def section_SimpleMarkupsWidget(self):
self.delayDisplay("Test SimpleMarkupsWidget", self.delayMs)
simpleMarkupsWidget = slicer.qSlicerSimpleMarkupsWidget()
nodeSelector = slicer.util.findChildren(
simpleMarkupsWidget, "MarkupsFiducialNodeComboBox")[0]
simpleMarkupsWidget.setMRMLScene(slicer.mrmlScene)
simpleMarkupsWidget.show()
placeWidget = simpleMarkupsWidget.markupsPlaceWidget()
self.assertIsNotNone(placeWidget)
simpleMarkupsWidget.setCurrentNode(None)
simpleMarkupsWidget.enterPlaceModeOnNodeChange = False
placeWidget.placeModeEnabled = False
nodeSelector.setCurrentNode(self.markupsNode1)
self.assertFalse(placeWidget.placeModeEnabled)
simpleMarkupsWidget.enterPlaceModeOnNodeChange = True
nodeSelector.setCurrentNode(self.markupsNode2)
self.assertTrue(placeWidget.placeModeEnabled)
simpleMarkupsWidget.jumpToSliceEnabled = True
self.assertTrue(simpleMarkupsWidget.jumpToSliceEnabled)
simpleMarkupsWidget.jumpToSliceEnabled = False
self.assertFalse(simpleMarkupsWidget.jumpToSliceEnabled)
simpleMarkupsWidget.nodeSelectorVisible = False
self.assertFalse(simpleMarkupsWidget.nodeSelectorVisible)
simpleMarkupsWidget.nodeSelectorVisible = True
self.assertTrue(simpleMarkupsWidget.nodeSelectorVisible)
simpleMarkupsWidget.optionsVisible = False
self.assertFalse(simpleMarkupsWidget.optionsVisible)
simpleMarkupsWidget.optionsVisible = True
self.assertTrue(simpleMarkupsWidget.optionsVisible)
defaultColor = qt.QColor(0, 255, 0)
simpleMarkupsWidget.defaultNodeColor = defaultColor
self.assertEqual(simpleMarkupsWidget.defaultNodeColor, defaultColor)
self.markupsNode3 = nodeSelector.addNode()
displayNode3 = self.markupsNode3.GetDisplayNode()
color3 = displayNode3.GetColor()
self.assertEqual(color3[0] * 255, defaultColor.red())
self.assertEqual(color3[1] * 255, defaultColor.green())
self.assertEqual(color3[2] * 255, defaultColor.blue())
numberOfFiducialsAdded = 5
for i in range(numberOfFiducialsAdded):
self.markupsLogic.AddFiducial()
tableWidget = simpleMarkupsWidget.tableWidget()
self.assertEqual(tableWidget.rowCount, numberOfFiducialsAdded)
def section_SimpleMarkupsWidget(self):
self.delayDisplay("Test SimpleMarkupsWidget",self.delayMs)
simpleMarkupsWidget = slicer.qSlicerSimpleMarkupsWidget()
nodeSelector = slicer.util.findChildren(simpleMarkupsWidget,"MarkupsFiducialNodeComboBox")[0]
simpleMarkupsWidget.setMRMLScene(slicer.mrmlScene)
simpleMarkupsWidget.show()
placeWidget = simpleMarkupsWidget.markupsPlaceWidget()
self.assertIsNotNone(placeWidget)
simpleMarkupsWidget.setCurrentNode(None)
simpleMarkupsWidget.enterPlaceModeOnNodeChange = False
placeWidget.placeModeEnabled = False
nodeSelector.setCurrentNode(self.markupsNode1)
self.assertFalse(placeWidget.placeModeEnabled)
simpleMarkupsWidget.enterPlaceModeOnNodeChange = True
nodeSelector.setCurrentNode(self.markupsNode2)
self.assertTrue(placeWidget.placeModeEnabled)
simpleMarkupsWidget.jumpToSliceEnabled = True
self.assertTrue(simpleMarkupsWidget.jumpToSliceEnabled)
simpleMarkupsWidget.jumpToSliceEnabled = False
self.assertFalse(simpleMarkupsWidget.jumpToSliceEnabled)
simpleMarkupsWidget.nodeSelectorVisible = False
self.assertFalse(simpleMarkupsWidget.nodeSelectorVisible)
simpleMarkupsWidget.nodeSelectorVisible = True
self.assertTrue(simpleMarkupsWidget.nodeSelectorVisible)
simpleMarkupsWidget.optionsVisible = False
self.assertFalse(simpleMarkupsWidget.optionsVisible)
simpleMarkupsWidget.optionsVisible = True
self.assertTrue(simpleMarkupsWidget.optionsVisible)
defaultColor = qt.QColor(0,255,0)
simpleMarkupsWidget.defaultNodeColor = defaultColor
self.assertEqual(simpleMarkupsWidget.defaultNodeColor, defaultColor)
self.markupsNode3 = nodeSelector.addNode()
displayNode3 = self.markupsNode3.GetDisplayNode()
color3 = displayNode3.GetColor()
self.assertEqual(color3[0]*255, defaultColor.red())
self.assertEqual(color3[1]*255, defaultColor.green())
self.assertEqual(color3[2]*255, defaultColor.blue())
numberOfFiducialsAdded = 5
for i in range(numberOfFiducialsAdded):
self.markupsLogic.AddFiducial()
tableWidget = simpleMarkupsWidget.tableWidget()
self.assertEqual(tableWidget.rowCount, numberOfFiducialsAdded)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
try:
import vtkvmtkSegmentationPython as vtkvmtkSegmentation
except ImportError:
self.layout.addWidget(qt.QLabel("Failed to load VMTK libraries"))
return
#
# 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."
self.inputVolumeNodeSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.inputVolumeNodeSelector.noneEnabled = False
self.inputVolumeNodeSelector.addEnabled = False
self.inputVolumeNodeSelector.removeEnabled = False
ioFormLayout.addRow("Input Volume:", self.inputVolumeNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.inputVolumeNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
# seed selector
self.seedFiducialsNodeSelector = slicer.qSlicerSimpleMarkupsWidget()
self.seedFiducialsNodeSelector.objectName = 'seedFiducialsNodeSelector'
self.seedFiducialsNodeSelector = slicer.qSlicerSimpleMarkupsWidget()
self.seedFiducialsNodeSelector.objectName = 'seedFiducialsNodeSelector'
self.seedFiducialsNodeSelector.toolTip = "Select a point in the largest vessel. Preview will be shown around this point. This is point is also used for determining maximum vessel diameter if automatic filtering parameters computation is enabled."
self.seedFiducialsNodeSelector.setNodeBaseName("DiameterSeed")
self.seedFiducialsNodeSelector.tableWidget().hide()
self.seedFiducialsNodeSelector.defaultNodeColor = qt.QColor(255, 0,
0) # red
self.seedFiducialsNodeSelector.markupsSelectorComboBox(
).noneEnabled = False
self.seedFiducialsNodeSelector.markupsPlaceWidget(
).placeMultipleMarkups = slicer.qSlicerMarkupsPlaceWidget.ForcePlaceSingleMarkup
ioFormLayout.addRow("Seed point:", self.seedFiducialsNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.seedFiducialsNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
# outputVolume selector
self.outputVolumeNodeSelector = slicer.qMRMLNodeComboBox()
self.outputVolumeNodeSelector.toolTip = "Select the output labelmap."
self.outputVolumeNodeSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.outputVolumeNodeSelector.baseName = "VesselnessFiltered"
self.outputVolumeNodeSelector.noneEnabled = True
self.outputVolumeNodeSelector.noneDisplay = "Create new volume"
self.outputVolumeNodeSelector.addEnabled = True
self.outputVolumeNodeSelector.selectNodeUponCreation = True
self.outputVolumeNodeSelector.removeEnabled = True
ioFormLayout.addRow("Output Volume:", self.outputVolumeNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.outputVolumeNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
#
# Advanced area
#
self.advancedCollapsibleButton = ctk.ctkCollapsibleButton()
self.advancedCollapsibleButton.text = "Advanced"
self.advancedCollapsibleButton.collapsed = True
self.layout.addWidget(self.advancedCollapsibleButton)
advancedFormLayout = qt.QFormLayout(self.advancedCollapsibleButton)
# previewVolume selector
self.previewVolumeNodeSelector = slicer.qMRMLNodeComboBox()
self.previewVolumeNodeSelector.toolTip = "Select the preview volume."
self.previewVolumeNodeSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.previewVolumeNodeSelector.baseName = "VesselnessPreview"
self.previewVolumeNodeSelector.noneEnabled = True
self.previewVolumeNodeSelector.noneDisplay = "Create new volume"
self.previewVolumeNodeSelector.addEnabled = True
self.previewVolumeNodeSelector.selectNodeUponCreation = True
self.previewVolumeNodeSelector.removeEnabled = True
advancedFormLayout.addRow("Preview volume:",
self.previewVolumeNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.previewVolumeNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
self.displayThresholdSlider = ctk.ctkSliderWidget()
self.displayThresholdSlider.decimals = 2
self.displayThresholdSlider.minimum = 0
self.displayThresholdSlider.maximum = 1.0
self.displayThresholdSlider.singleStep = 0.01
self.displayThresholdSlider.toolTip = "Voxels below this vesselness value will be hidden. It does not change the voxel values, only how the vesselness volume is displayed."
advancedFormLayout.addRow("Display threshold:",
self.displayThresholdSlider)
self.displayThresholdSlider.connect('valueChanged(double)',
self.onDisplayThresholdChanged)
self.previewVolumeDiameterVoxelSlider = ctk.ctkSliderWidget()
self.previewVolumeDiameterVoxelSlider.decimals = 0
self.previewVolumeDiameterVoxelSlider.minimum = 10
self.previewVolumeDiameterVoxelSlider.maximum = 200
self.previewVolumeDiameterVoxelSlider.singleStep = 5
self.previewVolumeDiameterVoxelSlider.suffix = " voxels"
self.previewVolumeDiameterVoxelSlider.toolTip = "Diameter of the preview area in voxels."
advancedFormLayout.addRow("Preview volume size:",
self.previewVolumeDiameterVoxelSlider)
# detect filterint parameters
self.detectPushButton = qt.QPushButton()
self.detectPushButton.text = "Compute vessel diameters and contrast from seed point"
self.detectPushButton.checkable = True
self.detectPushButton.checked = True
advancedFormLayout.addRow(self.detectPushButton)
self.detectPushButton.connect("clicked()", self.onNodeSelectionChanged)
self.minimumDiameterSpinBox = qt.QSpinBox()
self.minimumDiameterSpinBox.minimum = 1
self.minimumDiameterSpinBox.maximum = 1000
self.minimumDiameterSpinBox.singleStep = 1
self.minimumDiameterSpinBox.suffix = " voxels"
self.minimumDiameterSpinBox.enabled = False
self.minimumDiameterSpinBox.toolTip = "Tubular structures that have minimum this diameter will be enhanced."
advancedFormLayout.addRow("Minimum vessel diameter:",
self.minimumDiameterSpinBox)
self.detectPushButton.connect("toggled(bool)",
self.minimumDiameterSpinBox.setDisabled)
self.maximumDiameterSpinBox = qt.QSpinBox()
self.maximumDiameterSpinBox.minimum = 0
self.maximumDiameterSpinBox.maximum = 1000
self.maximumDiameterSpinBox.singleStep = 1
self.maximumDiameterSpinBox.suffix = " voxels"
self.maximumDiameterSpinBox.enabled = False
self.maximumDiameterSpinBox.toolTip = "Tubular structures that have maximum this diameter will be enhanced."
advancedFormLayout.addRow("Maximum vessel diameter:",
self.maximumDiameterSpinBox)
self.detectPushButton.connect("toggled(bool)",
self.maximumDiameterSpinBox.setDisabled)
self.contrastSlider = ctk.ctkSliderWidget()
self.contrastSlider.decimals = 0
self.contrastSlider.minimum = 0
self.contrastSlider.maximum = 500
self.contrastSlider.singleStep = 10
self.contrastSlider.enabled = False
self.contrastSlider.toolTip = "If the intensity contrast in the input image between vessel and background is high, choose a high value else choose a low value."
advancedFormLayout.addRow("Vessel contrast:", self.contrastSlider)
self.detectPushButton.connect("toggled(bool)",
self.contrastSlider.setDisabled)
self.suppressPlatesSlider = ctk.ctkSliderWidget()
self.suppressPlatesSlider.decimals = 0
self.suppressPlatesSlider.minimum = 0
self.suppressPlatesSlider.maximum = 100
self.suppressPlatesSlider.singleStep = 1
self.suppressPlatesSlider.suffix = " %"
self.suppressPlatesSlider.toolTip = "A higher value filters out more plate-like structures."
advancedFormLayout.addRow("Suppress plates:",
self.suppressPlatesSlider)
self.suppressBlobsSlider = ctk.ctkSliderWidget()
self.suppressBlobsSlider.decimals = 0
self.suppressBlobsSlider.minimum = 0
self.suppressBlobsSlider.maximum = 100
self.suppressBlobsSlider.singleStep = 1
self.suppressBlobsSlider.suffix = " %"
self.suppressBlobsSlider.toolTip = "A higher value filters out more blob-like structures."
advancedFormLayout.addRow("Suppress blobs:", self.suppressBlobsSlider)
#
# 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.startButton = self.buttonBox.addButton(self.buttonBox.Apply)
self.startButton.setIcon(qt.QIcon())
self.startButton.text = "Start"
self.startButton.enabled = False
self.layout.addWidget(self.buttonBox)
self.resetButton.connect("clicked()", self.restoreDefaults)
self.previewButton.connect("clicked()", self.onPreviewButtonClicked)
self.startButton.connect("clicked()", self.onStartButtonClicked)
self.inputVolumeNodeSelector.setMRMLScene(slicer.mrmlScene)
self.seedFiducialsNodeSelector.setMRMLScene(slicer.mrmlScene)
self.outputVolumeNodeSelector.setMRMLScene(slicer.mrmlScene)
self.previewVolumeNodeSelector.setMRMLScene(slicer.mrmlScene)
self.inputVolumeNodeSelector.connect(
"currentNodeChanged(vtkMRMLNode*)", self.onNodeSelectionChanged)
self.seedFiducialsNodeSelector.markupsSelectorComboBox().connect(
"currentNodeChanged(vtkMRMLNode*)", self.onNodeSelectionChanged)
self.seedFiducialsNodeSelector.connect("updateFinished()",
self.onNodeSelectionChanged)
# set default values
self.restoreDefaults()
self.onNodeSelectionChanged()
# compress the layout
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#clear scene
# slicer.mrmlScene.Clear(0)
#Define Widgets layout
lm = slicer.app.layoutManager()
lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutThreeOverThreeView)
lm.sliceWidget('Red').setSliceOrientation('Axial')
lm.sliceWidget('Red+').setSliceOrientation('Axial')
lm.sliceWidget('Yellow').setSliceOrientation('Axial')
lm.sliceWidget('Yellow+').setSliceOrientation('Axial')
lm.sliceWidget('Green').setSliceOrientation('Axial')
lm.sliceWidget('Green+').setSliceOrientation('Axial')
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# input volume selector
#
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.inputSelector.selectNodeUponCreation = True
self.inputSelector.addEnabled = False
self.inputSelector.removeEnabled = False
self.inputSelector.noneEnabled = False
self.inputSelector.showHidden = False
self.inputSelector.showChildNodeTypes = False
self.inputSelector.setMRMLScene(slicer.mrmlScene)
self.inputSelector.setToolTip("Pick the input to the algorithm.")
#parametersFormLayout.addRow("Input Volume: ", self.inputSelector) Por ahora no lo mostramos.
#
# output volume selector
#
self.outputSelector = slicer.qMRMLNodeComboBox()
self.outputSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.outputSelector.selectNodeUponCreation = True
self.outputSelector.addEnabled = True
self.outputSelector.removeEnabled = True
self.outputSelector.noneEnabled = True
self.outputSelector.showHidden = False
self.outputSelector.showChildNodeTypes = False
self.outputSelector.setMRMLScene(slicer.mrmlScene)
self.outputSelector.setToolTip("Pick the output to the algorithm.")
parametersFormLayout.addRow("Volume: ", self.outputSelector)
#
# Take Working Image Button
#
self.takeImageButton = qt.QPushButton("Take working image")
self.takeImageButton.toolTip = "Take working image"
self.takeImageButton.enabled = True
parametersFormLayout.addRow(self.takeImageButton)
#
# Processing selector
#
self.processingSelector = qt.QComboBox()
self.processingSelector.addItem("original")
self.processingSelector.addItem("image smoothing")
self.processingSelector.addItem("image segmentation")
self.processingSelector.addItem("image segmentation + no holes")
self.processingSelector.addItem("contouring")
parametersFormLayout.addRow("Processing: ", self.processingSelector)
#
# SpinBoxes : numerical inputs
#
self.segmentationGroupBox = qt.QGroupBox("Segmentation Data")
self.segmentationVBoxLayout = qt.QVBoxLayout()
self.tempGroupBox = qt.QGroupBox("Temperature")
self.tempHBoxLayout = qt.QHBoxLayout()
self.qlabelMin = QLabel('Min:')
self.doubleMinTemp = ctk.ctkSliderWidget()
self.doubleMinTemp.setSizePolicy(QSizePolicy.Ignored,
QSizePolicy.Preferred)
self.doubleMinTemp.setDecimals(2)
self.doubleMinTemp.setValue(27.0)
self.tempHBoxLayout.addWidget(self.qlabelMin)
self.tempHBoxLayout.addWidget(self.doubleMinTemp)
self.labelMax = qt.QLabel("Max: ")
self.doubleMaxTemp = ctk.ctkSliderWidget()
self.doubleMaxTemp.setValue(35.0)
self.tempHBoxLayout.addWidget(self.labelMax)
self.tempHBoxLayout.addWidget(self.doubleMaxTemp)
self.tempGroupBox.setLayout(self.tempHBoxLayout)
self.segmentationVBoxLayout.addWidget(self.tempGroupBox)
#
# Button to get foot seed
#
self.seedBoxesGroup = qt.QGroupBox("Seed")
frameControlHBox = qt.QVBoxLayout()
self.seedCoords = {}
# Seed Left selector
self.seedLeftFiducialsNodeSelector = slicer.qSlicerSimpleMarkupsWidget(
)
self.seedLeftFiducialsNodeSelector.objectName = 'seedLeftFiducialsNodeSelector'
self.seedLeftFiducialsNodeSelector.toolTip = "Select a fiducial to use as the origin of the left segments."
self.seedLeftFiducialsNodeSelector.setNodeBaseName("Left")
self.seedLeftFiducialsNodeSelector.defaultNodeColor = qt.QColor(
0, 255, 0)
self.seedLeftFiducialsNodeSelector.tableWidget().hide()
self.seedLeftFiducialsNodeSelector.markupsSelectorComboBox(
).noneEnabled = False
self.seedLeftFiducialsNodeSelector.markupsPlaceWidget(
).placeMultipleMarkups = slicer.qSlicerMarkupsPlaceWidget.ForcePlaceSingleMarkup
self.seedLeftFiducialsNodeSelector.markupsPlaceWidget(
).buttonsVisible = False
self.seedLeftFiducialsNodeSelector.markupsPlaceWidget().placeButton(
).show()
self.seedLeftFiducialsNodeSelector.setMRMLScene(slicer.mrmlScene)
self.seedFiducialsBox = qt.QHBoxLayout()
self.seedLabelWidget = qt.QLabel("Choose left seed node:")
self.seedFiducialsBox.addWidget(self.seedLabelWidget)
self.seedFiducialsBox.addWidget(self.seedLeftFiducialsNodeSelector)
self.leftFiducial = qt.QGroupBox("Left: ")
self.leftFiducial.setLayout(self.seedFiducialsBox)
# Seed Right selector
self.seedRightFiducialsNodeSelector = slicer.qSlicerSimpleMarkupsWidget(
)
self.seedRightFiducialsNodeSelector.objectName = 'seedRightFiducialsNodeSelector'
self.seedRightFiducialsNodeSelector.toolTip = "Select a fiducial to use as the origin of the left segments."
self.seedRightFiducialsNodeSelector.setNodeBaseName("Right")
self.seedRightFiducialsNodeSelector.defaultNodeColor = qt.QColor(
0, 255, 0)
self.seedRightFiducialsNodeSelector.tableWidget().hide()
self.seedRightFiducialsNodeSelector.markupsSelectorComboBox(
).noneEnabled = False
self.seedRightFiducialsNodeSelector.markupsPlaceWidget(
).placeMultipleMarkups = slicer.qSlicerMarkupsPlaceWidget.ForcePlaceSingleMarkup
self.seedRightFiducialsNodeSelector.markupsPlaceWidget(
).buttonsVisible = False
self.seedRightFiducialsNodeSelector.markupsPlaceWidget().placeButton(
).show()
self.seedRightFiducialsNodeSelector.setMRMLScene(slicer.mrmlScene)
seedRightFiducialsNodeSelector = self.seedRightFiducialsNodeSelector
self.seedRightFiducialsBox = qt.QHBoxLayout()
self.seedRightLabelWidget = qt.QLabel("Choose right seed node:")
self.seedRightFiducialsBox.addWidget(self.seedRightLabelWidget)
self.seedRightFiducialsBox.addWidget(
self.seedRightFiducialsNodeSelector)
self.rightFiducial = qt.QGroupBox("Right: ")
self.rightFiducial.setLayout(self.seedRightFiducialsBox)
frameControlHBox.addWidget(self.leftFiducial)
frameControlHBox.addWidget(self.rightFiducial)
self.seedBoxesGroup.setLayout(frameControlHBox)
self.segmentationVBoxLayout.addWidget(self.seedBoxesGroup)
# #Set Group
self.segmentationGroupBox.setLayout(self.segmentationVBoxLayout)
parametersFormLayout.addRow(self.segmentationGroupBox)
#
# Processing Button
#
self.extractButton = qt.QPushButton("Apply Segmentation")
self.extractButton.toolTip = "Run the algorithm."
# self.extractButton.enabled = False
parametersFormLayout.addRow(self.extractButton)
# connections
self.extractButton.connect('clicked(bool)', self.onExtractButton)
self.takeImageButton.connect('clicked(bool)', self.onTakeImageButton)
self.outputSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelectWorkingImage)
self.processingSelector.connect('currentIndexChanged(QString)',
self.onProcessing)
# self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)', self.seedFiducialsNodeSelector, 'setMRMLScene(vtkMRMLScene*)')
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
#
# the I/O panel
#
inputsCollapsibleButton = ctk.ctkCollapsibleButton()
inputsCollapsibleButton.text = "Inputs"
self.layout.addWidget(inputsCollapsibleButton)
inputsFormLayout = qt.QFormLayout(inputsCollapsibleButton)
# 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
inputsFormLayout.addRow("Input Volume:", self.inputVolumeNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.inputVolumeNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
self.inputVolumeNodeSelector.connect(
'currentNodeChanged(vtkMRMLNode*)', self.onInputVolumeChanged)
# vesselnessVolume selector
self.vesselnessVolumeNodeSelector = slicer.qMRMLNodeComboBox()
self.vesselnessVolumeNodeSelector.objectName = 'vesselnessVolumeNodeSelector'
self.vesselnessVolumeNodeSelector.toolTip = "Select the input vesselness volume."
self.vesselnessVolumeNodeSelector.nodeTypes = [
'vtkMRMLScalarVolumeNode'
]
self.vesselnessVolumeNodeSelector.noneEnabled = True
self.vesselnessVolumeNodeSelector.addEnabled = False
self.vesselnessVolumeNodeSelector.removeEnabled = False
inputsFormLayout.addRow("Vesselness Volume:",
self.vesselnessVolumeNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.vesselnessVolumeNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
self.vesselnessVolumeNodeSelector.connect(
'currentNodeChanged(vtkMRMLNode*)', self.onVesselnessVolumeChanged)
self.vesselnessVolumeNodeSelector.setCurrentNode(None)
# seed selector
self.seedFiducialsNodeSelector = slicer.qSlicerSimpleMarkupsWidget()
self.seedFiducialsNodeSelector.objectName = 'seedFiducialsNodeSelector'
self.seedFiducialsNodeSelector.toolTip = "Select start and end point of the vessel branch. Only the first and last point in the list are used."
self.seedFiducialsNodeSelector.defaultNodeColor = qt.QColor(
0, 0, 255) # blue
self.seedFiducialsNodeSelector.jumpToSliceEnabled = True
self.seedFiducialsNodeSelector.markupsPlaceWidget(
).placeMultipleMarkups = slicer.qSlicerMarkupsPlaceWidget.ForcePlaceMultipleMarkups
self.seedFiducialsNodeSelector.setNodeBaseName("seeds")
self.seedFiducialsNodeSelector.markupsSelectorComboBox(
).baseName = "Seeds"
self.seedFiducialsNodeSelector.markupsSelectorComboBox(
).noneEnabled = False
self.seedFiducialsNodeSelector.markupsSelectorComboBox(
).removeEnabled = True
inputsFormLayout.addRow("Seeds:", self.seedFiducialsNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.seedFiducialsNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
# stopper selector
self.stopperFiducialsNodeSelector = slicer.qSlicerSimpleMarkupsWidget()
self.stopperFiducialsNodeSelector.objectName = 'stopperFiducialsNodeSelector'
self.stopperFiducialsNodeSelector.toolTip = "(Optional) Select a hierarchy containing the fiducials to use as Stoppers. Whenever one stopper is reached, the segmentation stops."
self.stopperFiducialsNodeSelector.defaultNodeColor = qt.QColor(
0, 0, 255) # blue
self.stopperFiducialsNodeSelector.setNodeBaseName("seeds")
self.stopperFiducialsNodeSelector.tableWidget().hide()
self.stopperFiducialsNodeSelector.markupsSelectorComboBox(
).baseName = "Stoppers"
self.stopperFiducialsNodeSelector.markupsSelectorComboBox(
).noneEnabled = True
self.stopperFiducialsNodeSelector.markupsSelectorComboBox(
).removeEnabled = True
inputsFormLayout.addRow("Stoppers:", self.stopperFiducialsNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.stopperFiducialsNodeSelector,
'setMRMLScene(vtkMRMLScene*)')
#
# Outputs
#
outputsCollapsibleButton = ctk.ctkCollapsibleButton()
outputsCollapsibleButton.text = "Outputs"
self.layout.addWidget(outputsCollapsibleButton)
outputsFormLayout = qt.QFormLayout(outputsCollapsibleButton)
# outputVolume selector
self.outputVolumeNodeSelector = slicer.qMRMLNodeComboBox()
self.outputVolumeNodeSelector.toolTip = "Select the output labelmap."
self.outputVolumeNodeSelector.nodeTypes = ['vtkMRMLLabelMapVolumeNode']
self.outputVolumeNodeSelector.baseName = "LevelSetSegmentation"
self.outputVolumeNodeSelector.noneEnabled = False
self.outputVolumeNodeSelector.addEnabled = True
self.outputVolumeNodeSelector.selectNodeUponCreation = True
self.outputVolumeNodeSelector.removeEnabled = True
outputsFormLayout.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.hideChildNodeTypes = [
'vtkMRMLAnnotationNode'
] # hide all annotation nodes
self.outputModelNodeSelector.baseName = "LevelSetSegmentationModel"
self.outputModelNodeSelector.noneEnabled = False
self.outputModelNodeSelector.addEnabled = True
self.outputModelNodeSelector.selectNodeUponCreation = True
self.outputModelNodeSelector.removeEnabled = True
outputsFormLayout.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" + (' ' * 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" + (' ' * 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" + (' ' * 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" + (
' ' * 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((' ' * 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.onPreviewButtonClicked)
self.startButton.connect("clicked()", self.onStartButtonClicked)
self.inputVolumeNodeSelector.setMRMLScene(slicer.mrmlScene)
self.seedFiducialsNodeSelector.setMRMLScene(slicer.mrmlScene)
self.vesselnessVolumeNodeSelector.setMRMLScene(slicer.mrmlScene)
self.outputVolumeNodeSelector.setMRMLScene(slicer.mrmlScene)
self.outputModelNodeSelector.setMRMLScene(slicer.mrmlScene)
self.stopperFiducialsNodeSelector.setMRMLScene(slicer.mrmlScene)
# set default values
self.restoreDefaults()
self.onInputVolumeChanged()
# compress the layout
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
#
# Inputs
#
inputsCollapsibleButton = ctk.ctkCollapsibleButton()
inputsCollapsibleButton.text = "Inputs"
self.layout.addWidget(inputsCollapsibleButton)
inputsFormLayout = qt.QFormLayout(inputsCollapsibleButton)
# inputVolume selector
self.inputModelNodeSelector = slicer.qMRMLNodeComboBox()
self.inputModelNodeSelector.objectName = 'inputModelNodeSelector'
self.inputModelNodeSelector.toolTip = "Select the input model."
self.inputModelNodeSelector.nodeTypes = ['vtkMRMLModelNode']
self.inputModelNodeSelector.hideChildNodeTypes = ['vtkMRMLAnnotationNode'] # hide all annotation nodes
self.inputModelNodeSelector.noneEnabled = False
self.inputModelNodeSelector.addEnabled = False
self.inputModelNodeSelector.removeEnabled = False
inputsFormLayout.addRow("Vessel tree model:", self.inputModelNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.inputModelNodeSelector, 'setMRMLScene(vtkMRMLScene*)')
# seed selector
self.seedFiducialsNodeSelector = slicer.qSlicerSimpleMarkupsWidget()
self.seedFiducialsNodeSelector.objectName = 'seedFiducialsNodeSelector'
self.seedFiducialsNodeSelector = slicer.qSlicerSimpleMarkupsWidget()
self.seedFiducialsNodeSelector.objectName = 'seedFiducialsNodeSelector'
self.seedFiducialsNodeSelector.toolTip = "Select a fiducial to use as the origin of the Centerline."
self.seedFiducialsNodeSelector.setNodeBaseName("OriginSeed")
self.seedFiducialsNodeSelector.defaultNodeColor = qt.QColor(0,255,0)
self.seedFiducialsNodeSelector.tableWidget().hide()
self.seedFiducialsNodeSelector.markupsSelectorComboBox().noneEnabled = False
self.seedFiducialsNodeSelector.markupsPlaceWidget().placeMultipleMarkups = slicer.qSlicerMarkupsPlaceWidget.ForcePlaceSingleMarkup
inputsFormLayout.addRow("Start point:", self.seedFiducialsNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.seedFiducialsNodeSelector, 'setMRMLScene(vtkMRMLScene*)')
#
# Outputs
#
outputsCollapsibleButton = ctk.ctkCollapsibleButton()
outputsCollapsibleButton.text = "Outputs"
self.layout.addWidget(outputsCollapsibleButton)
outputsFormLayout = qt.QFormLayout(outputsCollapsibleButton)
# outputModel selector
self.outputModelNodeSelector = slicer.qMRMLNodeComboBox()
self.outputModelNodeSelector.objectName = 'outputModelNodeSelector'
self.outputModelNodeSelector.toolTip = "Select the output model for the Centerlines."
self.outputModelNodeSelector.nodeTypes = ['vtkMRMLModelNode']
self.outputModelNodeSelector.baseName = "CenterlineComputationModel"
self.outputModelNodeSelector.hideChildNodeTypes = ['vtkMRMLAnnotationNode'] # hide all annotation nodes
self.outputModelNodeSelector.noneEnabled = True
self.outputModelNodeSelector.noneDisplay = "Create new model"
self.outputModelNodeSelector.addEnabled = True
self.outputModelNodeSelector.selectNodeUponCreation = True
self.outputModelNodeSelector.removeEnabled = True
outputsFormLayout.addRow("Centerline model:", self.outputModelNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.outputModelNodeSelector, 'setMRMLScene(vtkMRMLScene*)')
self.outputEndPointsNodeSelector = slicer.qMRMLNodeComboBox()
self.outputEndPointsNodeSelector.objectName = 'outputEndPointsNodeSelector'
self.outputEndPointsNodeSelector.toolTip = "Select the output model for the Centerlines."
self.outputEndPointsNodeSelector.nodeTypes = ['vtkMRMLMarkupsFiducialNode']
self.outputEndPointsNodeSelector.baseName = "Centerline endpoints"
self.outputEndPointsNodeSelector.noneEnabled = True
self.outputEndPointsNodeSelector.noneDisplay = "Create new markups fiducial"
self.outputEndPointsNodeSelector.addEnabled = True
self.outputEndPointsNodeSelector.selectNodeUponCreation = True
self.outputEndPointsNodeSelector.removeEnabled = True
outputsFormLayout.addRow("Centerline endpoints:", self.outputEndPointsNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.outputEndPointsNodeSelector, 'setMRMLScene(vtkMRMLScene*)')
# voronoiModel selector
self.voronoiModelNodeSelector = slicer.qMRMLNodeComboBox()
self.voronoiModelNodeSelector.objectName = 'voronoiModelNodeSelector'
self.voronoiModelNodeSelector.toolTip = "Select the output model for the Voronoi Diagram."
self.voronoiModelNodeSelector.nodeTypes = ['vtkMRMLModelNode']
self.voronoiModelNodeSelector.baseName = "VoronoiModel"
self.voronoiModelNodeSelector.hideChildNodeTypes = ['vtkMRMLAnnotationNode'] # hide all annotation nodes
self.voronoiModelNodeSelector.noneEnabled = True
self.voronoiModelNodeSelector.addEnabled = True
self.voronoiModelNodeSelector.selectNodeUponCreation = True
self.voronoiModelNodeSelector.removeEnabled = True
outputsFormLayout.addRow("Voronoi Model:", self.voronoiModelNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.voronoiModelNodeSelector, 'setMRMLScene(vtkMRMLScene*)')
#
# Reset, preview and apply buttons
#
self.buttonBox = qt.QDialogButtonBox()
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.previewButton.connect("clicked()", self.onPreviewButtonClicked)
self.startButton.connect("clicked()", self.onStartButtonClicked)
self.inputModelNodeSelector.setMRMLScene(slicer.mrmlScene)
self.seedFiducialsNodeSelector.setMRMLScene(slicer.mrmlScene)
self.outputModelNodeSelector.setMRMLScene(slicer.mrmlScene)
self.outputEndPointsNodeSelector.setMRMLScene(slicer.mrmlScene)
self.voronoiModelNodeSelector.setMRMLScene(slicer.mrmlScene)
# compress the layout
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
self.optionalInputSelector = slicer.qMRMLNodeComboBox()
self.optionalInputSelector.nodeTypes = ["vtkMRMLModelNode"]
self.optionalInputSelector.selectNodeUponCreation = True
self.optionalInputSelector.addEnabled = False
self.optionalInputSelector.removeEnabled = False
self.optionalInputSelector.noneEnabled = True
self.optionalInputSelector.showHidden = False
self.optionalInputSelector.showChildNodeTypes = False
self.optionalInputSelector.setMRMLScene(slicer.mrmlScene)
self.optionalInputSelector.setToolTip("Pick the input to the algorithm.")
parametersFormLayout.addRow("Input Initial (Optional): ", self.optionalInputSelector)
#input model selector
self.inputModelSelector = slicer.qMRMLNodeComboBox()
self.inputModelSelector.nodeTypes = [ "vtkMRMLModelNode" ]
self.inputModelSelector.selectNodeUponCreation = True
self.inputModelSelector.addEnabled = False
self.inputModelSelector.removeEnabled = False
self.inputModelSelector.noneEnabled = False
self.inputModelSelector.showHidden = False
self.inputModelSelector.showChildNodeTypes = False
self.inputModelSelector.setMRMLScene( slicer.mrmlScene )
self.inputModelSelector.setToolTip( "Pick the input to the algorithm." )
parametersFormLayout.addRow("Input Model: ", self.inputModelSelector)
#input left Fiducal selector
self.inputLFiducialSelector = slicer.qSlicerSimpleMarkupsWidget()
self.inputLFiducialSelector.tableWidget().hide()
self.inputLFiducialSelector.setMRMLScene(slicer.mrmlScene)
self.inputLFiducialSelector.setToolTip("Pick the fiducials to define the left breast region of interest.")
self.inputLFiducialSelector.setNodeBaseName ("LeftFiducials")
parametersFormLayout.addRow("Left fiducials: ", self.inputLFiducialSelector)
# Enable place multiple markups by default
placeWidget = self.inputLFiducialSelector.markupsPlaceWidget()
placeWidget.placeMultipleMarkups = slicer.qSlicerMarkupsPlaceWidget.ForcePlaceMultipleMarkups
placeWidget.placeModeEnabled = False
placeWidget.placeModeEnabled = True
# input right Fiducal selector
self.inputRFiducialSelector = slicer.qSlicerSimpleMarkupsWidget()
self.inputRFiducialSelector.tableWidget().hide()
self.inputRFiducialSelector.setMRMLScene(slicer.mrmlScene)
self.inputRFiducialSelector.setToolTip("Pick the fiducials to define the right breast region of interest.")
self.inputRFiducialSelector.setNodeBaseName("RightFiducials")
parametersFormLayout.addRow("Right fiducials: ", self.inputRFiducialSelector)
placeWidget = self.inputRFiducialSelector.markupsPlaceWidget()
placeWidget.placeMultipleMarkups = slicer.qSlicerMarkupsPlaceWidget.ForcePlaceMultipleMarkups
placeWidget.placeModeEnabled = False
placeWidget.placeModeEnabled = True
self.applyButton = qt.QPushButton("Apply")
self.applyButton.enabled = False
parametersFormLayout.addRow("Breast Volume Computations", self.applyButton)
# Volume and distance Labels
self.VolumeLabelLeft = qt.QLabel()
self.VolumeLabelLeft.setText("Volume in cc")
parametersFormLayout.addRow("Left Breast Volume: ", self.VolumeLabelLeft)
self.VolumeLabelRight = qt.QLabel()
self.VolumeLabelRight.setText("Volume in cc")
parametersFormLayout.addRow("Right Breast Volume: ", self.VolumeLabelRight)
self.VolumeLabelDifference = qt.QLabel()
self.VolumeLabelDifference.setText("Volume Difference in cc")
parametersFormLayout.addRow("Breast Volume Difference: ", self.VolumeLabelDifference)
self.MeanDistanceLabel = qt.QLabel()
self.MeanDistanceLabel.setText("Mean distance in mm")
parametersFormLayout.addRow("Mean Distance After Registration: ", self.MeanDistanceLabel)
# Checkboxes for different module input
self.noBreastCheck = qt.QCheckBox("")
self.noBreastCheck.setCheckState(False)
parametersFormLayout.addRow("Check to create torso mesh (No breast): ", self.noBreastCheck)
self.infoLabel = qt.QLabel()
self.infoLabel.setText("")
parametersFormLayout.addRow("Please see documentation for examples of the below check box use", self.infoLabel)
self.reverseNormalCheckL = qt.QCheckBox("")
self.reverseNormalCheckL.setCheckState(False)
parametersFormLayout.addRow("Check to reverse normal of left breast: ", self.reverseNormalCheckL)
self.reverseNormalCheckR = qt.QCheckBox("")
self.reverseNormalCheckR.setCheckState(False)
parametersFormLayout.addRow("Check to reverse normal of right breast: ", self.reverseNormalCheckR)
self.setInSideOutCheckL = qt.QCheckBox("")
self.setInSideOutCheckL.setCheckState(False)
parametersFormLayout.addRow("Check to set clip function to inside out of left breast: ", self.setInSideOutCheckL)
self.setInSideOutCheckR = qt.QCheckBox("")
self.setInSideOutCheckR.setCheckState(False)
parametersFormLayout.addRow("Check to set clip function to inside out of right breast: ", self.setInSideOutCheckR)
# connections
self.optionalInputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.inputModelSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.inputLFiducialSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.inputRFiducialSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.applyButton.connect('clicked(bool)', self.onApplyButton)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onSelect()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# Parameters Area
#
# self.segVolumeTotalNode = slicer.vtkMRMLModelHierarchyNode()
# self.segVolumeTotalNode.SetName('segVolumeTotalNode')
# self.segVolumeTotalNode.SetSingletonTag('segVolumeTotalNode')
# # self.segVolumeTotalNode.HideFromEditorsOn()
# slicer.mrmlScene.AddNode(self.segVolumeTotalNode)
self.segVolumeTotalNode = []
self.segCombineVol = None
inputCollapsibleButton = ctk.ctkCollapsibleButton()
inputCollapsibleButton.text = "Input Volumes"
self.layout.addWidget(inputCollapsibleButton)
self.pathText = qt.QLineEdit()
# self.__fixedShrinkFactor.setText("16, 16, 16")
self.pathText.setToolTip('Specify output path')
self.layout.addWidget(self.pathText)
# Layout within the dummy collapsible button
inputFormLayout = qt.QFormLayout(inputCollapsibleButton)
loadSpineVolumeButton = qt.QPushButton('Load spine volume')
loadSpineVolumeButton.connect('clicked()', self.loadVolume)
inputFormLayout.addRow('Load spine volume', loadSpineVolumeButton)
loadSegVolumeButton = qt.QPushButton('Load segmentation volume')
loadSegVolumeButton.connect('clicked()', self.loadVolume)
inputFormLayout.addRow('Load segmentation volume', loadSegVolumeButton)
# input volume selector
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.inputSelector.selectNodeUponCreation = True
self.inputSelector.addEnabled = False
self.inputSelector.removeEnabled = False
self.inputSelector.noneEnabled = False
self.inputSelector.showHidden = False
self.inputSelector.showChildNodeTypes = False
self.inputSelector.setMRMLScene(slicer.mrmlScene)
self.inputSelector.setToolTip("Select the CT spine volume.")
inputFormLayout.addRow("Input Volume: ", self.inputSelector)
#
# output volume selector
#
self.segmentationSelector = slicer.qMRMLNodeComboBox()
self.segmentationSelector.nodeTypes = ["vtkMRMLLabelMapVolumeNode"]
self.segmentationSelector.selectNodeUponCreation = True
self.segmentationSelector.addEnabled = True
self.segmentationSelector.removeEnabled = True
self.segmentationSelector.noneEnabled = True
self.segmentationSelector.showHidden = False
self.segmentationSelector.showChildNodeTypes = False
self.segmentationSelector.setMRMLScene(slicer.mrmlScene)
self.segmentationSelector.setToolTip(
"Select the ground truth segmentation "
"(if any exists) to compare with prediction.")
inputFormLayout.addRow("Segmentation Volume: ",
self.segmentationSelector)
cropCollapsibleButton = ctk.ctkCollapsibleButton()
cropCollapsibleButton.text = "Select Vertebrae"
self.layout.addWidget(cropCollapsibleButton)
# Layout within the dummy collapsible button
cropFormLayout = qt.QFormLayout(cropCollapsibleButton)
markerTable = slicer.qSlicerSimpleMarkupsWidget()
self.markerTableSelector = markerTable.MarkupsFiducialNodeComboBox
self.markerTableSelector.selectNodeUponCreation = False
self.markerTableSelector.addEnabled = True
self.markerTableSelector.removeEnabled = True
self.markerTableSelector.noneEnabled = True
self.markerTableSelector.renameEnabled = False
markerTable.setMRMLScene(slicer.mrmlScene)
markerTable.setCurrentNode(
slicer.mrmlScene.GetNodeByID(
slicer.modules.markups.logic().AddNewFiducialNode()))
markerTable.show()
cropFormLayout.addWidget(markerTable)
font = qt.QFont()
font.setBold(True)
# Segment vertebrae button
self.segmentationButton = qt.QPushButton('Segment Vertebrae')
self.segmentationButton.setFont(font)
self.segmentationButton.toolTip = 'Segment the selected vertebrae'
self.segmentationButton.enabled = False
# Segmentation button connections
self.segmentationButton.connect('clicked(bool)', self.onSegmentButton)
self.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
self.markerTableSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
self.layout.addWidget(self.segmentationButton)
# Combine Segmentations
combineCollapsibleButton = ctk.ctkCollapsibleButton()
combineCollapsibleButton.text = "Combine Segmentations"
self.layout.addWidget(combineCollapsibleButton)
# Layout within the dummy collapsible button
combineFormLayout = qt.QFormLayout(combineCollapsibleButton)
# Section to assign labels to segmentations and combine segmentations to a single volume
self.L5SegSelector = DefaultSegSelect()
self.L5SegSelector.setToolTip("Select L5 Segmentation")
combineFormLayout.addRow("L5: ", self.L5SegSelector)
# self.L5SegSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.displayLabel(self.L5SegSelector.currentNode()))
self.L5SegSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.displayLabel)
self.L4SegSelector = DefaultSegSelect()
self.L4SegSelector.setToolTip("Select L4 Segmentation")
combineFormLayout.addRow("L4: ", self.L4SegSelector)
self.L4SegSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.displayLabel)
self.L3SegSelector = DefaultSegSelect()
self.L3SegSelector.setToolTip("Select L3 Segmentation")
combineFormLayout.addRow("L3: ", self.L3SegSelector)
self.L3SegSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.displayLabel)
self.L2SegSelector = DefaultSegSelect()
self.L2SegSelector.setToolTip("Select L2 Segmentation")
combineFormLayout.addRow("L2: ", self.L2SegSelector)
self.L2SegSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.displayLabel)
self.L1SegSelector = DefaultSegSelect()
self.L1SegSelector.setToolTip("Select L1 Segmentation")
combineFormLayout.addRow("L1: ", self.L1SegSelector)
self.L1SegSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.displayLabel)
self.T12SegSelector = DefaultSegSelect()
self.T12SegSelector.setToolTip("Select T12 Segmentation")
combineFormLayout.addRow("T12: ", self.T12SegSelector)
self.T12SegSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.displayLabel)
self.T11SegSelector = DefaultSegSelect()
self.T11SegSelector.setToolTip("Select T11 Segmentation")
combineFormLayout.addRow("T11: ", self.T11SegSelector)
self.T11SegSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.displayLabel)
self.T10SegSelector = DefaultSegSelect()
self.T10SegSelector.setToolTip("Select T10 Segmentation")
combineFormLayout.addRow("T10: ", self.T10SegSelector)
self.T10SegSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.displayLabel)
self.T9SegSelector = DefaultSegSelect()
self.T9SegSelector.setToolTip("Select T9 Segmentation")
combineFormLayout.addRow("T9: ", self.T9SegSelector)
self.T9SegSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.displayLabel)
self.T8SegSelector = DefaultSegSelect()
self.T8SegSelector.setToolTip("Select T8 Segmentation")
combineFormLayout.addRow("T8: ", self.T8SegSelector)
self.T8SegSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.displayLabel)
self.T7SegSelector = DefaultSegSelect()
self.T7SegSelector.setToolTip("Select T7 Segmentation")
combineFormLayout.addRow("T7: ", self.T7SegSelector)
self.T7SegSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.displayLabel)
self.T6SegSelector = DefaultSegSelect()
self.T6SegSelector.setToolTip("Select T6 Segmentation")
combineFormLayout.addRow("T6: ", self.T6SegSelector)
self.T6SegSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.displayLabel)
self.SegSelectList = [
self.L5SegSelector,
self.L4SegSelector,
self.L3SegSelector,
self.L2SegSelector,
self.L1SegSelector,
self.T12SegSelector,
self.T11SegSelector,
self.T10SegSelector,
self.T9SegSelector,
self.T8SegSelector,
self.T7SegSelector,
self.T6SegSelector,
]
# Segmentation button connections
self.combineSegButton = qt.QPushButton('Combine Segmentations')
self.combineSegButton.toolTip = 'Combine Segmented Vertebrae'
self.combineSegButton.connect('clicked(bool)', self.onCombineSegButton)
self.combineSegButton.setFont(font)
combineFormLayout.addRow(self.combineSegButton)
# Reset segmentations and fiducial markers
self.resetSegButton = qt.QPushButton('Reset Segmentation and Markers')
self.resetSegButton.toolTip = "Reset fiducial markers and individual vertebrae segmentations"
self.resetSegButton.setFont(font)
self.resetSegButton.connect('clicked(bool)', self.onResetSegButton)
self.layout.addWidget(self.resetSegButton)
# Save segmentation button
self.saveButton = qt.QPushButton('Save')
self.saveButton.toolTip = "Save segmentation"
self.saveButton.setFont(font)
self.saveButton.connect('clicked(bool)', self.onSaveButton)
combineFormLayout.addRow(self.saveButton)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onSelect()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
#
# the I/O panel
#
inputsCollapsibleButton = ctk.ctkCollapsibleButton()
inputsCollapsibleButton.text = "Inputs"
self.layout.addWidget(inputsCollapsibleButton)
inputsFormLayout = qt.QFormLayout(inputsCollapsibleButton)
# 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
inputsFormLayout.addRow("Input Volume:", self.inputVolumeNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.inputVolumeNodeSelector, 'setMRMLScene(vtkMRMLScene*)')
self.inputVolumeNodeSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onInputVolumeChanged)
# vesselnessVolume selector
self.vesselnessVolumeNodeSelector = slicer.qMRMLNodeComboBox()
self.vesselnessVolumeNodeSelector.objectName = 'vesselnessVolumeNodeSelector'
self.vesselnessVolumeNodeSelector.toolTip = "Select the input vesselness volume."
self.vesselnessVolumeNodeSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.vesselnessVolumeNodeSelector.noneEnabled = True
self.vesselnessVolumeNodeSelector.addEnabled = False
self.vesselnessVolumeNodeSelector.removeEnabled = False
inputsFormLayout.addRow("Vesselness Volume:", self.vesselnessVolumeNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.vesselnessVolumeNodeSelector, 'setMRMLScene(vtkMRMLScene*)')
self.vesselnessVolumeNodeSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onVesselnessVolumeChanged)
self.vesselnessVolumeNodeSelector.setCurrentNode(None)
# seed selector
self.seedFiducialsNodeSelector = slicer.qSlicerSimpleMarkupsWidget()
self.seedFiducialsNodeSelector.objectName = 'seedFiducialsNodeSelector'
self.seedFiducialsNodeSelector.toolTip = "Select start and end point of the vessel branch. Only the first and last point in the list are used."
self.seedFiducialsNodeSelector.defaultNodeColor = qt.QColor(0,0,255) # blue
self.seedFiducialsNodeSelector.jumpToSliceEnabled = True
self.seedFiducialsNodeSelector.markupsPlaceWidget().placeMultipleMarkups = slicer.qSlicerMarkupsPlaceWidget.ForcePlaceMultipleMarkups
self.seedFiducialsNodeSelector.setNodeBaseName("seeds")
self.seedFiducialsNodeSelector.markupsSelectorComboBox().baseName = "Seeds"
self.seedFiducialsNodeSelector.markupsSelectorComboBox().noneEnabled = False
self.seedFiducialsNodeSelector.markupsSelectorComboBox().removeEnabled = True
inputsFormLayout.addRow("Seeds:", self.seedFiducialsNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.seedFiducialsNodeSelector, 'setMRMLScene(vtkMRMLScene*)')
# stopper selector
self.stopperFiducialsNodeSelector = slicer.qSlicerSimpleMarkupsWidget()
self.stopperFiducialsNodeSelector.objectName = 'stopperFiducialsNodeSelector'
self.stopperFiducialsNodeSelector.toolTip = "(Optional) Select a hierarchy containing the fiducials to use as Stoppers. Whenever one stopper is reached, the segmentation stops."
self.stopperFiducialsNodeSelector.defaultNodeColor = qt.QColor(0,0,255) # blue
self.stopperFiducialsNodeSelector.setNodeBaseName("seeds")
self.stopperFiducialsNodeSelector.tableWidget().hide()
self.stopperFiducialsNodeSelector.markupsSelectorComboBox().baseName = "Stoppers"
self.stopperFiducialsNodeSelector.markupsSelectorComboBox().noneEnabled = True
self.stopperFiducialsNodeSelector.markupsSelectorComboBox().removeEnabled = True
inputsFormLayout.addRow("Stoppers:", self.stopperFiducialsNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.stopperFiducialsNodeSelector, 'setMRMLScene(vtkMRMLScene*)')
#
# Outputs
#
outputsCollapsibleButton = ctk.ctkCollapsibleButton()
outputsCollapsibleButton.text = "Outputs"
self.layout.addWidget(outputsCollapsibleButton)
outputsFormLayout = qt.QFormLayout(outputsCollapsibleButton)
# outputVolume selector
self.outputVolumeNodeSelector = slicer.qMRMLNodeComboBox()
self.outputVolumeNodeSelector.toolTip = "Select the output labelmap."
self.outputVolumeNodeSelector.nodeTypes = ['vtkMRMLLabelMapVolumeNode']
self.outputVolumeNodeSelector.baseName = "LevelSetSegmentation"
self.outputVolumeNodeSelector.noneEnabled = False
self.outputVolumeNodeSelector.addEnabled = True
self.outputVolumeNodeSelector.selectNodeUponCreation = True
self.outputVolumeNodeSelector.removeEnabled = True
outputsFormLayout.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.hideChildNodeTypes = ['vtkMRMLAnnotationNode'] # hide all annotation nodes
self.outputModelNodeSelector.baseName = "LevelSetSegmentationModel"
self.outputModelNodeSelector.noneEnabled = False
self.outputModelNodeSelector.addEnabled = True
self.outputModelNodeSelector.selectNodeUponCreation = True
self.outputModelNodeSelector.removeEnabled = True
outputsFormLayout.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" + (' '*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" + (' '*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" + (' '*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" + (' '*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((' '*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.onPreviewButtonClicked)
self.startButton.connect("clicked()", self.onStartButtonClicked)
self.inputVolumeNodeSelector.setMRMLScene(slicer.mrmlScene)
self.seedFiducialsNodeSelector.setMRMLScene(slicer.mrmlScene)
self.vesselnessVolumeNodeSelector.setMRMLScene(slicer.mrmlScene)
self.outputVolumeNodeSelector.setMRMLScene(slicer.mrmlScene)
self.outputModelNodeSelector.setMRMLScene(slicer.mrmlScene)
self.stopperFiducialsNodeSelector.setMRMLScene(slicer.mrmlScene)
# set default values
self.restoreDefaults()
self.onInputVolumeChanged()
# compress the layout
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.logic = ProstateReportingLogic()
self.uiLoader = qt.QUiLoader()
self.patientName = None
self.lesionList = None
self.lesionListTags = []
# Instantiate and connect widgets ...
# Load UI files
self.scansWidget = self.loadUI('Scans')
self.sectorMapWidget = self.loadUI('SectorMap')
self.assessmentWidget = self.loadUI('Assessment')
self.reportWidget = self.loadUI('Report')
# Set up the sector relationships
self.SectorMap = None
self.initSectorMap()
#
# Volumes Area
#
scansCollapsibleButton = ctk.ctkCollapsibleButton()
scansCollapsibleButton.text = "Patient Scans"
self.layout.addWidget(scansCollapsibleButton)
# Layout within the dummy collapsible button
scansLayout = qt.QVBoxLayout(scansCollapsibleButton)
# Patient name
patientNameLayout = qt.QHBoxLayout()
patientNameLayout.addWidget(qt.QLabel("Patient Name:"))
self.patientNameLabel = qt.QLabel("")
patientNameLayout.addWidget(self.patientNameLabel)
scansLayout.addLayout(patientNameLayout)
# Scans
scansLayout.addWidget(self.scansWidget)
self.t2VolumeSelector = self.logic.getChild(self.scansWidget,
't2VolumeSelector')
self.t2VolumeSelector.setMRMLScene(slicer.mrmlScene)
self.t2ScanDateLabel = self.logic.getChild(self.scansWidget,
't2ScanDateLabel')
self.t1VolumeSelector = self.logic.getChild(self.scansWidget,
't1VolumeSelector')
self.t1VolumeSelector.setMRMLScene(slicer.mrmlScene)
self.t1ScanDateLabel = self.logic.getChild(self.scansWidget,
't1ScanDateLabel')
self.dwiVolumeSelector = self.logic.getChild(self.scansWidget,
'dwiVolumeSelector')
self.dwiVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.dwiScanDateLabel = self.logic.getChild(self.scansWidget,
'dwiScanDateLabel')
self.adcVolumeSelector = self.logic.getChild(self.scansWidget,
'adcVolumeSelector')
self.adcVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.adcScanDateLabel = self.logic.getChild(self.scansWidget,
'adcScanDateLabel')
self.dceVolumeSelector = self.logic.getChild(self.scansWidget,
'dceVolumeSelector')
self.dceVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.dceScanDateLabel = self.logic.getChild(self.scansWidget,
'dceScanDateLabel')
#
# Lesions Area
#
lesionsCollapsibleButton = ctk.ctkCollapsibleButton()
lesionsCollapsibleButton.text = "Lesions"
self.layout.addWidget(lesionsCollapsibleButton)
# Layout within the dummy collapsible button
lesionsLayout = qt.QVBoxLayout(lesionsCollapsibleButton)
# Sector map
sectorMapLabel = qt.QLabel()
sectorMapLabel.setText("Prostate sector:")
lesionsLayout.addWidget(sectorMapLabel)
lesionsLayout.addWidget(self.sectorMapWidget)
# Lesion target list
if 0:
self.targetListSelector = slicer.qMRMLNodeComboBox()
self.targetListSelector.nodeTypes = ["vtkMRMLMarkupsFiducialNode"]
self.targetListSelector.selectNodeUponCreation = True
self.targetListSelector.addEnabled = True
self.targetListSelector.removeEnabled = False
self.targetListSelector.noneEnabled = False
self.targetListSelector.showHidden = False
self.targetListSelector.showChildNodeTypes = False
self.targetListSelector.setMRMLScene(slicer.mrmlScene)
self.targetListSelector.setToolTip(
"Pick the list of target lesion fiducials.")
lesionsLayout.addWidget(self.targetListSelector)
# Add a lesion, will create a list if necessary. Will name it according
# to sector selection
self.addLesionButton = qt.QPushButton()
self.addLesionButton.text = 'Add Lesion'
lesionsLayout.addWidget(self.addLesionButton)
# show the lesions in a table
self.targetTableWidget = slicer.qSlicerSimpleMarkupsWidget()
self.targetTableWidget.setMRMLScene(slicer.mrmlScene)
lesionsLayout.addWidget(self.targetTableWidget)
self.targetListSelector = self.logic.getChild(
self.targetTableWidget, "MarkupsFiducialNodeComboBox")
# hide the place button as want to rename fids when adding
placeWidget = self.logic.getChild(self.targetTableWidget,
"PlaceButton")
placeWidget.hide()
#
# Assessment Area
#
assessmentCollapsibleButton = ctk.ctkCollapsibleButton()
assessmentCollapsibleButton.text = "Assessment"
self.layout.addWidget(assessmentCollapsibleButton)
# Layout within the dummy collapsible button
assessmentLayout = qt.QVBoxLayout(assessmentCollapsibleButton)
assessmentLayout.addWidget(self.assessmentWidget)
self.assessmentComboBox = self.logic.getChild(self.assessmentWidget,
"assessmentComboBox")
#
# Report Area
#
self.reportButton = qt.QPushButton()
self.reportButton.setText("Report")
self.layout.addWidget(self.reportButton)
# get the report widgets need to fill in
self.reportPatientName = self.logic.getChild(self.reportWidget,
"patientNameLabel")
self.reportScans = self.logic.getChild(self.reportWidget,
"patientScansTextEdit")
self.reportLesions = self.logic.getChild(self.reportWidget,
"patientLesionsTextEdit")
self.reportAssessment = self.logic.getChild(
self.reportWidget, "patientAssessmentTextEdit")
self.reportNotes = self.logic.getChild(self.reportWidget,
"patientNotesTextEdit")
self.reportSave = self.logic.getChild(self.reportWidget,
"savePushButton")
self.reportCancel = self.logic.getChild(self.reportWidget,
"cancelPushButton")
#
# Set up Connections
#
# Volumes
self.t2VolumeSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelectT2)
self.t1VolumeSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelectT1)
self.dwiVolumeSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelectDWI)
self.adcVolumeSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelectADC)
self.dceVolumeSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelectDCE)
# Lesions
self.targetListSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelectTargets)
# Sector map
self.LRComboBox.connect("currentIndexChanged(int)",
self.onSectorLRChanged)
self.ZoneComboBox.connect("currentIndexChanged(int)",
self.onSectorZoneChanged)
self.GlandComboBox.connect("currentIndexChanged(int)",
self.onSectorGlandChanged)
self.APComboBox.connect("currentIndexChanged(int)",
self.onSectorAPChanged)
self.addLesionButton.connect('clicked(bool)', self.onAddLesion)
# Report
self.reportButton.connect('clicked(bool)', self.onReportButton)
self.reportSave.connect('clicked(bool)', self.onReportSave)
self.reportCancel.connect('clicked(bool)', self.onReportCancel)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
try:
import vtkvmtkSegmentationPython as vtkvmtkSegmentation
except ImportError:
self.layout.addWidget(qt.QLabel("Failed to load VMTK libraries"))
return
#
# 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."
self.inputVolumeNodeSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.inputVolumeNodeSelector.noneEnabled = False
self.inputVolumeNodeSelector.addEnabled = False
self.inputVolumeNodeSelector.removeEnabled = False
ioFormLayout.addRow("Input Volume:", self.inputVolumeNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.inputVolumeNodeSelector, 'setMRMLScene(vtkMRMLScene*)')
# seed selector
self.seedFiducialsNodeSelector = slicer.qSlicerSimpleMarkupsWidget()
self.seedFiducialsNodeSelector.objectName = 'seedFiducialsNodeSelector'
self.seedFiducialsNodeSelector = slicer.qSlicerSimpleMarkupsWidget()
self.seedFiducialsNodeSelector.objectName = 'seedFiducialsNodeSelector'
self.seedFiducialsNodeSelector.toolTip = "Select a point in the largest vessel. Preview will be shown around this point. This is point is also used for determining maximum vessel diameter if automatic filtering parameters computation is enabled."
self.seedFiducialsNodeSelector.setNodeBaseName("DiameterSeed")
self.seedFiducialsNodeSelector.tableWidget().hide()
self.seedFiducialsNodeSelector.defaultNodeColor = qt.QColor(255,0,0) # red
self.seedFiducialsNodeSelector.markupsSelectorComboBox().noneEnabled = False
self.seedFiducialsNodeSelector.markupsPlaceWidget().placeMultipleMarkups = slicer.qSlicerMarkupsPlaceWidget.ForcePlaceSingleMarkup
ioFormLayout.addRow("Seed point:", self.seedFiducialsNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.seedFiducialsNodeSelector, 'setMRMLScene(vtkMRMLScene*)')
# outputVolume selector
self.outputVolumeNodeSelector = slicer.qMRMLNodeComboBox()
self.outputVolumeNodeSelector.toolTip = "Select the output labelmap."
self.outputVolumeNodeSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.outputVolumeNodeSelector.baseName = "VesselnessFiltered"
self.outputVolumeNodeSelector.noneEnabled = True
self.outputVolumeNodeSelector.noneDisplay = "Create new volume"
self.outputVolumeNodeSelector.addEnabled = True
self.outputVolumeNodeSelector.selectNodeUponCreation = True
self.outputVolumeNodeSelector.removeEnabled = True
ioFormLayout.addRow("Output Volume:", self.outputVolumeNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.outputVolumeNodeSelector, 'setMRMLScene(vtkMRMLScene*)')
#
# Advanced area
#
self.advancedCollapsibleButton = ctk.ctkCollapsibleButton()
self.advancedCollapsibleButton.text = "Advanced"
self.advancedCollapsibleButton.collapsed = True
self.layout.addWidget(self.advancedCollapsibleButton)
advancedFormLayout = qt.QFormLayout(self.advancedCollapsibleButton)
# previewVolume selector
self.previewVolumeNodeSelector = slicer.qMRMLNodeComboBox()
self.previewVolumeNodeSelector.toolTip = "Select the preview volume."
self.previewVolumeNodeSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
self.previewVolumeNodeSelector.baseName = "VesselnessPreview"
self.previewVolumeNodeSelector.noneEnabled = True
self.previewVolumeNodeSelector.noneDisplay = "Create new volume"
self.previewVolumeNodeSelector.addEnabled = True
self.previewVolumeNodeSelector.selectNodeUponCreation = True
self.previewVolumeNodeSelector.removeEnabled = True
advancedFormLayout.addRow("Preview volume:", self.previewVolumeNodeSelector)
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.previewVolumeNodeSelector, 'setMRMLScene(vtkMRMLScene*)')
self.displayThresholdSlider = ctk.ctkSliderWidget()
self.displayThresholdSlider.decimals = 2
self.displayThresholdSlider.minimum = 0
self.displayThresholdSlider.maximum = 1.0
self.displayThresholdSlider.singleStep = 0.01
self.displayThresholdSlider.toolTip = "Voxels below this vesselness value will be hidden. It does not change the voxel values, only how the vesselness volume is displayed."
advancedFormLayout.addRow("Display threshold:", self.displayThresholdSlider)
self.displayThresholdSlider.connect('valueChanged(double)', self.onDisplayThresholdChanged)
self.previewVolumeDiameterVoxelSlider = ctk.ctkSliderWidget()
self.previewVolumeDiameterVoxelSlider.decimals = 0
self.previewVolumeDiameterVoxelSlider.minimum = 10
self.previewVolumeDiameterVoxelSlider.maximum = 200
self.previewVolumeDiameterVoxelSlider.singleStep = 5
self.previewVolumeDiameterVoxelSlider.suffix = " voxels"
self.previewVolumeDiameterVoxelSlider.toolTip = "Diameter of the preview area in voxels."
advancedFormLayout.addRow("Preview volume size:", self.previewVolumeDiameterVoxelSlider)
# detect filterint parameters
self.detectPushButton = qt.QPushButton()
self.detectPushButton.text = "Compute vessel diameters and contrast from seed point"
self.detectPushButton.checkable = True
self.detectPushButton.checked = True
advancedFormLayout.addRow(self.detectPushButton)
self.detectPushButton.connect("clicked()", self.onNodeSelectionChanged)
self.minimumDiameterSpinBox = qt.QSpinBox()
self.minimumDiameterSpinBox.minimum = 1
self.minimumDiameterSpinBox.maximum = 1000
self.minimumDiameterSpinBox.singleStep = 1
self.minimumDiameterSpinBox.suffix = " voxels"
self.minimumDiameterSpinBox.enabled = False
self.minimumDiameterSpinBox.toolTip = "Tubular structures that have minimum this diameter will be enhanced."
advancedFormLayout.addRow("Minimum vessel diameter:", self.minimumDiameterSpinBox)
self.detectPushButton.connect("toggled(bool)", self.minimumDiameterSpinBox.setDisabled)
self.maximumDiameterSpinBox = qt.QSpinBox()
self.maximumDiameterSpinBox.minimum = 0
self.maximumDiameterSpinBox.maximum = 1000
self.maximumDiameterSpinBox.singleStep = 1
self.maximumDiameterSpinBox.suffix = " voxels"
self.maximumDiameterSpinBox.enabled = False
self.maximumDiameterSpinBox.toolTip = "Tubular structures that have maximum this diameter will be enhanced."
advancedFormLayout.addRow("Maximum vessel diameter:", self.maximumDiameterSpinBox)
self.detectPushButton.connect("toggled(bool)", self.maximumDiameterSpinBox.setDisabled)
self.contrastSlider = ctk.ctkSliderWidget()
self.contrastSlider.decimals = 0
self.contrastSlider.minimum = 0
self.contrastSlider.maximum = 500
self.contrastSlider.singleStep = 10
self.contrastSlider.enabled = False
self.contrastSlider.toolTip = "If the intensity contrast in the input image between vessel and background is high, choose a high value else choose a low value."
advancedFormLayout.addRow("Vessel contrast:", self.contrastSlider)
self.detectPushButton.connect("toggled(bool)", self.contrastSlider.setDisabled)
self.suppressPlatesSlider = ctk.ctkSliderWidget()
self.suppressPlatesSlider.decimals = 0
self.suppressPlatesSlider.minimum = 0
self.suppressPlatesSlider.maximum = 100
self.suppressPlatesSlider.singleStep = 1
self.suppressPlatesSlider.suffix = " %"
self.suppressPlatesSlider.toolTip = "A higher value filters out more plate-like structures."
advancedFormLayout.addRow("Suppress plates:", self.suppressPlatesSlider)
self.suppressBlobsSlider = ctk.ctkSliderWidget()
self.suppressBlobsSlider.decimals = 0
self.suppressBlobsSlider.minimum = 0
self.suppressBlobsSlider.maximum = 100
self.suppressBlobsSlider.singleStep = 1
self.suppressBlobsSlider.suffix = " %"
self.suppressBlobsSlider.toolTip = "A higher value filters out more blob-like structures."
advancedFormLayout.addRow("Suppress blobs:", self.suppressBlobsSlider)
#
# 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.startButton = self.buttonBox.addButton(self.buttonBox.Apply)
self.startButton.setIcon(qt.QIcon())
self.startButton.text = "Start"
self.startButton.enabled = False
self.layout.addWidget(self.buttonBox)
self.resetButton.connect("clicked()", self.restoreDefaults)
self.previewButton.connect("clicked()", self.onPreviewButtonClicked)
self.startButton.connect("clicked()", self.onStartButtonClicked)
self.inputVolumeNodeSelector.setMRMLScene(slicer.mrmlScene)
self.seedFiducialsNodeSelector.setMRMLScene(slicer.mrmlScene)
self.outputVolumeNodeSelector.setMRMLScene(slicer.mrmlScene)
self.previewVolumeNodeSelector.setMRMLScene(slicer.mrmlScene)
self.inputVolumeNodeSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onNodeSelectionChanged)
self.seedFiducialsNodeSelector.markupsSelectorComboBox().connect("currentNodeChanged(vtkMRMLNode*)", self.onNodeSelectionChanged)
self.seedFiducialsNodeSelector.connect("updateFinished()", self.onNodeSelectionChanged)
# set default values
self.restoreDefaults()
self.onNodeSelectionChanged()
# compress the layout
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.logic = LineProfileLogic()
# Instantiate and connect widgets ...
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# input volume selector
#
self.inputVolumeSelector = slicer.qMRMLNodeComboBox()
self.inputVolumeSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.inputVolumeSelector.selectNodeUponCreation = True
self.inputVolumeSelector.addEnabled = False
self.inputVolumeSelector.removeEnabled = False
self.inputVolumeSelector.noneEnabled = False
self.inputVolumeSelector.showHidden = False
self.inputVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.inputVolumeSelector.setToolTip("Pick the input to the algorithm which will be sampled along the line.")
parametersFormLayout.addRow("Input Volume: ", self.inputVolumeSelector)
#
# input line selector
#
self.inputLineWidget = slicer.qSlicerSimpleMarkupsWidget()
self.inputLineSelector = self.inputLineWidget.markupsSelectorComboBox()
self.inputLineSelector.nodeTypes = ["vtkMRMLMarkupsLineNode", "vtkMRMLMarkupsCurveNode"]
self.inputLineSelector.selectNodeUponCreation = True
self.inputLineSelector.addEnabled = True
self.inputLineSelector.removeEnabled = True
self.inputLineSelector.noneEnabled = False
self.inputLineSelector.showHidden = False
self.inputLineWidget.tableWidget().setVisible(False)
self.inputLineWidget.setDefaultNodeColor(qt.QColor().fromRgbF(1,1,0))
self.inputLineWidget.setMRMLScene( slicer.mrmlScene )
self.inputLineWidget.setToolTip("Pick line or curve to take image samples along.")
parametersFormLayout.addRow("Input line: ", self.inputLineWidget)
#
# output table selector
#
self.outputTableSelector = slicer.qMRMLNodeComboBox()
self.outputTableSelector.nodeTypes = ["vtkMRMLTableNode"]
self.outputTableSelector.addEnabled = True
self.outputTableSelector.renameEnabled = True
self.outputTableSelector.removeEnabled = True
self.outputTableSelector.noneEnabled = True
self.outputTableSelector.showHidden = False
self.outputTableSelector.setMRMLScene( slicer.mrmlScene )
self.outputTableSelector.setToolTip( "Pick the output table to the algorithm." )
parametersFormLayout.addRow("Output table: ", self.outputTableSelector)
#
# output plot selector
#
self.outputPlotSeriesSelector = slicer.qMRMLNodeComboBox()
self.outputPlotSeriesSelector.nodeTypes = ["vtkMRMLPlotSeriesNode"]
self.outputPlotSeriesSelector.addEnabled = True
self.outputPlotSeriesSelector.renameEnabled = True
self.outputPlotSeriesSelector.removeEnabled = True
self.outputPlotSeriesSelector.noneEnabled = True
self.outputPlotSeriesSelector.showHidden = False
self.outputPlotSeriesSelector.setMRMLScene( slicer.mrmlScene )
self.outputPlotSeriesSelector.setToolTip( "Pick the output plot series to the algorithm." )
parametersFormLayout.addRow("Output plot series: ", self.outputPlotSeriesSelector)
#
# line resolution
#
self.lineResolutionSliderWidget = ctk.ctkSliderWidget()
self.lineResolutionSliderWidget.singleStep = 1
self.lineResolutionSliderWidget.minimum = 2
self.lineResolutionSliderWidget.maximum = 1000
self.lineResolutionSliderWidget.value = 100
self.lineResolutionSliderWidget.decimals = 0
self.lineResolutionSliderWidget.setToolTip("Number of points to sample along the line.")
parametersFormLayout.addRow("Line resolution", self.lineResolutionSliderWidget)
#
# Proportional percent distance from start
#
self.plotProportionalDistanceCheckBox = qt.QCheckBox(" ")
self.plotProportionalDistanceCheckBox.checked = False
self.plotProportionalDistanceCheckBox.setToolTip("If checked, distance along the line in plot is not absolute, but the percent distance from the start of the line.")
parametersFormLayout.addRow("Proportional distance (%):", self.plotProportionalDistanceCheckBox)
#
# Apply Button
#
self.applyButton = ctk.ctkCheckablePushButton()
self.applyButton.text = "Compute intensity profile"
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = False
self.applyButton.checkable = False
self.applyButton.checkBoxControlsButtonToggleState = True
parametersFormLayout.addRow(self.applyButton)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.applyButton.connect('checkBoxToggled(bool)', self.onApplyButtonToggled)
self.inputVolumeSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelectNode)
self.inputLineSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelectNode)
self.outputPlotSeriesSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelectNode)
self.outputTableSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelectNode)
self.lineResolutionSliderWidget.connect("valueChanged(double)", self.onSetLineResolution)
self.plotProportionalDistanceCheckBox.connect("clicked()", self.onProportionalDistance)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onSelectNode()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# Parameters Area
#
inputCollapsibleButton = ctk.ctkCollapsibleButton()
inputCollapsibleButton.text = "Input Volumes"
self.layout.addWidget(inputCollapsibleButton)
# Layout within the dummy collapsible button
inputFormLayout = qt.QFormLayout(inputCollapsibleButton)
loadSpineVolumeButton = qt.QPushButton('Load spine volume')
loadSpineVolumeButton.connect('clicked()', self.loadVolume)
inputFormLayout.addRow('Load spine volume', loadSpineVolumeButton)
loadSegVolumeButton = qt.QPushButton('Load segmentation volume')
loadSegVolumeButton.connect('clicked()', self.loadVolume)
inputFormLayout.addRow('Load segmentation volume', loadSegVolumeButton)
# TODO Add functionality so that if the segmentation is NOT imported as a label map, it is converted to one immediately
#
# input volume selector
#
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.inputSelector.selectNodeUponCreation = True
self.inputSelector.addEnabled = False
self.inputSelector.removeEnabled = False
self.inputSelector.noneEnabled = False
self.inputSelector.showHidden = False
self.inputSelector.showChildNodeTypes = False
self.inputSelector.setMRMLScene(slicer.mrmlScene)
self.inputSelector.setToolTip("Select the CT spine volume.")
inputFormLayout.addRow("Input Volume: ", self.inputSelector)
#
# output volume selector
#
self.segmentationSelector = slicer.qMRMLNodeComboBox()
self.segmentationSelector.nodeTypes = ["vtkMRMLLabelMapVolumeNode"]
self.segmentationSelector.selectNodeUponCreation = True
self.segmentationSelector.addEnabled = True
self.segmentationSelector.removeEnabled = True
self.segmentationSelector.noneEnabled = True
self.segmentationSelector.showHidden = False
self.segmentationSelector.showChildNodeTypes = False
self.segmentationSelector.setMRMLScene(slicer.mrmlScene)
self.segmentationSelector.setToolTip(
"Select the ground truth segmentation "
"(if any exists) to compare with prediction.")
inputFormLayout.addRow("Segmentation Volume: ",
self.segmentationSelector)
# TODO Add a save resampled volume
cropCollapsibleButton = ctk.ctkCollapsibleButton()
cropCollapsibleButton.text = "Select Vertebrae"
self.layout.addWidget(cropCollapsibleButton)
# Layout within the dummy collapsible button
cropFormLayout = qt.QFormLayout(cropCollapsibleButton)
markerTable = slicer.qSlicerSimpleMarkupsWidget()
self.markerTableSelector = markerTable.MarkupsFiducialNodeComboBox
self.markerTableSelector.selectNodeUponCreation = False
self.markerTableSelector.addEnabled = True
self.markerTableSelector.removeEnabled = True
self.markerTableSelector.noneEnabled = False
self.markerTableSelector.renameEnabled = True
markerTable.setMRMLScene(slicer.mrmlScene)
markerTable.setCurrentNode(
slicer.mrmlScene.GetNodeByID(
slicer.modules.markups.logic().AddNewFiducialNode()))
markerTable.show()
cropFormLayout.addWidget(markerTable)
# # crop output volume selector
# self.cropOutputSelector = slicer.qMRMLNodeComboBox()
# self.cropOutputSelector.nodeTypes = ['vtkMRMLScalarVolumeNode']
# self.cropOutputSelector.toolTip = "Crop volumes for vertebrae levels"
# self.cropOutputSelector.setMRMLScene(slicer.mrmlScene)
# self.cropOutputSelector.renameEnabled = True
# self.cropOutputSelector.addEnabled = True
# self.cropOutputSelector.noneEnabled = True
# self.cropOutputSelector.selectNodeUponCreation = True
# self.cropOutputSelector.noneDisplay = 'Define name for cropped volume'
# self.cropOutputSelector.removeEnabled = True
# self.cropOutputSelector.showHidden = True
#
#
# cropFormLayout.addRow("Output Crop Volume: ", self.cropOutputSelector)
#
#
# # crop button
# cropButton = qt.QPushButton("Crop Vertebrae")
# cropButton.connect("clicked(bool)", self.onCropButton)
# cropFormLayout.addRow("Crop Vertebrae", cropButton)
# Segment vertebrae button
self.segmentationButton = qt.QPushButton('Segment Vertebrae')
self.segmentationButton.toolTip = 'Segment the selected vertebrae'
self.segmentationButton.enabled = False
# Segmentation button connections
self.segmentationButton.connect('clicked(bool)', self.onSegmentButton)
self.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
self.markerTableSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
self.layout.addWidget(self.segmentationButton)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onSelect()
