This UI takes advantage of a pre-built slicer thresholding widget.
"""
self.__layout = self.__parent.createUserInterface()
step_label = qt.QLabel(
"""Use the slider bar below to set an intensity threshold. Any pixels within your ROI and within the intensity threshold will be selected."""
)
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)
self.__thresholdGroupBox = qt.QGroupBox()
self.__thresholdGroupBox.setTitle('Threshold Range')
self.__thresholdGroupBoxLayout = qt.QFormLayout(
self.__thresholdGroupBox)
threshLabel = qt.QLabel('Select Intensity Range:')
threshLabel.alignment = 4
self.__threshRange = slicer.qMRMLRangeWidget()
self.__threshRange.decimals = 0
self.__threshRange.singleStep = 1
self.__thresholdGroupBoxLayout.addRow(threshLabel)
self.__thresholdGroupBoxLayout.addRow(self.__threshRange)
self.__layout.addRow(self.__thresholdGroupBox)
self.__threshRange.connect('valuesChanged(double,double)',
self.onThresholdChanged)
qt.QTimer.singleShot(0, self.killButton)
def createUserInterface( self ):
'''
'''
self.skip = 0
self.__layout = self.__parent.createUserInterface()
self.__basicFrame = ctk.ctkCollapsibleButton()
self.__basicFrame.text = "Basic settings"
self.__basicFrame.collapsed = 0
basicFrameLayout = qt.QFormLayout(self.__basicFrame)
self.__layout.addRow(self.__basicFrame)
self.__advancedFrame = ctk.ctkCollapsibleButton()
self.__advancedFrame.text = "Advanced settings"
self.__advancedFrame.collapsed = 1
advFrameLayout = qt.QFormLayout(self.__advancedFrame)
self.__layout.addRow(self.__advancedFrame)
threshLabel = qt.QLabel('1/ Make the holes visible:')
self.__threshRange = slicer.qMRMLRangeWidget()
self.__threshRange.decimals = 0
self.__threshRange.singleStep = 1
self.__useThresholdsCheck = qt.QCheckBox()
self.__useThresholdsCheck.setEnabled(0)
threshCheckLabel = qt.QLabel('Use thresholds for segmentation')
roiLabel = qt.QLabel( 'Select segmentation:' )
self.__roiLabelSelector = slicer.qMRMLNodeComboBox()
self.__roiLabelSelector.nodeTypes = ( 'vtkMRMLScalarVolumeNode', '' )
self.__roiLabelSelector.addAttribute('vtkMRMLScalarVolumeNode','LabelMap','1')
self.__roiLabelSelector.toolTip = "Choose the ROI segmentation"
self.__roiLabelSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__roiLabelSelector.addEnabled = 0
self.__roiLabelSelector.setMRMLScene(slicer.mrmlScene)
self.__applyButton = qt.QPushButton('2/ Make a 3D Model')
self.__applyButton.connect('clicked()', self.applyModelMaker)
basicFrameLayout.addRow(threshLabel, self.__threshRange)
basicFrameLayout.addRow(self.__applyButton)
advFrameLayout.addRow(threshCheckLabel, self.__useThresholdsCheck)
advFrameLayout.addRow( roiLabel, self.__roiLabelSelector )
self.__threshRange.connect('valuesChanged(double,double)', self.onThresholdChanged)
self.__useThresholdsCheck.connect('stateChanged(int)', self.onThresholdsCheckChanged)
self.__secondReg = qt.QPushButton('3/ ICP Registration')
self.__secondReg.connect('clicked()', self.ICPRegistration)
self.__secondReg.setEnabled(0)
self.__layout.addRow(self.__secondReg)
self.fiducialButton = qt.QPushButton('Manual Registration')
self.fiducialButton.checkable = True
self.__layout.addRow(self.fiducialButton)
self.fiducialButton.connect('toggled(bool)', self.onRunButtonToggled)
def createUserInterface( self ):
""" This UI takes advantage of a pre-built slicer thresholding widget.
"""
self.__layout = self.__parent.createUserInterface()
threshLabel = qt.QLabel('Choose threshold:')
self.__threshRange = slicer.qMRMLRangeWidget()
self.__threshRange.decimals = 0
self.__threshRange.singleStep = 1
self.__layout.addRow(threshLabel, self.__threshRange)
self.__threshRange.connect('valuesChanged(double,double)', self.onThresholdChanged)
qt.QTimer.singleShot(0, self.killButton)
def createUserInterface( self ):
""" This UI takes advantage of a pre-built slicer thresholding widget.
"""
self.__layout = self.__parent.createUserInterface()
threshLabel = qt.QLabel('Choose threshold:')
self.__threshRange = slicer.qMRMLRangeWidget()
self.__threshRange.decimals = 0
self.__threshRange.singleStep = 1
self.__layout.addRow(threshLabel, self.__threshRange)
self.__threshRange.connect('valuesChanged(double,double)', self.onThresholdChanged)
qt.QTimer.singleShot(0, self.killButton)
def createUserInterface( self ):
""" This step is mostly empty. A volume rendering threshold is added to be useful.
"""
self.__layout = self.__parent.createUserInterface()
threshLabel = qt.QLabel('Choose Volume Rendering Threshold:')
self.__threshRange = slicer.qMRMLRangeWidget()
self.__threshRange.decimals = 0
self.__threshRange.singleStep = 1
self.__layout.addRow(threshLabel, self.__threshRange)
self.__threshRange.connect('valuesChanged(double,double)', self.onThresholdChanged)
qt.QTimer.singleShot(0, self.killButton)
def createUserInterface( self ):
self.__layout = qt.QFormLayout( self )
self.__layout.setVerticalSpacing( 5 )
# Add empty rows
self.__layout.addRow( "", qt.QWidget() )
self.__layout.addRow( "", qt.QWidget() )
#label for ROI selector
vertLabel = qt.QLabel( 'Vertebrae Labels:' )
font = vertLabel.font
font.setBold(True)
vertLabel.setFont(font)
labelText = qt.QLabel("Add Labels: ")
self.identify = qt.QPushButton("Click to Identify")
self.identify.connect('clicked(bool)', self.addFiducials)
self.identify.setMaximumWidth(170)
blank = qt.QLabel(" ")
blank.setMaximumWidth(30)
self.vertebraeGridBox = qt.QFormLayout()
self.vertebraeGridBox.addRow(vertLabel)
self.vertebraeGridBox.addRow(labelText,self.identify)
self.__layout.addRow(self.vertebraeGridBox)
# Hide Threshold Details
threshCollapsibleButton = ctk.ctkCollapsibleButton()
#roiCollapsibleButton.setMaximumWidth(320)
threshCollapsibleButton.text = "Bone Threshold Details"
self.__layout.addWidget(threshCollapsibleButton)
threshCollapsibleButton.collapsed = False
# Layout
threshLayout = qt.QFormLayout(threshCollapsibleButton)
self.__loadThreshButton = qt.QPushButton("Show Threshold Label")
threshLayout.addRow(self.__loadThreshButton)
self.__loadThreshButton.connect('clicked(bool)', self.showThreshold)
self.__corticalRange = slicer.qMRMLRangeWidget()
self.__corticalRange.decimals = 0
self.__corticalRange.singleStep = 1
cortLabel = qt.QLabel('Choose Cortical Bone Threshold:')
self.__corticalRange.connect('valuesChanged(double,double)', self.onCorticalChanged)
threshLayout.addRow(cortLabel)
threshLayout.addRow(self.__corticalRange)
# Hide ROI Details
roiCollapsibleButton = ctk.ctkCollapsibleButton()
roiCollapsibleButton.text = "Advanced Options"
self.__layout.addWidget(roiCollapsibleButton)
roiCollapsibleButton.collapsed = True
roiCollapsibleButton.visible = False
# Layout
roiLayout = qt.QFormLayout(roiCollapsibleButton)
self.__loadLandmarksButton = qt.QPushButton("Show Crop Landmarks")
roiLayout.addRow(self.__loadLandmarksButton)
self.__loadLandmarksButton.connect('clicked(bool)', self.showLandmarks)
#label for ROI selector
roiLabel = qt.QLabel( 'Select ROI:' )
font = roiLabel.font
font.setBold(True)
roiLabel.setFont(font)
#creates combobox and populates it with all vtkMRMLAnnotationROINodes in the scene
self.__roiSelector = slicer.qMRMLNodeComboBox()
self.__roiSelector.nodeTypes = ['vtkMRMLAnnotationROINode']
self.__roiSelector.toolTip = "ROI defining the structure of interest"
self.__roiSelector.setMRMLScene(slicer.mrmlScene)
self.__roiSelector.addEnabled = 1
#add label + combobox
roiLayout.addRow( roiLabel, self.__roiSelector )
self.__roiSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onROIChanged)
# the ROI parameters
# GroupBox to hold ROI Widget
voiGroupBox = qt.QGroupBox()
voiGroupBox.setTitle( 'Define VOI' )
roiLayout.addRow( voiGroupBox )
# create form layout for GroupBox
voiGroupBoxLayout = qt.QFormLayout( voiGroupBox )
# create ROI Widget and add it to the form layout of the GroupBox
self.__roiWidget = PythonQt.qSlicerAnnotationsModuleWidgets.qMRMLAnnotationROIWidget()
voiGroupBoxLayout.addRow( self.__roiWidget )
# Hide VR Details
vrCollapsibleButton = ctk.ctkCollapsibleButton()
#roiCollapsibleButton.setMaximumWidth(320)
vrCollapsibleButton.text = "Rendering Details"
self.__layout.addWidget(vrCollapsibleButton)
vrCollapsibleButton.collapsed = True
vrCollapsibleButton.visible = False
# Layout
vrLayout = qt.QFormLayout(vrCollapsibleButton)
# the ROI parameters
# GroupBox to hold ROI Widget
vrGroupBox = qt.QGroupBox()
vrGroupBox.setTitle( 'Define Rendering' )
vrLayout.addRow( vrGroupBox )
# create form layout for GroupBox
vrGroupBoxLayout = qt.QFormLayout( vrGroupBox )
# create ROI Widget and add it to the form layout of the GroupBox
self.__vrWidget = PythonQt.qSlicerVolumeRenderingModuleWidgets.qSlicerPresetComboBox()
#self.__vrWidget = PythonQt.qSlicerVolumeRenderingModuleWidgets.qMRMLVolumePropertyNodeWidget()
vrGroupBoxLayout.addRow( self.__vrWidget )
# initialize VR
self.__vrLogic = slicer.modules.volumerendering.logic()
lm = slicer.app.layoutManager()
redWidget = lm.sliceWidget('Red')
self.__redController = redWidget.sliceController()
self.__redLogic = redWidget.sliceLogic()
yellowWidget = lm.sliceWidget('Yellow')
self.__yellowController = yellowWidget.sliceController()
self.__yellowLogic = yellowWidget.sliceLogic()
greenWidget = lm.sliceWidget('Green')
self.__greenController = greenWidget.sliceController()
self.__greenLogic = greenWidget.sliceLogic()
qt.QTimer.singleShot(0, self.killButton)
def createUserInterface( self ):
'''
'''
self.__layout = self.__parent.createUserInterface()
self.__registrationStatus = qt.QLabel('Register Template and Scan')
self.__layout.addRow(self.__registrationStatus)
self.automaticRegistrationButton = qt.QPushButton('Auto Register Template')
self.automaticRegistrationButton.connect('clicked()', self.automaticRegistration)
self.__layout.addRow(self.automaticRegistrationButton)
typeOfRegLabel = qt.QLabel('Or Manually Register the Template')
self.__layout.addRow(typeOfRegLabel)
self.fiducialButton = qt.QPushButton('1. Choose Fiducial Points')
self.fiducialButton.checkable = True
self.__layout.addRow(self.fiducialButton)
self.fiducialButton.connect('toggled(bool)', self.onRunButtonToggled)
self.firstRegButton = qt.QPushButton('2. Run Initial Registration')
self.firstRegButton.checkable = False
self.__layout.addRow(self.firstRegButton)
self.firstRegButton.connect('clicked()', self.firstRegistration)
self.resetRegistration = qt.QPushButton('Reset Registration')
self.resetRegistration.checkable = False
self.__layout.addRow(self.resetRegistration)
self.resetRegistration.connect('clicked()', self.backToInitialRegistration)
# # define cropping area
# self.drawRectlangelButton = qt.QPushButton('Outline Area Containing Fiducial Points')
# self.drawRectlangelButton.checkable = True
# self.__layout.addRow(self.drawRectlangelButton)
# self.drawRectlangelButton.connect('toggled(bool)',self.onDrawRectangleButtonToggled)
# Hough parameters - Cropping box: used to limit the volume where to find the circles
self.__houghFrame = ctk.ctkCollapsibleButton()
self.__houghFrame.text = "Registration Parameters"
self.__houghFrame.collapsed = 1
houghFrame = qt.QFormLayout(self.__houghFrame)
# option for horizontal template
self.horizontalTemplate=qt.QCheckBox('Horizontal Template')
houghFrame.addRow(self.horizontalTemplate)
# Use Hough Transform?
self.withHT = qt.QCheckBox('Use Hough Transform to Detect Circles (needs separate CLI Module)')
self.withHT.checked = False
houghFrame.addRow(self.withHT)
# Auto-value option
self.autoLimit = qt.QCheckBox('Limit fiducial search computation volume')
self.autoLimit.checked = True
houghFrame.addRow(self.autoLimit)
# Auto-value option
# self.autoValue = qt.QCheckBox('Automatic values?')
# self.autoValue.checked = False
# houghFrame.addRow(self.autoValue)
# Ratio height
self.ratioHeightCroppedVolume = qt.QSpinBox()
self.ratioHeightCroppedVolume.setMinimum(1)
self.ratioHeightCroppedVolume.setMaximum(15)
self.ratioHeightCroppedVolume.setValue(2)
ratioHeightCroppedVolumeLabel = qt.QLabel("Divide the height by: ")
houghFrame.addRow(ratioHeightCroppedVolumeLabel, self.ratioHeightCroppedVolume)
# Ratio width
# self.ratioWidthCroppedVolume = qt.QSpinBox()
# self.ratioWidthCroppedVolume.setMinimum(1)
# self.ratioWidthCroppedVolume.setMaximum(15)
# self.ratioWidthCroppedVolume.setValue(4)
# ratioWidthCroppedVolumeLabel = qt.QLabel("Divide the width by: ")
# houghFrame.addRow(ratioWidthCroppedVolumeLabel, self.ratioWidthCroppedVolume)
# # Ratio length
# self.ratioLengthCroppedVolume = qt.QSpinBox()
# self.ratioLengthCroppedVolume.setMinimum(1)
# self.ratioLengthCroppedVolume.setMaximum(15)
# self.ratioLengthCroppedVolume.setValue(4)
# ratioLengthCroppedVolumeLabel = qt.QLabel("Divide the length by: ")
# houghFrame.addRow(ratioLengthCroppedVolumeLabel, self.ratioLengthCroppedVolume)
# Get Maximum Threshold Value
red_logic = slicer.app.layoutManager().sliceWidget("Red").sliceLogic()
imageData = red_logic.GetImageData()
minMax = imageData.GetScalarRange()
maxThresh = minMax[1]
# Threshold slider for template segmentation
threshLabel = qt.QLabel('Threshold for CHT:')
self.__threshRange = slicer.qMRMLRangeWidget()
self.__threshRange.decimals = 0
self.__threshRange.singleStep = 1
self.__threshRange.minimum = 150
self.__threshRange.minimumValue = 150
self.__threshRange.maximum = maxThresh
self.__threshRange.maximumValue = maxThresh
houghFrame.addRow(threshLabel,self.__threshRange)
self.__layout.addRow(self.__houghFrame)
# Threshold slider for template segmentation
thresholdSliderLabel = qt.QLabel('Speed of registration (increases inaccuracy) 1-10')
self.thresholdSlider=qt.QSlider(0x1)
self.thresholdSlider.toolTip = "Select Threshold."
self.thresholdSlider.enabled = True
self.thresholdSlider.setMinimum(1)
self.thresholdSlider.setMaximum(10)
self.thresholdSlider.setValue(2)
houghFrame.addRow(thresholdSliderLabel,self.thresholdSlider)
self.__layout.addRow(self.__houghFrame)
# reset module button
# resetButton = qt.QPushButton( 'Reset Module' )
# resetButton.connect( 'clicked()', self.onResetButton )
# self.__layout.addWidget( resetButton )
qt.QTimer.singleShot(0, self.killButton)
def setup( self ):
# check if the SlicerVmtk module is installed properly
# self.__vmtkInstalled = SlicerVmtkCommonLib.Helper.CheckIfVmtkIsInstalled()
# Helper.Debug("VMTK found: " + self.__vmtkInstalled)
#
# the I/O panel
#
ioCollapsibleButton = ctk.ctkCollapsibleButton()
ioCollapsibleButton.text = "Input/Output"
self.layout.addWidget( ioCollapsibleButton )
ioFormLayout = qt.QFormLayout( ioCollapsibleButton )
# inputVolume selector
self.__inputVolumeNodeSelector = slicer.qMRMLNodeComboBox()
self.__inputVolumeNodeSelector.objectName = 'inputVolumeNodeSelector'
self.__inputVolumeNodeSelector.toolTip = "Select the input volume. This should always be the original image and not a vesselness image, if possible."
self.__inputVolumeNodeSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__inputVolumeNodeSelector.noneEnabled = False
self.__inputVolumeNodeSelector.addEnabled = False
self.__inputVolumeNodeSelector.removeEnabled = False
self.__inputVolumeNodeSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", "0" )
ioFormLayout.addRow( "Input Volume:", self.__inputVolumeNodeSelector )
self.parent.connect( 'mrmlSceneChanged(vtkMRMLScene*)',
self.__inputVolumeNodeSelector, 'setMRMLScene(vtkMRMLScene*)' )
self.__inputVolumeNodeSelector.connect( 'currentNodeChanged(vtkMRMLNode*)', self.onInputVolumeChanged )
self.__inputVolumeNodeSelector.connect( 'nodeActivated(vtkMRMLNode*)', self.onInputVolumeChanged )
# seed selector
self.__seedFiducialsNodeSelector = slicer.qMRMLNodeComboBox()
self.__seedFiducialsNodeSelector.objectName = 'seedFiducialsNodeSelector'
self.__seedFiducialsNodeSelector.toolTip = "Select a hierarchy containing the fiducials to use as Seeds."
self.__seedFiducialsNodeSelector.nodeTypes = ['vtkMRMLAnnotationHierarchyNode']
self.__seedFiducialsNodeSelector.baseName = "Seeds"
self.__seedFiducialsNodeSelector.noneEnabled = False
self.__seedFiducialsNodeSelector.addEnabled = False
self.__seedFiducialsNodeSelector.removeEnabled = False
ioFormLayout.addRow( "Seeds:", self.__seedFiducialsNodeSelector )
self.parent.connect( 'mrmlSceneChanged(vtkMRMLScene*)',
self.__seedFiducialsNodeSelector, 'setMRMLScene(vtkMRMLScene*)' )
self.__ioAdvancedToggle = qt.QCheckBox( "Show Advanced I/O Properties" )
self.__ioAdvancedToggle.setChecked( False )
ioFormLayout.addRow( self.__ioAdvancedToggle )
#
# I/O advanced panel
#
self.__ioAdvancedPanel = qt.QFrame( ioCollapsibleButton )
self.__ioAdvancedPanel.hide()
self.__ioAdvancedPanel.setFrameStyle( 6 )
ioFormLayout.addRow( self.__ioAdvancedPanel )
self.__ioAdvancedToggle.connect( "clicked()", self.onIOAdvancedToggle )
ioAdvancedFormLayout = qt.QFormLayout( self.__ioAdvancedPanel )
# inputVolume selector
self.__vesselnessVolumeNodeSelector = slicer.qMRMLNodeComboBox()
self.__vesselnessVolumeNodeSelector.objectName = 'vesselnessVolumeNodeSelector'
self.__vesselnessVolumeNodeSelector.toolTip = "Select the input vesselness volume. This is optional input."
self.__vesselnessVolumeNodeSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__vesselnessVolumeNodeSelector.noneEnabled = True
self.__vesselnessVolumeNodeSelector.addEnabled = False
self.__vesselnessVolumeNodeSelector.removeEnabled = False
self.__vesselnessVolumeNodeSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", "0" )
ioAdvancedFormLayout.addRow( "Vesselness Volume:", self.__vesselnessVolumeNodeSelector )
self.parent.connect( 'mrmlSceneChanged(vtkMRMLScene*)',
self.__vesselnessVolumeNodeSelector, 'setMRMLScene(vtkMRMLScene*)' )
self.__vesselnessVolumeNodeSelector.setCurrentNode( None )
# stopper selector
self.__stopperFiducialsNodeSelector = slicer.qMRMLNodeComboBox()
self.__stopperFiducialsNodeSelector.objectName = 'stopperFiducialsNodeSelector'
self.__stopperFiducialsNodeSelector.toolTip = "Select a hierarchy containing the fiducials to use as Stoppers. Whenever one stopper is reached, the segmentation stops."
self.__stopperFiducialsNodeSelector.nodeTypes = ['vtkMRMLAnnotationHierarchyNode']
self.__stopperFiducialsNodeSelector.baseName = "Stoppers"
self.__stopperFiducialsNodeSelector.noneEnabled = False
self.__stopperFiducialsNodeSelector.addEnabled = True
self.__stopperFiducialsNodeSelector.removeEnabled = False
ioAdvancedFormLayout.addRow( "Stoppers:", self.__stopperFiducialsNodeSelector )
self.parent.connect( 'mrmlSceneChanged(vtkMRMLScene*)',
self.__stopperFiducialsNodeSelector, 'setMRMLScene(vtkMRMLScene*)' )
# outputVolume selector
self.__outputVolumeNodeSelector = slicer.qMRMLNodeComboBox()
self.__outputVolumeNodeSelector.toolTip = "Select the output labelmap."
self.__outputVolumeNodeSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__outputVolumeNodeSelector.baseName = "LevelSetSegmentation"
self.__outputVolumeNodeSelector.noneEnabled = False
self.__outputVolumeNodeSelector.addEnabled = True
self.__outputVolumeNodeSelector.selectNodeUponCreation = True
self.__outputVolumeNodeSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", "1" )
self.__outputVolumeNodeSelector.removeEnabled = True
ioAdvancedFormLayout.addRow( "Output Labelmap:", self.__outputVolumeNodeSelector )
self.parent.connect( 'mrmlSceneChanged(vtkMRMLScene*)',
self.__outputVolumeNodeSelector, 'setMRMLScene(vtkMRMLScene*)' )
# outputModel selector
self.__outputModelNodeSelector = slicer.qMRMLNodeComboBox()
self.__outputModelNodeSelector.objectName = 'outputModelNodeSelector'
self.__outputModelNodeSelector.toolTip = "Select the output model."
self.__outputModelNodeSelector.nodeTypes = ['vtkMRMLModelNode']
self.__outputModelNodeSelector.baseName = "LevelSetSegmentationModel"
self.__outputModelNodeSelector.hideChildNodeTypes = ['vtkMRMLAnnotationNode'] # hide all annotation nodes
self.__outputModelNodeSelector.noneEnabled = False
self.__outputModelNodeSelector.addEnabled = True
self.__outputModelNodeSelector.selectNodeUponCreation = True
self.__outputModelNodeSelector.removeEnabled = True
ioAdvancedFormLayout.addRow( "Output Model:", self.__outputModelNodeSelector )
self.parent.connect( 'mrmlSceneChanged(vtkMRMLScene*)',
self.__outputModelNodeSelector, 'setMRMLScene(vtkMRMLScene*)' )
#
# the segmentation panel
#
segmentationCollapsibleButton = ctk.ctkCollapsibleButton()
segmentationCollapsibleButton.text = "Segmentation"
self.layout.addWidget( segmentationCollapsibleButton )
segmentationFormLayout = qt.QFormLayout( segmentationCollapsibleButton )
# Threshold slider
thresholdLabel = qt.QLabel()
thresholdLabel.text = "Thresholding" + SlicerVmtkCommonLib.Helper.CreateSpace( 7 )
thresholdLabel.toolTip = "Choose the intensity range to segment."
thresholdLabel.setAlignment( 4 )
segmentationFormLayout.addRow( thresholdLabel )
self.__thresholdSlider = slicer.qMRMLRangeWidget()
segmentationFormLayout.addRow( self.__thresholdSlider )
self.__thresholdSlider.connect( 'valuesChanged(double,double)', self.onThresholdSliderChanged )
self.__segmentationAdvancedToggle = qt.QCheckBox( "Show Advanced Segmentation Properties" )
self.__segmentationAdvancedToggle.setChecked( False )
segmentationFormLayout.addRow( self.__segmentationAdvancedToggle )
#
# segmentation advanced panel
#
self.__segmentationAdvancedPanel = qt.QFrame( segmentationCollapsibleButton )
self.__segmentationAdvancedPanel.hide()
self.__segmentationAdvancedPanel.setFrameStyle( 6 )
segmentationFormLayout.addRow( self.__segmentationAdvancedPanel )
self.__segmentationAdvancedToggle.connect( "clicked()", self.onSegmentationAdvancedToggle )
segmentationAdvancedFormLayout = qt.QFormLayout( self.__segmentationAdvancedPanel )
# inflation slider
inflationLabel = qt.QLabel()
inflationLabel.text = "less inflation <-> more inflation" + SlicerVmtkCommonLib.Helper.CreateSpace( 14 )
inflationLabel.setAlignment( 4 )
inflationLabel.toolTip = "Define how fast the segmentation expands."
segmentationAdvancedFormLayout.addRow( inflationLabel )
self.__inflationSlider = ctk.ctkSliderWidget()
self.__inflationSlider.decimals = 0
self.__inflationSlider.minimum = -100
self.__inflationSlider.maximum = 100
self.__inflationSlider.singleStep = 10
self.__inflationSlider.toolTip = inflationLabel.toolTip
segmentationAdvancedFormLayout.addRow( self.__inflationSlider )
# curvature slider
curvatureLabel = qt.QLabel()
curvatureLabel.text = "less curvature <-> more curvature" + SlicerVmtkCommonLib.Helper.CreateSpace( 14 )
curvatureLabel.setAlignment( 4 )
curvatureLabel.toolTip = "Choose a high curvature to generate a smooth segmentation."
segmentationAdvancedFormLayout.addRow( curvatureLabel )
self.__curvatureSlider = ctk.ctkSliderWidget()
self.__curvatureSlider.decimals = 0
self.__curvatureSlider.minimum = -100
self.__curvatureSlider.maximum = 100
self.__curvatureSlider.singleStep = 10
self.__curvatureSlider.toolTip = curvatureLabel.toolTip
segmentationAdvancedFormLayout.addRow( self.__curvatureSlider )
# attraction slider
attractionLabel = qt.QLabel()
attractionLabel.text = "less attraction to gradient <-> more attraction to gradient" + SlicerVmtkCommonLib.Helper.CreateSpace( 14 )
attractionLabel.setAlignment( 4 )
attractionLabel.toolTip = "Configure how the segmentation travels towards gradient ridges (vessel lumen wall)."
segmentationAdvancedFormLayout.addRow( attractionLabel )
self.__attractionSlider = ctk.ctkSliderWidget()
self.__attractionSlider.decimals = 0
self.__attractionSlider.minimum = -100
self.__attractionSlider.maximum = 100
self.__attractionSlider.singleStep = 10
self.__attractionSlider.toolTip = attractionLabel.toolTip
segmentationAdvancedFormLayout.addRow( self.__attractionSlider )
# iteration spinbox
self.__iterationSpinBox = qt.QSpinBox()
self.__iterationSpinBox.minimum = 0
self.__iterationSpinBox.maximum = 5000
self.__iterationSpinBox.singleStep = 10
self.__iterationSpinBox.toolTip = "Choose the number of evolution iterations."
segmentationAdvancedFormLayout.addRow( SlicerVmtkCommonLib.Helper.CreateSpace( 100 ) + "Iterations:", self.__iterationSpinBox )
#
# Reset, preview and apply buttons
#
self.__buttonBox = qt.QDialogButtonBox()
self.__resetButton = self.__buttonBox.addButton( self.__buttonBox.RestoreDefaults )
self.__resetButton.toolTip = "Click to reset all input elements to default."
self.__previewButton = self.__buttonBox.addButton( self.__buttonBox.Discard )
self.__previewButton.setIcon( qt.QIcon() )
self.__previewButton.text = "Preview.."
self.__previewButton.toolTip = "Click to refresh the preview."
self.__startButton = self.__buttonBox.addButton( self.__buttonBox.Apply )
self.__startButton.setIcon( qt.QIcon() )
self.__startButton.text = "Start!"
self.__startButton.enabled = False
self.__startButton.toolTip = "Click to start the filtering."
self.layout.addWidget( self.__buttonBox )
self.__resetButton.connect( "clicked()", self.restoreDefaults )
self.__previewButton.connect( "clicked()", self.onRefreshButtonClicked )
self.__startButton.connect( "clicked()", self.onStartButtonClicked )
# be ready for events
self.__updating = 0
# set default values
self.restoreDefaults()
# compress the layout
self.layout.addStretch( 1 )
def setup(self):
# check if the SlicerVmtk module is installed properly
# self.__vmtkInstalled = SlicerVmtkCommonLib.Helper.CheckIfVmtkIsInstalled()
# Helper.Debug("VMTK found: " + self.__vmtkInstalled)
#
# the I/O panel
#
ioCollapsibleButton = ctk.ctkCollapsibleButton()
ioCollapsibleButton.text = "Input/Output"
self.layout.addWidget(ioCollapsibleButton)
ioFormLayout = qt.QFormLayout(ioCollapsibleButton)
# inputVolume selector
self.__inputVolumeNodeSelector = slicer.qMRMLNodeComboBox()
self.__inputVolumeNodeSelector.objectName = 'inputVolumeNodeSelector'
self.__inputVolumeNodeSelector.toolTip = "Select the input volume. This should always be the original image and not a vesselness image, if possible."
self.__inputVolumeNodeSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__inputVolumeNodeSelector.noneEnabled = False
self.__inputVolumeNodeSelector.addEnabled = False
self.__inputVolumeNodeSelector.removeEnabled = False
self.__inputVolumeNodeSelector.addAttribute("vtkMRMLScalarVolumeNode",
"LabelMap", "0")
ioFormLayout.addRow("Input Volume:", self.__inputVolumeNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.__inputVolumeNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
self.__inputVolumeNodeSelector.connect(
'currentNodeChanged(vtkMRMLNode*)', self.onInputVolumeChanged)
self.__inputVolumeNodeSelector.connect('nodeActivated(vtkMRMLNode*)',
self.onInputVolumeChanged)
# seed selector
self.__seedFiducialsNodeSelector = slicer.qMRMLNodeComboBox()
self.__seedFiducialsNodeSelector.objectName = 'seedFiducialsNodeSelector'
self.__seedFiducialsNodeSelector.toolTip = "Select a hierarchy containing the fiducials to use as Seeds."
self.__seedFiducialsNodeSelector.nodeTypes = [
'vtkMRMLAnnotationHierarchyNode'
]
self.__seedFiducialsNodeSelector.baseName = "Seeds"
self.__seedFiducialsNodeSelector.noneEnabled = False
self.__seedFiducialsNodeSelector.addEnabled = False
self.__seedFiducialsNodeSelector.removeEnabled = False
ioFormLayout.addRow("Seeds:", self.__seedFiducialsNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.__seedFiducialsNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
self.__ioAdvancedToggle = qt.QCheckBox("Show Advanced I/O Properties")
self.__ioAdvancedToggle.setChecked(False)
ioFormLayout.addRow(self.__ioAdvancedToggle)
#
# I/O advanced panel
#
self.__ioAdvancedPanel = qt.QFrame(ioCollapsibleButton)
self.__ioAdvancedPanel.hide()
self.__ioAdvancedPanel.setFrameStyle(6)
ioFormLayout.addRow(self.__ioAdvancedPanel)
self.__ioAdvancedToggle.connect("clicked()", self.onIOAdvancedToggle)
ioAdvancedFormLayout = qt.QFormLayout(self.__ioAdvancedPanel)
# inputVolume selector
self.__vesselnessVolumeNodeSelector = slicer.qMRMLNodeComboBox()
self.__vesselnessVolumeNodeSelector.objectName = 'vesselnessVolumeNodeSelector'
self.__vesselnessVolumeNodeSelector.toolTip = "Select the input vesselness volume. This is optional input."
self.__vesselnessVolumeNodeSelector.nodeTypes = [
'vtkMRMLScalarVolumeNode'
]
self.__vesselnessVolumeNodeSelector.noneEnabled = True
self.__vesselnessVolumeNodeSelector.addEnabled = False
self.__vesselnessVolumeNodeSelector.removeEnabled = False
self.__vesselnessVolumeNodeSelector.addAttribute(
"vtkMRMLScalarVolumeNode", "LabelMap", "0")
ioAdvancedFormLayout.addRow("Vesselness Volume:",
self.__vesselnessVolumeNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.__vesselnessVolumeNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
self.__vesselnessVolumeNodeSelector.setCurrentNode(None)
# stopper selector
self.__stopperFiducialsNodeSelector = slicer.qMRMLNodeComboBox()
self.__stopperFiducialsNodeSelector.objectName = 'stopperFiducialsNodeSelector'
self.__stopperFiducialsNodeSelector.toolTip = "Select a hierarchy containing the fiducials to use as Stoppers. Whenever one stopper is reached, the segmentation stops."
self.__stopperFiducialsNodeSelector.nodeTypes = [
'vtkMRMLAnnotationHierarchyNode'
]
self.__stopperFiducialsNodeSelector.baseName = "Stoppers"
self.__stopperFiducialsNodeSelector.noneEnabled = False
self.__stopperFiducialsNodeSelector.addEnabled = True
self.__stopperFiducialsNodeSelector.removeEnabled = False
ioAdvancedFormLayout.addRow("Stoppers:",
self.__stopperFiducialsNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.__stopperFiducialsNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
# outputVolume selector
self.__outputVolumeNodeSelector = slicer.qMRMLNodeComboBox()
self.__outputVolumeNodeSelector.toolTip = "Select the output labelmap."
self.__outputVolumeNodeSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.__outputVolumeNodeSelector.baseName = "LevelSetSegmentation"
self.__outputVolumeNodeSelector.noneEnabled = False
self.__outputVolumeNodeSelector.addEnabled = True
self.__outputVolumeNodeSelector.selectNodeUponCreation = True
self.__outputVolumeNodeSelector.addAttribute("vtkMRMLScalarVolumeNode",
"LabelMap", "1")
self.__outputVolumeNodeSelector.removeEnabled = True
ioAdvancedFormLayout.addRow("Output Labelmap:",
self.__outputVolumeNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.__outputVolumeNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
# outputModel selector
self.__outputModelNodeSelector = slicer.qMRMLNodeComboBox()
self.__outputModelNodeSelector.objectName = 'outputModelNodeSelector'
self.__outputModelNodeSelector.toolTip = "Select the output model."
self.__outputModelNodeSelector.nodeTypes = ['vtkMRMLModelNode']
self.__outputModelNodeSelector.baseName = "LevelSetSegmentationModel"
self.__outputModelNodeSelector.hideChildNodeTypes = [
'vtkMRMLAnnotationNode'
] # hide all annotation nodes
self.__outputModelNodeSelector.noneEnabled = False
self.__outputModelNodeSelector.addEnabled = True
self.__outputModelNodeSelector.selectNodeUponCreation = True
self.__outputModelNodeSelector.removeEnabled = True
ioAdvancedFormLayout.addRow("Output Model:",
self.__outputModelNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.__outputModelNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
#
# the segmentation panel
#
segmentationCollapsibleButton = ctk.ctkCollapsibleButton()
segmentationCollapsibleButton.text = "Segmentation"
self.layout.addWidget(segmentationCollapsibleButton)
segmentationFormLayout = qt.QFormLayout(segmentationCollapsibleButton)
# Threshold slider
thresholdLabel = qt.QLabel()
thresholdLabel.text = "Thresholding" + SlicerVmtkCommonLib.Helper.CreateSpace(
7)
thresholdLabel.toolTip = "Choose the intensity range to segment."
thresholdLabel.setAlignment(4)
segmentationFormLayout.addRow(thresholdLabel)
self.__thresholdSlider = slicer.qMRMLRangeWidget()
segmentationFormLayout.addRow(self.__thresholdSlider)
self.__thresholdSlider.connect('valuesChanged(double,double)',
self.onThresholdSliderChanged)
self.__segmentationAdvancedToggle = qt.QCheckBox(
"Show Advanced Segmentation Properties")
self.__segmentationAdvancedToggle.setChecked(False)
segmentationFormLayout.addRow(self.__segmentationAdvancedToggle)
#
# segmentation advanced panel
#
self.__segmentationAdvancedPanel = qt.QFrame(
segmentationCollapsibleButton)
self.__segmentationAdvancedPanel.hide()
self.__segmentationAdvancedPanel.setFrameStyle(6)
segmentationFormLayout.addRow(self.__segmentationAdvancedPanel)
self.__segmentationAdvancedToggle.connect(
"clicked()", self.onSegmentationAdvancedToggle)
segmentationAdvancedFormLayout = qt.QFormLayout(
self.__segmentationAdvancedPanel)
# inflation slider
inflationLabel = qt.QLabel()
inflationLabel.text = "less inflation <-> more inflation" + SlicerVmtkCommonLib.Helper.CreateSpace(
14)
inflationLabel.setAlignment(4)
inflationLabel.toolTip = "Define how fast the segmentation expands."
segmentationAdvancedFormLayout.addRow(inflationLabel)
self.__inflationSlider = ctk.ctkSliderWidget()
self.__inflationSlider.decimals = 0
self.__inflationSlider.minimum = -100
self.__inflationSlider.maximum = 100
self.__inflationSlider.singleStep = 10
self.__inflationSlider.toolTip = inflationLabel.toolTip
segmentationAdvancedFormLayout.addRow(self.__inflationSlider)
# curvature slider
curvatureLabel = qt.QLabel()
curvatureLabel.text = "less curvature <-> more curvature" + SlicerVmtkCommonLib.Helper.CreateSpace(
14)
curvatureLabel.setAlignment(4)
curvatureLabel.toolTip = "Choose a high curvature to generate a smooth segmentation."
segmentationAdvancedFormLayout.addRow(curvatureLabel)
self.__curvatureSlider = ctk.ctkSliderWidget()
self.__curvatureSlider.decimals = 0
self.__curvatureSlider.minimum = -100
self.__curvatureSlider.maximum = 100
self.__curvatureSlider.singleStep = 10
self.__curvatureSlider.toolTip = curvatureLabel.toolTip
segmentationAdvancedFormLayout.addRow(self.__curvatureSlider)
# attraction slider
attractionLabel = qt.QLabel()
attractionLabel.text = "less attraction to gradient <-> more attraction to gradient" + SlicerVmtkCommonLib.Helper.CreateSpace(
14)
attractionLabel.setAlignment(4)
attractionLabel.toolTip = "Configure how the segmentation travels towards gradient ridges (vessel lumen wall)."
segmentationAdvancedFormLayout.addRow(attractionLabel)
self.__attractionSlider = ctk.ctkSliderWidget()
self.__attractionSlider.decimals = 0
self.__attractionSlider.minimum = -100
self.__attractionSlider.maximum = 100
self.__attractionSlider.singleStep = 10
self.__attractionSlider.toolTip = attractionLabel.toolTip
segmentationAdvancedFormLayout.addRow(self.__attractionSlider)
# iteration spinbox
self.__iterationSpinBox = qt.QSpinBox()
self.__iterationSpinBox.minimum = 0
self.__iterationSpinBox.maximum = 5000
self.__iterationSpinBox.singleStep = 10
self.__iterationSpinBox.toolTip = "Choose the number of evolution iterations."
segmentationAdvancedFormLayout.addRow(
SlicerVmtkCommonLib.Helper.CreateSpace(100) + "Iterations:",
self.__iterationSpinBox)
#
# Reset, preview and apply buttons
#
self.__buttonBox = qt.QDialogButtonBox()
self.__resetButton = self.__buttonBox.addButton(
self.__buttonBox.RestoreDefaults)
self.__resetButton.toolTip = "Click to reset all input elements to default."
self.__previewButton = self.__buttonBox.addButton(
self.__buttonBox.Discard)
self.__previewButton.setIcon(qt.QIcon())
self.__previewButton.text = "Preview.."
self.__previewButton.toolTip = "Click to refresh the preview."
self.__startButton = self.__buttonBox.addButton(self.__buttonBox.Apply)
self.__startButton.setIcon(qt.QIcon())
self.__startButton.text = "Start!"
self.__startButton.enabled = False
self.__startButton.toolTip = "Click to start the filtering."
self.layout.addWidget(self.__buttonBox)
self.__resetButton.connect("clicked()", self.restoreDefaults)
self.__previewButton.connect("clicked()", self.onRefreshButtonClicked)
self.__startButton.connect("clicked()", self.onStartButtonClicked)
# be ready for events
self.__updating = 0
# set default values
self.restoreDefaults()
# compress the layout
self.layout.addStretch(1)