def create(self):
"""create the segmentation helper box"""
#
# Master Frame
#
self.masterFrame = qt.QFrame(self.parent)
self.masterFrame.setLayout(qt.QVBoxLayout())
self.parent.layout().addWidget(self.masterFrame)
#
# the master volume selector
#
self.masterSelectorFrame = qt.QFrame(self.parent)
self.masterSelectorFrame.objectName = 'MasterVolumeFrame'
self.masterSelectorFrame.setLayout(qt.QHBoxLayout())
self.masterFrame.layout().addWidget(self.masterSelectorFrame)
self.masterSelectorLabel = qt.QLabel("Master Volume: ", self.masterSelectorFrame)
self.masterSelectorLabel.setToolTip( "Select the master volume (background grayscale scalar volume node)")
self.masterSelectorFrame.layout().addWidget(self.masterSelectorLabel)
self.masterSelector = slicer.qMRMLNodeComboBox(self.masterSelectorFrame)
self.masterSelector.objectName = 'MasterVolumeNodeSelector'
# TODO
self.masterSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
self.masterSelector.selectNodeUponCreation = False
self.masterSelector.addEnabled = False
self.masterSelector.removeEnabled = False
self.masterSelector.noneEnabled = True
self.masterSelector.showHidden = False
self.masterSelector.showChildNodeTypes = False
self.masterSelector.setMRMLScene( slicer.mrmlScene )
# TODO: need to add a QLabel
# self.masterSelector.SetLabelText( "Master Volume:" )
self.masterSelector.setToolTip( "Pick the master structural volume to define the segmentation. A label volume with the with \"%s\" appended to the name will be created if it doesn't already exist." % self.mergeVolumePostfix)
self.masterSelectorFrame.layout().addWidget(self.masterSelector)
#
# merge label name and set button
#
self.mergeSelectorFrame = qt.QFrame(self.masterFrame)
self.mergeSelectorFrame.objectName = 'MergeVolumeFrame'
self.mergeSelectorFrame.setLayout(qt.QHBoxLayout())
self.masterFrame.layout().addWidget(self.mergeSelectorFrame)
mergeNameToolTip = "Composite label map containing the merged structures (be aware that merge operations will overwrite any edits applied to this volume)"
self.mergeNameLabel = qt.QLabel("Merge Volume: ", self.mergeSelectorFrame)
self.mergeNameLabel.setToolTip( mergeNameToolTip )
self.mergeSelectorFrame.layout().addWidget(self.mergeNameLabel)
self.mergeSelector = slicer.qMRMLNodeComboBox(self.mergeSelectorFrame)
self.mergeSelector.objectName = 'MergeVolumeNodeSelector'
self.mergeSelector.setToolTip( mergeNameToolTip )
self.mergeSelector.nodeTypes = ( ("vtkMRMLLabelMapVolumeNode"), "" )
self.mergeSelector.addEnabled = False
self.mergeSelector.removeEnabled = False
self.mergeSelector.noneEnabled = False
self.mergeSelector.showHidden = False
self.mergeSelector.showChildNodeTypes = False
self.mergeSelector.setMRMLScene( slicer.mrmlScene )
self.mergeSelectorFrame.layout().addWidget(self.mergeSelector)
self.newMergeVolumeAction = qt.QAction("Create new LabelMapVolume", self.mergeSelector)
self.newMergeVolumeAction.connect("triggered()", self.newMerge)
self.mergeSelector.addMenuAction(self.newMergeVolumeAction)
#
# Structures Frame
#
self.structuresFrame = ctk.ctkCollapsibleGroupBox(self.masterFrame)
self.structuresFrame.objectName = 'PerStructureVolumesFrame'
self.structuresFrame.title = "Per-Structure Volumes"
self.structuresFrame.collapsed = True
self.structuresFrame.setLayout(qt.QVBoxLayout())
self.masterFrame.layout().addWidget(self.structuresFrame)
self.structureListWidget = LabelStructureListWidget()
self.structureListWidget.mergeVolumePostfix = self.mergeVolumePostfix
self.structuresFrame.layout().addWidget(self.structureListWidget)
#
# signals, slots, and observers
#
# signals/slots on qt widgets are automatically when
# this class destructs, but observers of the scene must be explicitly
# removed in the destuctor
# node selected
self.masterSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.mergeSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onMergeSelect)
# so buttons will initially be disabled
self.master = None
self.structureListWidget.updateStructures()
def setupNavigationPanel(self):
logging.debug("setupNavigationPanel")
self.sliderTranslationDefaultMm = 0
self.sliderTranslationMinMm = -500
self.sliderTranslationMaxMm = 500
self.sliderViewAngleDefaultDeg = 30
self.cameraViewAngleMinDeg = 5.0 # maximum magnification
self.cameraViewAngleMaxDeg = 150.0 # minimum magnification
self.sliderSingleStepValue = 1
self.sliderPageStepValue = 10
self.navigationCollapsibleButton.setProperty("collapsedHeight", 20)
setButtonStyle(self.navigationCollapsibleButton, 2.0)
self.navigationCollapsibleButton.text = "Navigation"
self.sliceletPanelLayout.addWidget(self.navigationCollapsibleButton)
self.navigationCollapsibleLayout = qt.QFormLayout(self.navigationCollapsibleButton)
self.navigationCollapsibleLayout.setContentsMargins(12, 4, 4, 4)
self.navigationCollapsibleLayout.setSpacing(4)
self.rightCameraButton = qt.QPushButton("Setup right camera")
self.rightCameraButton.setCheckable(True)
setButtonStyle(self.rightCameraButton)
self.leftCameraButton = qt.QPushButton("Setup left camera")
self.leftCameraButton.setCheckable(True)
setButtonStyle(self.leftCameraButton)
hbox = qt.QHBoxLayout()
hbox.addWidget(self.leftCameraButton)
hbox.addWidget(self.rightCameraButton)
self.navigationCollapsibleLayout.addRow(hbox)
# "Camera Control" Collapsible
self.zoomCollapsibleButton = ctk.ctkCollapsibleGroupBox()
self.zoomCollapsibleButton.collapsed = True
self.zoomCollapsibleButton.title = "Zoom"
self.navigationCollapsibleLayout.addRow(self.zoomCollapsibleButton)
# Layout within the collapsible button
self.zoomFormLayout = qt.QFormLayout(self.zoomCollapsibleButton)
# Camera distance to focal point slider
self.cameraViewAngleLabel = qt.QLabel(qt.Qt.Horizontal, None)
self.cameraViewAngleLabel.setText("Field of view [degrees]: ")
self.cameraViewAngleSlider = slicer.qMRMLSliderWidget()
self.cameraViewAngleSlider.minimum = self.cameraViewAngleMinDeg
self.cameraViewAngleSlider.maximum = self.cameraViewAngleMaxDeg
self.cameraViewAngleSlider.value = self.sliderViewAngleDefaultDeg
self.cameraViewAngleSlider.singleStep = self.sliderSingleStepValue
self.cameraViewAngleSlider.pageStep = self.sliderPageStepValue
self.cameraViewAngleSlider.setDisabled(True)
self.zoomFormLayout.addRow(self.cameraViewAngleLabel, self.cameraViewAngleSlider)
# "Camera Control" Collapsible
self.translationCollapsibleButton = ctk.ctkCollapsibleGroupBox()
self.translationCollapsibleButton.title = "Translation"
self.translationCollapsibleButton.collapsed = True
self.navigationCollapsibleLayout.addRow(self.translationCollapsibleButton)
# Layout within the collapsible button
self.translationFormLayout = qt.QFormLayout(self.translationCollapsibleButton)
self.cameraXPosLabel = qt.QLabel(qt.Qt.Horizontal, None)
self.cameraXPosLabel.text = "Left/Right [mm]: "
self.cameraXPosSlider = slicer.qMRMLSliderWidget()
setButtonStyle(self.cameraXPosSlider)
self.cameraXPosSlider.minimum = self.sliderTranslationMinMm
self.cameraXPosSlider.maximum = self.sliderTranslationMaxMm
self.cameraXPosSlider.value = self.sliderTranslationDefaultMm
self.cameraXPosSlider.singleStep = self.sliderSingleStepValue
self.cameraXPosSlider.pageStep = self.sliderPageStepValue
self.cameraXPosSlider.setDisabled(True)
self.translationFormLayout.addRow(self.cameraXPosLabel, self.cameraXPosSlider)
self.cameraYPosLabel = qt.QLabel(qt.Qt.Horizontal, None)
self.cameraYPosLabel.setText("Down/Up [mm]: ")
self.cameraYPosSlider = slicer.qMRMLSliderWidget()
setButtonStyle(self.cameraYPosSlider)
self.cameraYPosSlider.minimum = self.sliderTranslationMinMm
self.cameraYPosSlider.maximum = self.sliderTranslationMaxMm
self.cameraYPosSlider.value = self.sliderTranslationDefaultMm
self.cameraYPosSlider.singleStep = self.sliderSingleStepValue
self.cameraYPosSlider.pageStep = self.sliderPageStepValue
self.cameraYPosSlider.setDisabled(True)
self.translationFormLayout.addRow(self.cameraYPosLabel, self.cameraYPosSlider)
self.cameraZPosLabel = qt.QLabel(qt.Qt.Horizontal, None)
self.cameraZPosLabel.setText("Front/Back [mm]: ")
self.cameraZPosSlider = slicer.qMRMLSliderWidget()
setButtonStyle(self.cameraZPosSlider)
self.cameraZPosSlider.minimum = self.sliderTranslationMinMm
self.cameraZPosSlider.maximum = self.sliderTranslationMaxMm
self.cameraZPosSlider.value = self.sliderTranslationDefaultMm
self.cameraZPosSlider.singleStep = self.sliderSingleStepValue
self.cameraZPosSlider.pageStep = self.sliderPageStepValue
self.cameraZPosSlider.setDisabled(True)
self.translationFormLayout.addRow(self.cameraZPosLabel, self.cameraZPosSlider)
# "Contour adjustment" Collapsible
self.contourAdjustmentCollapsibleButton = ctk.ctkCollapsibleGroupBox()
self.contourAdjustmentCollapsibleButton.title = "Contour adjustment"
self.contourAdjustmentCollapsibleButton.collapsed = True
self.navigationCollapsibleLayout.addRow(self.contourAdjustmentCollapsibleButton)
# Layout within the collapsible button
self.contourAdjustmentFormLayout = qt.QFormLayout(self.contourAdjustmentCollapsibleButton)
self.placeTumorPointAtCauteryTipButton = qt.QPushButton("Mark point at cautery tip")
setButtonStyle(self.placeTumorPointAtCauteryTipButton)
self.contourAdjustmentFormLayout.addRow(self.placeTumorPointAtCauteryTipButton)
self.deleteLastFiducialDuringNavigationButton = qt.QPushButton("Delete last")
self.deleteLastFiducialDuringNavigationButton.setIcon(qt.QIcon(":/Icons/MarkupsDelete.png"))
setButtonStyle(self.deleteLastFiducialDuringNavigationButton)
self.deleteLastFiducialDuringNavigationButton.setEnabled(False)
self.contourAdjustmentFormLayout.addRow(self.deleteLastFiducialDuringNavigationButton)
def setup(self):
#Instantiate and Connect Widgets
#################################################
#HeterogeneityCAD Inputs Collapsible Button
self.inputHeterogeneityCADCollapsibleButton = ctk.ctkCollapsibleButton()
self.inputHeterogeneityCADCollapsibleButton.text = "HeterogeneityCAD Input"
self.layout.addWidget(self.inputHeterogeneityCADCollapsibleButton)
self.inputHeterogeneityCADLayout = qt.QFormLayout(self.inputHeterogeneityCADCollapsibleButton)
##Input Volume as a PET/CT/MRI image or parameter map converted to a volume
self.inputVolHetFrame = qt.QFrame(self.inputHeterogeneityCADCollapsibleButton)
self.inputVolHetFrame.setLayout(qt.QHBoxLayout())
self.inputHeterogeneityCADLayout.addRow(self.inputVolHetFrame)
# label for selecting individual node
self.inputVolHet = qt.QLabel("Input Node: ", self.inputVolHetFrame)
self.inputVolHetFrame.layout().addWidget(self.inputVolHet)
# select individual nodes
self.inputSelectorVolHet = slicer.qMRMLNodeComboBox(self.inputVolHetFrame)
self.inputSelectorVolHet.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
self.inputSelectorVolHet.selectNodeUponCreation = False
self.inputSelectorVolHet.addEnabled = False
self.inputSelectorVolHet.removeEnabled = False
self.inputSelectorVolHet.setMRMLScene( slicer.mrmlScene )
self.inputVolHetFrame.layout().addWidget(self.inputSelectorVolHet)
# add Data Node button
self.addDataNodeButton = qt.QPushButton("Add Node", self.inputVolHetFrame)
self.addDataNodeButton.objectName = 'AddDataNodeButton'
self.addDataNodeButton.setToolTip( "Add a Node to Queue" )
self.addDataNodeButton.connect('clicked()', self.onAddDataNodeButtonClicked)
self.inputVolHetFrame.layout().addWidget(self.addDataNodeButton)
## data nodes Frame
self.dataNodesFrame = ctk.ctkCollapsibleGroupBox(self.inputHeterogeneityCADCollapsibleButton)
self.dataNodesFrame.title = "Nodes List"
self.dataNodesFrame.collapsed = False
self.dataNodesFrame.setLayout(qt.QVBoxLayout())
# all buttons frame
self.allButtonsFrame = qt.QFrame(self.inputHeterogeneityCADCollapsibleButton)
self.allButtonsFrame.objectName = 'AllButtonsFrameButton'
self.allButtonsFrame.setLayout(qt.QVBoxLayout())
self.inputHeterogeneityCADLayout.addRow(self.dataNodesFrame, self.allButtonsFrame)
# Data Nodes view
# Use list view here with scroll area widget.
self.dataScrollArea = qt.QScrollArea()
self.dataNodesListWidget = qt.QListWidget()
self.dataNodesListWidget.name = 'dataNodesListWidget'
self.dataScrollArea.setWidget(self.dataNodesListWidget)
self.dataNodesListWidget.resize(350,100)
self.dataNodesFrame.layout().addWidget(self.dataScrollArea)
#self.listWidget.setProperty('SH_ItemView_ActivateItemOnSingleClick', 1)
#self.listWidget.connect('activated(QModelIndex)', self.onActivated)
# add all Data Nodes from scene button
self.addAllDataNodesButton = qt.QPushButton("Add All Nodes From Scene", self.allButtonsFrame)
self.addAllDataNodesButton.objectName = 'AddAllDataNodesButton'
self.addAllDataNodesButton.setToolTip( "Add all Nodes from the Scene to Queue" )
self.addAllDataNodesButton.connect('clicked()', self.onAddAllDataNodesButtonClicked)
self.allButtonsFrame.layout().addWidget(self.addAllDataNodesButton)
# remove single Data Node
self.removeDataNodeButton = qt.QPushButton("Remove Node", self.allButtonsFrame)
self.removeDataNodeButton.objectName = 'RemoveDataNodeButton'
self.removeDataNodeButton.setToolTip( "Removes Selected Node from the Queue." )
self.removeDataNodeButton.connect('clicked()', self.onRemoveDataNodeButtonClicked)
self.allButtonsFrame.layout().addWidget(self.removeDataNodeButton)
# remove all Data Nodes button
self.removeAllDataNodesButton = qt.QPushButton("Remove All Nodes", self.allButtonsFrame)
self.removeAllDataNodesButton.objectName = 'RemoveAllDataNodesButton'
self.removeAllDataNodesButton.setToolTip( "Removes All Nodes from the Queue." )
self.removeAllDataNodesButton.connect('clicked()', self.onRemoveAllDataNodesButtonClicked)
self.allButtonsFrame.layout().addWidget(self.removeAllDataNodesButton)
# Use Label Map as ROI(segmentation output or user-selected ROI)
self.inputLabelROIFrame = qt.QFrame(self.inputHeterogeneityCADCollapsibleButton)
self.inputLabelROIFrame.setLayout(qt.QHBoxLayout())
self.inputHeterogeneityCADLayout.addRow(self.inputLabelROIFrame)
# Enable Input Label Map as ROI
self.inputLabelROI = qt.QLabel("Label Map ROI: ", self.inputLabelROIFrame)
self.inputLabelROIFrame.layout().addWidget(self.inputLabelROI)
# Select Input Label Map as ROI
self.inputSelectorLabel = slicer.qMRMLNodeComboBox(self.inputLabelROIFrame)
self.inputSelectorLabel.nodeTypes = ( ("vtkMRMLLabelMapVolumeNode"), "" )
self.inputSelectorLabel.selectNodeUponCreation = False
self.inputSelectorLabel.renameEnabled = True
self.inputSelectorLabel.removeEnabled = False
self.inputSelectorLabel.noneEnabled = True
self.inputSelectorLabel.addEnabled = False
self.inputSelectorLabel.setMRMLScene( slicer.mrmlScene )
self.inputLabelROIFrame.layout().addWidget(self.inputSelectorLabel)
#End HeterogeneityCAD Inputs Collapsible Button
#################################################
#HeterogeneityCAD Features Collapsible Button
self.HeterogeneityCADCollapsibleButton = ctk.ctkCollapsibleButton()
self.HeterogeneityCADCollapsibleButton.text = "HeterogeneityCAD Features Selection"
self.layout.addWidget(self.HeterogeneityCADCollapsibleButton)
self.featuresHeterogeneityCADLayout = qt.QFormLayout(self.HeterogeneityCADCollapsibleButton)
# auto-generate QTabWidget Tabs and QCheckBoxes (subclassed in FeatureWidgetHelperLib)
self.tabsFeatureClasses = FeatureWidgetHelperLib.CheckableTabWidget()
self.featuresHeterogeneityCADLayout.addRow(self.tabsFeatureClasses)
gridWidth, gridHeight = 3, 9
for featureClass in self.featureClassKeys:
# by default, features from the following features classes are checked:
if featureClass in ["Node Information", "First-Order Statistics", "Morphology and Shape", "Texture: GLCM", "Texture: GLRL"]:
check = True
else:
check = False
tabFeatureClass = qt.QWidget()
tabFeatureClass.setLayout(qt.QGridLayout())
#featureList = (feature for feature in self.featureClassKeys[featureClass])
gridLayoutCoordinates = ((row,col) for col in range(gridWidth) for row in range(gridHeight))
for featureName in self.featureClassKeys[featureClass]:
row, col = next(gridLayoutCoordinates, None)
if featureName is None or row is None or col is None:
break
featureCheckboxWidget = FeatureWidgetHelperLib.FeatureWidget()
featureCheckboxWidget.Setup(featureName=featureName, checkStatus=check)
tabFeatureClass.layout().addWidget(featureCheckboxWidget, row, col)
self.featureWidgets[featureClass].append(featureCheckboxWidget)
self.tabsFeatureClasses.addTab(tabFeatureClass, featureClass, self.featureWidgets[featureClass], checkStatus=check)
self.tabsFeatureClasses.setCurrentIndex(1)
# note: try using itertools list merging with lists of GLRL diagonal
self.heterogeneityFeatureWidgets = list(itertools.chain.from_iterable(self.featureWidgets.values()))
self.classes = list(self.featureWidgets.keys())
# or reduce(lambda x,y: x+y, self.featureWidgets.values())
########## Parameter options
# add parameters for top-level feature classes
self.tabsFeatureClasses.addParameter("Geometrical Measures", "Extrusion Parameter 1")
self.tabsFeatureClasses.addParameter("Texture: GLCM", "GLCM Matrix Parameter 1")
self.tabsFeatureClasses.addParameter("Texture: GLRL", "GLRL Matrix Parameter 1")
# compile dict of feature classes with parameter names and values
self.featureClassParametersDict = collections.OrderedDict()
for featureClassWidget in self.tabsFeatureClasses.getFeatureClassWidgets():
featureClassName = featureClassWidget.getName()
self.featureClassParametersDict[featureClassName] = collections.OrderedDict()
self.updateFeatureClassParameterDict(0,featureClassWidget)
for parameterName in featureClassWidget.widgetMenu.parameters:
featureClassWidget.getParameterEditWindow(parameterName).connect('intValueChanged(int)', lambda intValue, featureClassWidget=featureClassWidget: self.updateFeatureClassParameterDict(intValue, featureClassWidget))
# add parameters for individual features
for featureWidget in self.heterogeneityFeatureWidgets:
if featureWidget.getName() == "Voxel Count":
featureWidget.addParameter("Example Parameter 1")
featureWidget.addParameter("Example Parameter 2")
if featureWidget.getName() == "Gray Levels":
featureWidget.addParameter("Example Parameter 1-GL")
featureWidget.addParameter("Example Parameter 2-GL")
# compile dict of features with parameter names and values
self.featureParametersDict = collections.OrderedDict()
for featureWidget in self.heterogeneityFeatureWidgets:
featureName = featureWidget.getName()
self.featureParametersDict[featureName] = collections.OrderedDict()
self.updateFeatureParameterDict(0,featureWidget)
for parameterName in featureWidget.widgetMenu.parameters:
featureWidget.getParameterEditWindow(parameterName).connect('intValueChanged(int)', lambda intValue, featureWidget=featureWidget: self.updateFeatureParameterDict(intValue, featureWidget)) #connect intvaluechanged signals to updateParamaterDict function
##########
# Feature Buttons Frame and Layout
self.featureButtonFrame = qt.QFrame(self.HeterogeneityCADCollapsibleButton)
self.featureButtonFrame.setLayout(qt.QHBoxLayout())
self.featuresHeterogeneityCADLayout.addRow(self.featureButtonFrame)
# HeterogeneityCAD Apply Button
self.HeterogeneityCADButton = qt.QPushButton("Apply HeterogeneityCAD", self.featureButtonFrame)
self.HeterogeneityCADButton.toolTip = "Analyze input volume using selected Heterogeneity Features."
self.featureButtonFrame.layout().addWidget(self.HeterogeneityCADButton)
self.HeterogeneityCADButton.connect('clicked()', self.onHeterogeneityCADButtonClicked)
# Save Button
self.saveButton = qt.QPushButton("Save to File", self.featureButtonFrame)
self.saveButton.toolTip = "Save analyses to CSV file"
self.saveButton.enabled = False
self.featureButtonFrame.layout().addWidget(self.saveButton)
self.saveButton.connect('clicked()', self.onSave)
#End HeterogeneityCAD Features Collapsible Button
#################################################
#Feature Summary Chart
#Complete chart options, export list of user-selected options identified via connections to labelstatistics module
self.chartOptions = ("Count", "Volume mm^3", "Volume cc", "Min", "Max", "Mean", "StdDev")
self.StatisticsChartCollapsibleButton = ctk.ctkCollapsibleButton()
self.StatisticsChartCollapsibleButton.text = "HeterogeneityCAD Features Summary"
self.layout.addWidget(self.StatisticsChartCollapsibleButton)
self.StatisticsChartLayout = qt.QFormLayout(self.StatisticsChartCollapsibleButton)
self.StatisticsChartCollapsibleButton.collapsed = False
#Table View to display Label statistics
self.view = qt.QTableView(self.StatisticsChartCollapsibleButton)
self.view.sortingEnabled = True
self.StatisticsChartLayout.addWidget(self.view)
self.view.minimumHeight = 175
def create(self):
super(InteractiveConnectedComponentsUsingParzenPDFsOptions,
self).create()
ioCollapsibleButton = ctk.ctkCollapsibleGroupBox()
ioCollapsibleButton.title = "IO"
ioCollapsibleButton.collapsed = 0
self.frame.layout().addWidget(ioCollapsibleButton)
# Layout within the io collapsible button
ioFormLayout = qt.QFormLayout(ioCollapsibleButton)
self.additionalInputNodeSelectors = []
for i in range(0, 2):
self.additionalInputNodeSelectors.append(
self.addInputNodeSelector(i, ioFormLayout))
self.additionalInputNodeSelectors[
0].toolTip = "Select the 1st additional input volume to be segmented"
self.additionalInputNodeSelectors[
1].toolTip = "Select the 2nd additional input volume to be segmented"
# Objects
objectCollapsibleGroupBox = ctk.ctkCollapsibleGroupBox()
objectCollapsibleGroupBox.title = "Objects"
self.frame.layout().addWidget(objectCollapsibleGroupBox)
# Layout within the io collapsible button
objectFormLayout = qt.QFormLayout(objectCollapsibleGroupBox)
foregroundLayout = qt.QHBoxLayout()
foregroundLabel = slicer.qMRMLLabelComboBox()
foregroundLabel.objectName = 'Foreground label'
foregroundLabel.setMRMLScene(slicer.mrmlScene)
foregroundLabel.setMRMLColorNode(self.editUtil.getColorNode())
foregroundLabel.labelValueVisible = True
foregroundLabel.currentColor = 1
self.foregroundLabel = foregroundLabel
self.connections.append(
(self.foregroundLabel, 'currentColorChanged(int)',
self.updateMRMLFromGUI))
foregroundWeightSpinBox = qt.QDoubleSpinBox(foregroundLabel)
self.foregroundWeightSpinBox = foregroundWeightSpinBox
foregroundWeightSpinBox.setRange(0.0, 1.0)
foregroundWeightSpinBox.setSingleStep(0.1)
foregroundWeightSpinBox.value = 1.0
foregroundPopup = ctk.ctkPopupWidget(foregroundWeightSpinBox)
foregroundPopupLayout = qt.QHBoxLayout(foregroundPopup)
foregroundPopupSlider = ctk.ctkDoubleSlider(foregroundPopup)
self.foregroundPopupSlider = foregroundPopupSlider
foregroundPopupSlider.maximum = 1.0
foregroundPopupSlider.minimum = 0.0
foregroundPopupSlider.singleStep = 0.1
foregroundPopupSlider.connect('valueChanged(double)',
self.foregroundWeightSpinBox.setValue)
foregroundWeightSpinBox.connect('valueChanged(double)',
self.foregroundPopupSlider.setValue)
self.connections.append(
(self.foregroundWeightSpinBox, 'valueChanged(double)',
self.updateMRMLFromGUI))
foregroundLayout.addWidget(foregroundLabel)
foregroundLayout.addWidget(foregroundWeightSpinBox)
foregroundPopupLayout.addWidget(foregroundPopupSlider)
objectFormLayout.addRow("Foreground Label:", foregroundLayout)
self.objectLabel = foregroundLabel
# http://qt-project.org/doc/qt-4.7/qt.html
foregroundPopup.alignment = 0x0082 # Qt::AlignVCenter | Qt::AlignRight
foregroundPopup.horizontalDirection = 0 # Qt::LeftToRight
foregroundPopup.verticalDirection = 0 # Qt::TopToBottom
foregroundPopup.animationEffect = 1 # Qt::ScrollEffect
backgroundLayout = qt.QHBoxLayout()
backgroundLabel = slicer.qMRMLLabelComboBox()
backgroundLabel.objectName = 'Background label'
backgroundLabel.setMRMLScene(slicer.mrmlScene)
backgroundLabel.setMRMLColorNode(self.editUtil.getColorNode())
backgroundLabel.labelValueVisible = True
backgroundLabel.currentColor = 2
self.backgroundLabel = backgroundLabel
self.connections.append(
(self.backgroundLabel, 'currentColorChanged(int)',
self.updateMRMLFromGUI))
backgroundWeightSpinBox = qt.QDoubleSpinBox(backgroundLabel)
self.backgroundWeightSpinBox = backgroundWeightSpinBox
backgroundWeightSpinBox.setRange(0.0, 1.0)
backgroundWeightSpinBox.setSingleStep(0.1)
backgroundWeightSpinBox.value = 1.0
backgroundPopup = ctk.ctkPopupWidget(backgroundWeightSpinBox)
backgroundPopupLayout = qt.QHBoxLayout(backgroundPopup)
backgroundPopupSlider = ctk.ctkDoubleSlider(backgroundPopup)
self.backgroundPopupSlider = backgroundPopupSlider
backgroundPopupSlider.maximum = 1.0
backgroundPopupSlider.minimum = 0.0
backgroundPopupSlider.singleStep = 0.1
backgroundPopupSlider.connect('valueChanged(double)',
self.backgroundWeightSpinBox.setValue)
backgroundWeightSpinBox.connect('valueChanged(double)',
self.backgroundPopupSlider.setValue)
self.connections.append(
(self.backgroundWeightSpinBox, 'valueChanged(double)',
self.updateMRMLFromGUI))
backgroundLayout.addWidget(backgroundLabel)
backgroundLayout.addWidget(backgroundWeightSpinBox)
backgroundPopupLayout.addWidget(backgroundPopupSlider)
objectFormLayout.addRow("Background Label:", backgroundLayout)
self.backgroundLabel = backgroundLabel
# http://qt-project.org/doc/qt-4.7/qt.html
backgroundPopup.alignment = 0x0082 # Qt::AlignVCenter | Qt::AlignRight
backgroundPopup.horizontalDirection = 0 # Qt::LeftToRight
backgroundPopup.verticalDirection = 0 # Qt::TopToBottom
backgroundPopup.animationEffect = 1 # Qt::ScrollEffect
# Presets
# Placeholder
presetsCollapsibleGroupBox = ctk.ctkCollapsibleGroupBox()
presetsCollapsibleGroupBox.title = "Preset"
self.frame.layout().addWidget(presetsCollapsibleGroupBox)
presetComboBox = slicer.qSlicerPresetComboBox()
# Advanced Parameters
paramsCollapsibleGroupBox = ctk.ctkCollapsibleGroupBox()
paramsCollapsibleGroupBox.title = "Advanced Parameters"
paramsCollapsibleGroupBox.collapsed = 1
self.frame.layout().addWidget(paramsCollapsibleGroupBox)
# Layout within the io collapsible button
paramsFormLayout = qt.QFormLayout(paramsCollapsibleGroupBox)
erosionSpinBox = qt.QSpinBox()
erosionSpinBox.objectName = 'erosionSpinBox'
erosionSpinBox.toolTip = "Set the erosion radius."
erosionSpinBox.setMinimum(0)
erosionSpinBox.setValue(5) # Default
paramsFormLayout.addRow("Erosion Radius:", erosionSpinBox)
self.erosionSpinBox = erosionSpinBox
self.connections.append(
(self.erosionSpinBox, "valueChanged(int)", self.updateMRMLFromGUI))
holeFillSpinBox = qt.QSpinBox()
holeFillSpinBox.objectName = 'holeFillSpinBox'
holeFillSpinBox.toolTip = "Set the hole fill iterations."
holeFillSpinBox.setMinimum(0)
holeFillSpinBox.setValue(5) #Default
paramsFormLayout.addRow("Hole Fill Iterations:", holeFillSpinBox)
self.holeFillSpinBox = holeFillSpinBox
self.connections.append((self.holeFillSpinBox, "valueChanged(int)",
self.updateMRMLFromGUI))
# probabilitySmoothingStandardDeviation spin box
probabilitySmoothingStdDevSpinBox = qt.QDoubleSpinBox()
probabilitySmoothingStdDevSpinBox.objectName = 'probabilitySmoothingStdDevSpinBox'
probabilitySmoothingStdDevSpinBox.toolTip = "Standard deviation of blur applied to probability images prior to computing maximum likelihood of each class at each pixel."
probabilitySmoothingStdDevSpinBox.setMinimum(0.0)
probabilitySmoothingStdDevSpinBox.setValue(1.0) # Default
probabilitySmoothingStdDevSpinBox.setSingleStep(0.5)
paramsFormLayout.addRow("Probability Smoothing Standard Deviation:",
probabilitySmoothingStdDevSpinBox)
self.probabilitySmoothingStdDevSpinBox = probabilitySmoothingStdDevSpinBox
self.connections.append(
(self.probabilitySmoothingStdDevSpinBox, "valueChanged(double)",
self.updateMRMLFromGUI))
# histogramSmoothingStandardDeviation spin box
histogramSmoothingStdDevSpinBox = qt.QDoubleSpinBox()
histogramSmoothingStdDevSpinBox.objectName = 'histogramSmoothingStdDevSpinBox'
histogramSmoothingStdDevSpinBox.toolTip = "Standard deviation of blur applied to histograms to convert them to probability density function estimates."
histogramSmoothingStdDevSpinBox.setMinimum(0.0)
histogramSmoothingStdDevSpinBox.setValue(5.0) # Default
histogramSmoothingStdDevSpinBox.setSingleStep(0.5)
paramsFormLayout.addRow("Probability Smoothing Standard Deviation:",
histogramSmoothingStdDevSpinBox)
self.histogramSmoothingStdDevSpinBox = histogramSmoothingStdDevSpinBox
self.connections.append(
(self.histogramSmoothingStdDevSpinBox, "valueChanged(double)",
self.updateMRMLFromGUI))
# draft check box
draftCheckBox = qt.QCheckBox()
draftCheckBox.objectName = 'draftCheckBox'
draftCheckBox.toolTip = "Downsamples results by a factor of 4."
paramsFormLayout.addRow("Draft Mode:", draftCheckBox)
self.draftCheckBox = draftCheckBox
self.connections.append(
(self.draftCheckBox, "stateChanged(int)", self.updateMRMLFromGUI))
# force classification check box
forceClassificationCheckBox = qt.QCheckBox()
forceClassificationCheckBox.objectName = 'forceClassificationCheckBox'
forceClassificationCheckBox.toolTip = "Perform the classification of all voxels?"
forceClassificationCheckBox.setChecked(False)
paramsFormLayout.addRow("Classify all voxels: ",
forceClassificationCheckBox)
self.forceClassificationCheckBox = forceClassificationCheckBox
self.connections.append((self.forceClassificationCheckBox,
"stateChanged(int)", self.updateMRMLFromGUI))
# dilate first check box
dilateFirstCheckBox = qt.QCheckBox()
dilateFirstCheckBox.objectName = 'dilateFirstCheckBox'
dilateFirstCheckBox.toolTip = "Dilate and then erode so as to fill-in holes?"
dilateFirstCheckBox.setChecked(False)
paramsFormLayout.addRow("Dilate First: ", dilateFirstCheckBox)
self.dilateFirstCheckBox = dilateFirstCheckBox
self.connections.append((self.dilateFirstCheckBox, "stateChanged(int)",
self.updateMRMLFromGUI))
self.helpLabel = qt.QLabel(
"Run the PDF Segmentation on the current label map.", self.frame)
self.frame.layout().addWidget(self.helpLabel)
self.apply = qt.QPushButton("Apply", self.frame)
self.apply.setToolTip(
"Apply to run segmentation.\nCreates a new label volume using the current volume as input"
)
self.frame.layout().addWidget(self.apply)
self.widgets.append(self.apply)
EditorLib.HelpButton(
self.frame,
"Use this tool to apply segmentation using Parzen windowed PDFs.\n\n Select different label colors and paint on the foreground or background voxels using the paint effect.\nTo run segmentation correctly, you need to supply a minimum or two class labels."
)
self.connections.append((self.apply, 'clicked()', self.onApply))
def create(self):
"""create the segmentation helper box"""
#
# Master Frame
#
self.masterFrame = qt.QFrame(self.parent)
self.masterFrame.setLayout(qt.QVBoxLayout())
self.parent.layout().addWidget(self.masterFrame)
#
# the master volume selector
#
self.masterSelectorFrame = qt.QFrame(self.parent)
self.masterSelectorFrame.setLayout(qt.QHBoxLayout())
self.masterFrame.layout().addWidget(self.masterSelectorFrame)
self.masterSelectorLabel = qt.QLabel("Master Volume: ", self.masterSelectorFrame)
self.masterSelectorLabel.setToolTip( "Select the master volume (background grayscale scalar volume node)")
self.masterSelectorFrame.layout().addWidget(self.masterSelectorLabel)
self.masterSelector = slicer.qMRMLNodeComboBox(self.masterSelectorFrame)
# TODO
self.masterSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
self.masterSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", 0 )
self.masterSelector.selectNodeUponCreation = False
self.masterSelector.addEnabled = False
self.masterSelector.removeEnabled = False
self.masterSelector.noneEnabled = True
self.masterSelector.showHidden = False
self.masterSelector.showChildNodeTypes = False
self.masterSelector.setMRMLScene( slicer.mrmlScene )
# TODO: need to add a QLabel
# self.masterSelector.SetLabelText( "Master Volume:" )
self.masterSelector.setToolTip( "Pick the master structural volume to define the segmentation. A label volume with the with \"-label\" appended to the name will be created if it doesn't already exist." )
self.masterSelectorFrame.layout().addWidget(self.masterSelector)
#
# merge label name and set button
#
self.mergeFrame = qt.QFrame(self.masterFrame)
self.mergeFrame.setLayout(qt.QHBoxLayout())
self.masterFrame.layout().addWidget(self.mergeFrame)
mergeNameToolTip = "Composite label map containing the merged structures (be aware that merge operations will overwrite any edits applied to this volume)"
self.mergeNameLabel = qt.QLabel("Merge Volume: ", self.mergeFrame)
self.mergeNameLabel.setToolTip( mergeNameToolTip )
self.mergeFrame.layout().addWidget(self.mergeNameLabel)
self.mergeName = qt.QLabel("", self.mergeFrame)
self.mergeName.setToolTip( mergeNameToolTip )
self.mergeFrame.layout().addWidget(self.mergeName)
self.setMergeButton = qt.QPushButton("Set...", self.mergeFrame)
self.setMergeButton.setToolTip( "Set the merge volume to use with this master." )
self.mergeFrame.layout().addWidget(self.setMergeButton)
#
# Structures Frame
#
self.structuresFrame = ctk.ctkCollapsibleGroupBox(self.masterFrame)
self.structuresFrame.title = "Per-Structure Volumes"
self.structuresFrame.collapsed = True
self.structuresFrame.setLayout(qt.QVBoxLayout())
self.masterFrame.layout().addWidget(self.structuresFrame)
# buttons frame
self.structureButtonsFrame = qt.QFrame(self.structuresFrame)
self.structureButtonsFrame.setLayout(qt.QHBoxLayout())
self.structuresFrame.layout().addWidget(self.structureButtonsFrame)
# add button
self.addStructureButton = qt.QPushButton("Add Structure", self.structureButtonsFrame)
self.addStructureButton.setToolTip( "Add a label volume for a structure to edit" )
self.structureButtonsFrame.layout().addWidget(self.addStructureButton)
# split button
self.splitButton = qt.QPushButton("Split Merge Volume", self.structuresFrame)
self.splitButton.setToolTip( "Split distinct labels from merge volume into new volumes" )
self.structureButtonsFrame.layout().addWidget(self.splitButton)
# structures view
self.structuresView = qt.QTreeView()
self.structuresView.sortingEnabled = True
self.structuresFrame.layout().addWidget(self.structuresView)
# all buttons frame
self.allButtonsFrame = qt.QFrame(self.structuresFrame)
self.allButtonsFrame.setLayout(qt.QHBoxLayout())
self.structuresFrame.layout().addWidget(self.allButtonsFrame)
# delete structures button
self.deleteStructuresButton = qt.QPushButton("Delete Structures", self.allButtonsFrame)
self.deleteStructuresButton.setToolTip( "Delete all the structure volumes from the scene.\n\nNote: to delete individual structure volumes, use the Data Module." )
self.allButtonsFrame.layout().addWidget(self.deleteStructuresButton)
# merge button
self.mergeButton = qt.QPushButton("Merge All", self.allButtonsFrame)
self.mergeButton.setToolTip( "Merge all structures into Merge Volume" )
self.allButtonsFrame.layout().addWidget(self.mergeButton)
# merge and build button
self.mergeAndBuildButton = qt.QPushButton("Merge And Build", self.allButtonsFrame)
self.mergeAndBuildButton.setToolTip( "Merge all structures into Merge Volume and build models from all structures")
self.allButtonsFrame.layout().addWidget(self.mergeAndBuildButton)
# options frame
self.optionsFrame = qt.QFrame(self.structuresFrame)
self.optionsFrame.setLayout(qt.QHBoxLayout())
self.structuresFrame.layout().addWidget(self.optionsFrame)
# replace models button
self.replaceModels = qt.QCheckBox("Replace Models", self.optionsFrame)
self.replaceModels.setToolTip( "Replace any existing models when building" )
self.replaceModels.setChecked(1)
self.optionsFrame.layout().addWidget(self.replaceModels)
#
# signals, slots, and observers
#
# signals/slots on qt widgets are automatically when
# this class destructs, but observers of the scene must be explicitly
# removed in the destuctor
# node selected
self.masterSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
# buttons pressed
self.addStructureButton.connect("clicked()", self.addStructure)
self.deleteStructuresButton.connect("clicked()", self.deleteStructures)
# selection changed event
self.structuresView.connect("clicked(QModelIndex)", self.onStructuresClicked)
# invoked event
self.splitButton.connect("clicked()", self.split)
self.mergeButton.connect("clicked()", self.mergeStructures)
self.mergeAndBuildButton.connect("clicked()", self.onMergeAndBuild)
self.setMergeButton.connect("clicked()", self.labelSelectDialog)
# new scene, node added or removed events
# TODO: allow observers on speific events: 66000, 66001, 66002
tag = slicer.mrmlScene.AddObserver("ModifiedEvent", self.updateStructures)
self.observerTags.append( (slicer.mrmlScene, tag) )
# so buttons will initially be disabled
self.master = None
self.updateStructures()
def create(self):
super(InteractiveConnectedComponentsUsingParzenPDFsOptions,self).create()
ioCollapsibleButton = ctk.ctkCollapsibleGroupBox()
ioCollapsibleButton.title = "IO"
ioCollapsibleButton.collapsed = 0
self.frame.layout().addWidget(ioCollapsibleButton)
# Layout within the io collapsible button
ioFormLayout = qt.QFormLayout(ioCollapsibleButton)
self.additionalInputNodeSelectors = []
for i in range(0,2):
self.additionalInputNodeSelectors.append(self.addInputNodeSelector(i, ioFormLayout))
self.additionalInputNodeSelectors[0].toolTip = "Select the 1st additional input volume to be segmented"
self.additionalInputNodeSelectors[1].toolTip = "Select the 2nd additional input volume to be segmented"
# Objects
objectCollapsibleGroupBox = ctk.ctkCollapsibleGroupBox()
objectCollapsibleGroupBox.title = "Objects"
self.frame.layout().addWidget(objectCollapsibleGroupBox)
# Layout within the io collapsible button
objectFormLayout = qt.QFormLayout(objectCollapsibleGroupBox)
foregroundLayout = qt.QHBoxLayout()
foregroundLabel = slicer.qMRMLLabelComboBox()
foregroundLabel.objectName = 'Foreground label'
foregroundLabel.setMRMLScene(slicer.mrmlScene)
foregroundLabel.setMRMLColorNode(self.editUtil.getColorNode())
foregroundLabel.labelValueVisible = True
foregroundLabel.currentColor = 1
self.foregroundLabel = foregroundLabel
self.connections.append( (self.foregroundLabel, 'currentColorChanged(int)', self.updateMRMLFromGUI ) )
foregroundWeightSpinBox = qt.QDoubleSpinBox(foregroundLabel)
self.foregroundWeightSpinBox = foregroundWeightSpinBox
foregroundWeightSpinBox.setRange(0.0, 1.0)
foregroundWeightSpinBox.setSingleStep(0.1)
foregroundWeightSpinBox.value = 1.0
foregroundPopup = ctk.ctkPopupWidget( foregroundWeightSpinBox )
foregroundPopupLayout = qt.QHBoxLayout( foregroundPopup )
foregroundPopupSlider = ctk.ctkDoubleSlider( foregroundPopup )
self.foregroundPopupSlider = foregroundPopupSlider
foregroundPopupSlider.maximum = 1.0
foregroundPopupSlider.minimum = 0.0
foregroundPopupSlider.singleStep = 0.1
foregroundPopupSlider.connect('valueChanged(double)', self.foregroundWeightSpinBox.setValue)
foregroundWeightSpinBox.connect('valueChanged(double)', self.foregroundPopupSlider.setValue)
self.connections.append( (self.foregroundWeightSpinBox, 'valueChanged(double)', self.updateMRMLFromGUI ) )
foregroundLayout.addWidget( foregroundLabel )
foregroundLayout.addWidget( foregroundWeightSpinBox )
foregroundPopupLayout.addWidget( foregroundPopupSlider )
objectFormLayout.addRow("Foreground Label:", foregroundLayout )
self.objectLabel = foregroundLabel
# http://qt-project.org/doc/qt-4.7/qt.html
foregroundPopup.alignment = 0x0082 # Qt::AlignVCenter | Qt::AlignRight
foregroundPopup.horizontalDirection = 0 # Qt::LeftToRight
foregroundPopup.verticalDirection = 0 # Qt::TopToBottom
foregroundPopup.animationEffect = 1 # Qt::ScrollEffect
backgroundLayout = qt.QHBoxLayout()
backgroundLabel = slicer.qMRMLLabelComboBox()
backgroundLabel.objectName = 'Background label'
backgroundLabel.setMRMLScene(slicer.mrmlScene)
backgroundLabel.setMRMLColorNode(self.editUtil.getColorNode())
backgroundLabel.labelValueVisible = True
backgroundLabel.currentColor = 2
self.backgroundLabel = backgroundLabel
self.connections.append( (self.backgroundLabel, 'currentColorChanged(int)', self.updateMRMLFromGUI ) )
backgroundWeightSpinBox = qt.QDoubleSpinBox(backgroundLabel)
self.backgroundWeightSpinBox = backgroundWeightSpinBox
backgroundWeightSpinBox.setRange(0.0, 1.0)
backgroundWeightSpinBox.setSingleStep(0.1)
backgroundWeightSpinBox.value = 1.0
backgroundPopup = ctk.ctkPopupWidget( backgroundWeightSpinBox )
backgroundPopupLayout = qt.QHBoxLayout( backgroundPopup )
backgroundPopupSlider = ctk.ctkDoubleSlider( backgroundPopup )
self.backgroundPopupSlider = backgroundPopupSlider
backgroundPopupSlider.maximum = 1.0
backgroundPopupSlider.minimum = 0.0
backgroundPopupSlider.singleStep = 0.1
backgroundPopupSlider.connect('valueChanged(double)', self.backgroundWeightSpinBox.setValue)
backgroundWeightSpinBox.connect('valueChanged(double)', self.backgroundPopupSlider.setValue)
self.connections.append( (self.backgroundWeightSpinBox, 'valueChanged(double)', self.updateMRMLFromGUI ) )
backgroundLayout.addWidget( backgroundLabel )
backgroundLayout.addWidget( backgroundWeightSpinBox )
backgroundPopupLayout.addWidget( backgroundPopupSlider )
objectFormLayout.addRow("Background Label:", backgroundLayout)
self.backgroundLabel = backgroundLabel
# http://qt-project.org/doc/qt-4.7/qt.html
backgroundPopup.alignment = 0x0082 # Qt::AlignVCenter | Qt::AlignRight
backgroundPopup.horizontalDirection = 0 # Qt::LeftToRight
backgroundPopup.verticalDirection = 0 # Qt::TopToBottom
backgroundPopup.animationEffect = 1 # Qt::ScrollEffect
# Presets
# Placeholder
presetsCollapsibleGroupBox = ctk.ctkCollapsibleGroupBox()
presetsCollapsibleGroupBox.title = "Preset"
self.frame.layout().addWidget(presetsCollapsibleGroupBox)
presetComboBox = slicer.qSlicerPresetComboBox()
# Advanced Parameters
paramsCollapsibleGroupBox = ctk.ctkCollapsibleGroupBox()
paramsCollapsibleGroupBox.title = "Advanced Parameters"
paramsCollapsibleGroupBox.collapsed = 1
self.frame.layout().addWidget(paramsCollapsibleGroupBox)
# Layout within the io collapsible button
paramsFormLayout = qt.QFormLayout(paramsCollapsibleGroupBox)
erosionSpinBox = qt.QSpinBox()
erosionSpinBox.objectName = 'erosionSpinBox'
erosionSpinBox.toolTip = "Set the erosion radius."
erosionSpinBox.setMinimum(0)
erosionSpinBox.setValue(5) # Default
paramsFormLayout.addRow("Erosion Radius:", erosionSpinBox)
self.erosionSpinBox = erosionSpinBox
self.connections.append( (self.erosionSpinBox, "valueChanged(int)", self.updateMRMLFromGUI ) )
holeFillSpinBox = qt.QSpinBox()
holeFillSpinBox.objectName = 'holeFillSpinBox'
holeFillSpinBox.toolTip = "Set the hole fill iterations."
holeFillSpinBox.setMinimum(0)
holeFillSpinBox.setValue(5) #Default
paramsFormLayout.addRow("Hole Fill Iterations:", holeFillSpinBox)
self.holeFillSpinBox = holeFillSpinBox
self.connections.append( (self.holeFillSpinBox, "valueChanged(int)", self.updateMRMLFromGUI ) )
# probabilitySmoothingStandardDeviation spin box
probabilitySmoothingStdDevSpinBox = qt.QDoubleSpinBox()
probabilitySmoothingStdDevSpinBox.objectName = 'probabilitySmoothingStdDevSpinBox'
probabilitySmoothingStdDevSpinBox.toolTip = "Standard deviation of blur applied to probability images prior to computing maximum likelihood of each class at each pixel."
probabilitySmoothingStdDevSpinBox.setMinimum(0.0)
probabilitySmoothingStdDevSpinBox.setValue(1.0) # Default
probabilitySmoothingStdDevSpinBox.setSingleStep(0.5)
paramsFormLayout.addRow("Probability Smoothing Standard Deviation:", probabilitySmoothingStdDevSpinBox)
self.probabilitySmoothingStdDevSpinBox = probabilitySmoothingStdDevSpinBox
self.connections.append( (self.probabilitySmoothingStdDevSpinBox, "valueChanged(double)", self.updateMRMLFromGUI ) )
# histogramSmoothingStandardDeviation spin box
histogramSmoothingStdDevSpinBox = qt.QDoubleSpinBox()
histogramSmoothingStdDevSpinBox.objectName = 'histogramSmoothingStdDevSpinBox'
histogramSmoothingStdDevSpinBox.toolTip = "Standard deviation of blur applied to histograms to convert them to probability density function estimates."
histogramSmoothingStdDevSpinBox.setMinimum(0.0)
histogramSmoothingStdDevSpinBox.setValue(5.0) # Default
histogramSmoothingStdDevSpinBox.setSingleStep(0.5)
paramsFormLayout.addRow("Probability Smoothing Standard Deviation:", histogramSmoothingStdDevSpinBox)
self.histogramSmoothingStdDevSpinBox = histogramSmoothingStdDevSpinBox
self.connections.append( (self.histogramSmoothingStdDevSpinBox, "valueChanged(double)", self.updateMRMLFromGUI ) )
# draft check box
draftCheckBox = qt.QCheckBox()
draftCheckBox.objectName = 'draftCheckBox'
draftCheckBox.toolTip = "Downsamples results by a factor of 4."
paramsFormLayout.addRow("Draft Mode:", draftCheckBox)
self.draftCheckBox = draftCheckBox
self.connections.append( (self.draftCheckBox, "stateChanged(int)", self.updateMRMLFromGUI ) )
# force classification check box
forceClassificationCheckBox = qt.QCheckBox()
forceClassificationCheckBox.objectName = 'forceClassificationCheckBox'
forceClassificationCheckBox.toolTip = "Perform the classification of all voxels?"
forceClassificationCheckBox.setChecked(False)
paramsFormLayout.addRow("Classify all voxels: ", forceClassificationCheckBox)
self.forceClassificationCheckBox = forceClassificationCheckBox
self.connections.append( (self.forceClassificationCheckBox, "stateChanged(int)", self.updateMRMLFromGUI ) )
# dilate first check box
dilateFirstCheckBox = qt.QCheckBox()
dilateFirstCheckBox.objectName = 'dilateFirstCheckBox'
dilateFirstCheckBox.toolTip = "Dilate and then erode so as to fill-in holes?"
dilateFirstCheckBox.setChecked(False)
paramsFormLayout.addRow("Dilate First: ", dilateFirstCheckBox)
self.dilateFirstCheckBox = dilateFirstCheckBox
self.connections.append( (self.dilateFirstCheckBox, "stateChanged(int)", self.updateMRMLFromGUI ) )
self.helpLabel = qt.QLabel("Run the PDF Segmentation on the current label map.", self.frame)
self.frame.layout().addWidget(self.helpLabel)
self.apply = qt.QPushButton("Apply", self.frame)
self.apply.setToolTip("Apply to run segmentation.\nCreates a new label volume using the current volume as input")
self.frame.layout().addWidget(self.apply)
self.widgets.append(self.apply)
EditorLib.HelpButton(self.frame, "Use this tool to apply segmentation using Parzen windowed PDFs.\n\n Select different label colors and paint on the foreground or background voxels using the paint effect.\nTo run segmentation correctly, you need to supply a minimum or two class labels.")
self.connections.append( (self.apply, 'clicked()', self.onApply) )
def setup(self):
# TODO: The following line is strictly for debug purposes, should be removed when this module is done
slicer.tvwidget = self
# Collapsible buttons
self.parametersCollapsibleButton = ctk.ctkCollapsibleButton()
self.parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(self.parametersCollapsibleButton)
# Layout within the collapsible button
self.parametersFormLayout = qt.QFormLayout(self.parametersCollapsibleButton)
# Transform combobox
self.transformLabel = qt.QLabel()
self.transformLabel.setText("toolCameraToToolTransform: ")
self.transformSelector = slicer.qMRMLNodeComboBox()
self.transformSelector.nodeTypes = ( ("vtkMRMLLinearTransformNode"), "" )
self.transformSelector.noneEnabled = False
self.transformSelector.addEnabled = False
self.transformSelector.removeEnabled = False
self.transformSelector.setMRMLScene( slicer.mrmlScene )
self.transformSelector.setToolTip("Pick the transform that the camera should follow, e.g. 'cauteryCameraToCauteryTransform'")
self.parametersFormLayout.addRow(self.transformLabel, self.transformSelector)
# Camera combobox
self.cameraLabel = qt.QLabel()
self.cameraLabel.setText("Scene Camera: ")
self.cameraSelector = slicer.qMRMLNodeComboBox()
self.cameraSelector.nodeTypes = ( ("vtkMRMLCameraNode"), "" )
self.cameraSelector.noneEnabled = False
self.cameraSelector.addEnabled = False
self.cameraSelector.removeEnabled = False
self.cameraSelector.setMRMLScene( slicer.mrmlScene )
self.cameraSelector.setToolTip("Pick the camera which should be moved, e.g. 'Default Scene Camera'")
self.parametersFormLayout.addRow(self.cameraLabel, self.cameraSelector)
# "Camera Control" Collapsible
self.cameraControlCollapsibleButton = ctk.ctkCollapsibleButton()
self.cameraControlCollapsibleButton.text = "Camera Control"
self.layout.addWidget(self.cameraControlCollapsibleButton)
# Layout within the collapsible button
self.cameraControlFormLayout = qt.QFormLayout(self.cameraControlCollapsibleButton)
# "Degrees of Freedom" Collapsible button
self.degreesOfFreedomCollapsibleButton = ctk.ctkCollapsibleGroupBox()
self.degreesOfFreedomCollapsibleButton.title = "Degrees of Freedom"
self.cameraControlFormLayout.addRow(self.degreesOfFreedomCollapsibleButton)
# Layout within the collapsible button
self.degreesOfFreedomFormLayout = qt.QFormLayout(self.degreesOfFreedomCollapsibleButton)
# A series of radio buttons for changing the degrees of freedom
self.degreesOfFreedom3Label = qt.QLabel(qt.Qt.Horizontal,None)
self.degreesOfFreedom3Label.setText("3DOF: ")
self.degreesOfFreedom3RadioButton = qt.QRadioButton()
self.degreesOfFreedom3RadioButton.setToolTip("The camera will always look at the target model (or if unselected will act like 5DOF)")
self.degreesOfFreedomFormLayout.addRow(self.degreesOfFreedom3Label,self.degreesOfFreedom3RadioButton)
self.degreesOfFreedom5Label = qt.QLabel(qt.Qt.Horizontal,None)
self.degreesOfFreedom5Label.setText("5DOF: ")
self.degreesOfFreedom5RadioButton = qt.QRadioButton()
self.degreesOfFreedom5RadioButton.setToolTip("The camera will always be oriented with the selected 'up direction'")
self.degreesOfFreedomFormLayout.addRow(self.degreesOfFreedom5Label,self.degreesOfFreedom5RadioButton)
self.degreesOfFreedom6Label = qt.QLabel(qt.Qt.Horizontal,None)
self.degreesOfFreedom6Label.setText("6DOF: ")
self.degreesOfFreedom6RadioButton = qt.QRadioButton()
self.degreesOfFreedom6RadioButton.setToolTip("The camera will be virtually attached to the tool, and rotate together with it")
self.degreesOfFreedom6RadioButton.setChecked(True)
self.degreesOfFreedomFormLayout.addRow(self.degreesOfFreedom6Label,self.degreesOfFreedom6RadioButton)
# "Up Direction" Collapsible button
self.upDirectionCollapsibleButton = ctk.ctkCollapsibleGroupBox()
self.upDirectionCollapsibleButton.title = "Up Direction"
self.upDirectionCollapsibleButton.setVisible(False)
self.cameraControlFormLayout.addRow(self.upDirectionCollapsibleButton)
# Layout within the collapsible button
self.upDirectionFormLayout = qt.QFormLayout(self.upDirectionCollapsibleButton)
# Radio buttons for each of the anatomical directions
self.upDirectionAnteriorLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.upDirectionAnteriorLabel.setText("Anterior: ")
self.upDirectionAnteriorRadioButton = qt.QRadioButton()
self.upDirectionAnteriorRadioButton.setChecked(True)
self.upDirectionFormLayout.addRow(self.upDirectionAnteriorLabel,self.upDirectionAnteriorRadioButton)
self.upDirectionPosteriorLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.upDirectionPosteriorLabel.setText("Posterior: ")
self.upDirectionPosteriorRadioButton = qt.QRadioButton()
self.upDirectionFormLayout.addRow(self.upDirectionPosteriorLabel,self.upDirectionPosteriorRadioButton)
self.upDirectionRightLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.upDirectionRightLabel.setText("Right: ")
self.upDirectionRightRadioButton = qt.QRadioButton()
self.upDirectionFormLayout.addRow(self.upDirectionRightLabel,self.upDirectionRightRadioButton)
self.upDirectionLeftLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.upDirectionLeftLabel.setText("Left: ")
self.upDirectionLeftRadioButton = qt.QRadioButton()
self.upDirectionFormLayout.addRow(self.upDirectionLeftLabel,self.upDirectionLeftRadioButton)
self.upDirectionSuperiorLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.upDirectionSuperiorLabel.setText("Superior: ")
self.upDirectionSuperiorRadioButton = qt.QRadioButton()
self.upDirectionFormLayout.addRow(self.upDirectionSuperiorLabel,self.upDirectionSuperiorRadioButton)
self.upDirectionInferiorLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.upDirectionInferiorLabel.setText("Inferior: ")
self.upDirectionInferiorRadioButton = qt.QRadioButton()
self.upDirectionFormLayout.addRow(self.upDirectionInferiorLabel,self.upDirectionInferiorRadioButton)
# "Target Model" Collapsible button
self.targetModelCollapsibleButton = ctk.ctkCollapsibleGroupBox()
self.targetModelCollapsibleButton.title = "Target Model"
self.targetModelCollapsibleButton.setVisible(False)
self.cameraControlFormLayout.addRow(self.targetModelCollapsibleButton)
# Layout within the collapsible button
self.targetModelFormLayout = qt.QFormLayout(self.targetModelCollapsibleButton)
# Selection of the target model
self.targetModelLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.targetModelLabel.text = "Target model: "
self.targetModelSelector = slicer.qMRMLNodeComboBox()
self.targetModelSelector.nodeTypes = ( ("vtkMRMLModelNode"), "" )
self.targetModelSelector.noneEnabled = False
self.targetModelSelector.addEnabled = False
self.targetModelSelector.removeEnabled = False
self.targetModelSelector.setMRMLScene( slicer.mrmlScene )
self.targetModelSelector.setToolTip("This model be the center of rotation using 3DOF Viewpoint (e.g. tumour)")
self.targetModelFormLayout.addRow(self.targetModelLabel,self.targetModelSelector)
# "Zoom" Collapsible button
self.zoomCollapsibleButton = ctk.ctkCollapsibleGroupBox()
self.zoomCollapsibleButton.title = "Zoom"
self.cameraControlFormLayout.addRow(self.zoomCollapsibleButton)
# Layout within the collapsible button
self.zoomFormLayout = qt.QFormLayout(self.zoomCollapsibleButton)
# Camera viewing angle (perspective projection only)
self.cameraViewAngleLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.cameraViewAngleLabel.setText("View angle (degrees): ")
self.cameraViewAngleSlider = slicer.qMRMLSliderWidget()
self.cameraViewAngleSlider.minimum = self.cameraViewAngleMinDeg
self.cameraViewAngleSlider.maximum = self.cameraViewAngleMaxDeg
self.cameraViewAngleSlider.value = self.sliderViewAngleDefaultDeg
self.cameraViewAngleSlider.singleStep = self.sliderSingleStepValue
self.cameraViewAngleSlider.pageStep = self.sliderPageStepValue
self.cameraViewAngleSlider.setToolTip("Make the current viewing target look larger/smaller.")
self.zoomFormLayout.addRow(self.cameraViewAngleLabel,self.cameraViewAngleSlider)
# Camera parallel scale (parallel projection only)
self.cameraParallelScaleLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.cameraParallelScaleLabel.setText("View scale: ")
self.cameraParallelScaleLabel.setVisible(False)
self.cameraParallelScaleSlider = slicer.qMRMLSliderWidget()
self.cameraParallelScaleSlider.minimum = self.cameraParallelScaleMinDeg
self.cameraParallelScaleSlider.maximum = self.cameraParallelScaleMaxDeg
self.cameraParallelScaleSlider.value = self.sliderParallelScaleDefaultDeg
self.cameraParallelScaleSlider.singleStep = self.sliderSingleStepValue
self.cameraParallelScaleSlider.pageStep = self.sliderPageStepValue
self.cameraParallelScaleSlider.setToolTip("Make the current viewing target look larger/smaller.")
self.cameraParallelScaleSlider.setVisible(False)
self.zoomFormLayout.addRow(self.cameraParallelScaleLabel,self.cameraParallelScaleSlider)
# "Translation" Collapsible
self.translationCollapsibleButton = ctk.ctkCollapsibleGroupBox()
self.translationCollapsibleButton.title = "Translation"
self.cameraControlFormLayout.addRow(self.translationCollapsibleButton)
# Layout within the collapsible button
self.translationFormLayout = qt.QFormLayout(self.translationCollapsibleButton)
self.cameraXPosLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.cameraXPosLabel.text = "Left/Right (mm): "
self.cameraXPosSlider = slicer.qMRMLSliderWidget()
self.cameraXPosSlider.minimum = self.sliderTranslationMinMm
self.cameraXPosSlider.maximum = self.sliderTranslationMaxMm
self.cameraXPosSlider.value = self.sliderTranslationDefaultMm
self.cameraXPosSlider.singleStep = self.sliderSingleStepValue
self.cameraXPosSlider.pageStep = self.sliderPageStepValue
self.translationFormLayout.addRow(self.cameraXPosLabel,self.cameraXPosSlider)
self.cameraYPosLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.cameraYPosLabel.setText("Down/Up (mm): ")
self.cameraYPosSlider = slicer.qMRMLSliderWidget()
self.cameraYPosSlider.minimum = self.sliderTranslationMinMm
self.cameraYPosSlider.maximum = self.sliderTranslationMaxMm
self.cameraYPosSlider.value = self.sliderTranslationDefaultMm
self.cameraYPosSlider.singleStep = self.sliderSingleStepValue
self.cameraYPosSlider.pageStep = self.sliderPageStepValue
self.translationFormLayout.addRow(self.cameraYPosLabel,self.cameraYPosSlider)
self.cameraZPosLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.cameraZPosLabel.setText("Front/Back (mm): ")
self.cameraZPosSlider = slicer.qMRMLSliderWidget()
self.cameraZPosSlider.minimum = self.sliderTranslationMinMm
self.cameraZPosSlider.maximum = self.sliderTranslationMaxMm
self.cameraZPosSlider.value = self.sliderTranslationDefaultMm
self.cameraZPosSlider.singleStep = self.sliderSingleStepValue
self.cameraZPosSlider.pageStep = self.sliderPageStepValue
self.translationFormLayout.addRow(self.cameraZPosLabel,self.cameraZPosSlider)
# "Model Visibility" Collapsible
self.modelVisibilityCollapsibleButton = ctk.ctkCollapsibleGroupBox()
self.modelVisibilityCollapsibleButton.title = "Model Visibility"
self.cameraControlFormLayout.addRow(self.modelVisibilityCollapsibleButton)
# Layout within the collapsible button
self.modelVisibilityFormLayout = qt.QFormLayout(self.modelVisibilityCollapsibleButton)
self.modelOnlyViewpointOnLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.modelOnlyViewpointOnLabel.text = "Model visible only for Viewpoint on: "
self.modelOnlyViewpointOnSelector = slicer.qMRMLNodeComboBox()
self.modelOnlyViewpointOnSelector.nodeTypes = ( ("vtkMRMLModelNode"), "" )
self.modelOnlyViewpointOnSelector.noneEnabled = True
self.modelOnlyViewpointOnSelector.addEnabled = False
self.modelOnlyViewpointOnSelector.removeEnabled = False
self.modelOnlyViewpointOnSelector.setMRMLScene( slicer.mrmlScene )
self.modelOnlyViewpointOnSelector.setToolTip("This model be visible if Viewpoint mode is enabled, and invisible otherwise")
self.modelVisibilityFormLayout.addRow(self.modelOnlyViewpointOnLabel,self.modelOnlyViewpointOnSelector)
self.modelOnlyViewpointOffLabel = qt.QLabel(qt.Qt.Horizontal,None)
self.modelOnlyViewpointOffLabel.text = "Model visible only for Viewpoint off: "
self.modelOnlyViewpointOffSelector = slicer.qMRMLNodeComboBox()
self.modelOnlyViewpointOffSelector.nodeTypes = ( ("vtkMRMLModelNode"), "" )
self.modelOnlyViewpointOffSelector.noneEnabled = True
self.modelOnlyViewpointOffSelector.addEnabled = False
self.modelOnlyViewpointOffSelector.removeEnabled = False
self.modelOnlyViewpointOffSelector.setMRMLScene( slicer.mrmlScene )
self.modelOnlyViewpointOffSelector.setToolTip("This model be visible if Viewpoint Mode is disabled, and invisible otherwise")
self.modelVisibilityFormLayout.addRow(self.modelOnlyViewpointOffLabel,self.modelOnlyViewpointOffSelector)
# Camera parallel projection checkbox
self.cameraParallelProjectionLabel = qt.QLabel()
self.cameraParallelProjectionLabel.setText("Parallel Projection")
self.cameraParallelProjectionCheckbox = qt.QCheckBox()
self.cameraParallelProjectionCheckbox.setCheckState(0)
self.cameraParallelProjectionCheckbox.setToolTip("If checked, render with parallel projection (box-shaped view). Otherwise render with perspective projection (cone-shaped view).")
self.cameraControlFormLayout.addRow(self.cameraParallelProjectionLabel,self.cameraParallelProjectionCheckbox)
# "Toggle Tool Point of View" button
self.enableViewpointButton = qt.QPushButton()
self.enableViewpointButton.setToolTip("The camera will continuously update its position so that it follows the tool.")
self.enableViewpointButton.setText(self.enableViewpointButtonTextState0)
self.cameraControlFormLayout.addRow(self.enableViewpointButton)
#Connections
self.enableViewpointButton.connect('clicked()', self.enableViewpointButtonPressed)
self.cameraParallelProjectionCheckbox.connect('stateChanged(int)', self.toggleCameraParallelProjectionCheckboxPressed)
self.cameraViewAngleSlider.connect('valueChanged(double)', self.logic.SetCameraViewAngleDeg)
self.cameraParallelScaleSlider.connect('valueChanged(double)', self.logic.SetCameraParallelScale)
self.cameraXPosSlider.connect('valueChanged(double)', self.logic.SetCameraXPosMm)
self.cameraYPosSlider.connect('valueChanged(double)', self.logic.SetCameraYPosMm)
self.cameraZPosSlider.connect('valueChanged(double)', self.logic.SetCameraZPosMm)
self.upDirectionAnteriorRadioButton.connect('clicked()', self.changeUpToAnterior)
self.upDirectionPosteriorRadioButton.connect('clicked()', self.changeUpToPosterior)
self.upDirectionLeftRadioButton.connect('clicked()', self.changeUpToLeft)
self.upDirectionRightRadioButton.connect('clicked()', self.changeUpToRight)
self.upDirectionSuperiorRadioButton.connect('clicked()', self.changeUpToSuperior)
self.upDirectionInferiorRadioButton.connect('clicked()', self.changeUpToInferior)
self.degreesOfFreedom3RadioButton.connect('clicked()', self.changeInterfaceTo3DOFMode)
self.degreesOfFreedom5RadioButton.connect('clicked()', self.changeInterfaceTo5DOFMode)
self.degreesOfFreedom6RadioButton.connect('clicked()', self.changeInterfaceTo6DOFMode)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
# Instantiate and connect widgets ...
# Status text
statusCollapsibleButton = ctk.ctkCollapsibleButton()
statusCollapsibleButton.text = "Status"
self.layout.addWidget(statusCollapsibleButton)
self.statusFormLayout = qt.QFormLayout(statusCollapsibleButton)
self.overallStatus = qt.QLabel()
self.overallStatus.text = "Idle"
self.statusFormLayout.addRow("New Process:", self.overallStatus)
self.processes = list()
#
# Volumes
#
self.inputImagesCollapsibleButton = ctk.ctkCollapsibleButton()
self.inputImagesCollapsibleButton.text = "Input Images"
self.layout.addWidget(self.inputImagesCollapsibleButton)
# Layout within the collapsible button
inputImagesFormLayout = qt.QFormLayout(self.inputImagesCollapsibleButton)
# input volume selector
self.fixedVolumeSelector = slicer.qMRMLNodeComboBox()
self.fixedVolumeSelector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.fixedVolumeSelector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap", 0)
self.fixedVolumeSelector.selectNodeUponCreation = True
self.fixedVolumeSelector.addEnabled = True
self.fixedVolumeSelector.removeEnabled = True
self.fixedVolumeSelector.noneEnabled = False
self.fixedVolumeSelector.showHidden = False
self.fixedVolumeSelector.showChildNodeTypes = False
self.fixedVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.fixedVolumeSelector.setToolTip("Pick the fixed input to the algorithm.")
inputImagesFormLayout.addRow("Fixed Image Volume: ", self.fixedVolumeSelector)
# Moving volume selector
self.movingVolumeSelector = slicer.qMRMLCheckableNodeComboBox()
# self.movingVolumeSelector = slicer.qMRMLNodeComboBox()
self.movingVolumeSelector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.movingVolumeSelector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap", 0)
self.movingVolumeSelector.selectNodeUponCreation = True
self.movingVolumeSelector.addEnabled = True
self.movingVolumeSelector.removeEnabled = True
self.movingVolumeSelector.noneEnabled = False
self.movingVolumeSelector.showHidden = False
self.movingVolumeSelector.showChildNodeTypes = False
self.movingVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.movingVolumeSelector.setToolTip("Pick the moving volume to the algorithm.")
inputImagesFormLayout.addRow("Moving Volume: ", self.movingVolumeSelector)
#
# Crop parameters
#
self.cropParametersCollapsibleButton = ctk.ctkCollapsibleButton()
self.cropParametersCollapsibleButton.text = "Crop Parameters"
self.layout.addWidget(self.cropParametersCollapsibleButton)
cropParametersFormLayout = qt.QFormLayout(self.cropParametersCollapsibleButton)
cropParametersFormLayout
# Input ROI
self.annotationROISelector = slicer.qMRMLNodeComboBox()
self.annotationROISelector.nodeTypes = (("vtkMRMLAnnotationROINode"), "")
self.annotationROISelector.editEnabled = True
self.annotationROISelector.renameEnabled = True
self.annotationROISelector.setMRMLScene(slicer.mrmlScene)
self.annotationROISelector.setToolTip("Pick the fixed input to the algorithm.")
cropParametersFormLayout.addRow("Input ROI: ", self.annotationROISelector)
# ROI Visibility
self.ROIVisibilityButton = qt.QToolButton()
visibilityIcon = qt.QIcon()
visibilityIcon.addPixmap(qt.QPixmap(":/Icons/VisibleOff.png"), qt.QIcon().Normal, qt.QIcon().Off)
visibilityIcon.addPixmap(qt.QPixmap(":/Icons/VisibleOn.png"), qt.QIcon().Normal, qt.QIcon().On)
self.ROIVisibilityButton.setIcon(visibilityIcon)
self.ROIVisibilityButton.setCheckable(True)
cropParametersFormLayout.addRow("Visibility ROI:", self.ROIVisibilityButton)
# Cropping technique
croppingTechniqueLayout = qt.QHBoxLayout()
self.interpolationButton = qt.QRadioButton("Interpolated cropping")
self.interpolationButton.setChecked(True)
self.voxelBasedButton = qt.QRadioButton("Voxel based cropping")
croppingTechniqueLayout.addWidget(self.interpolationButton)
croppingTechniqueLayout.addWidget(self.voxelBasedButton)
cropParametersFormLayout.addRow("Technique: ", croppingTechniqueLayout)
# Interpolation options
self.interpolationOptionsCollapsibleGroupBox = ctk.ctkCollapsibleGroupBox()
self.interpolationOptionsCollapsibleGroupBox.title = "Interpolation options"
cropParametersFormLayout.addRow("", self.interpolationOptionsCollapsibleGroupBox)
interpolationOptionsLayout = qt.QFormLayout(self.interpolationOptionsCollapsibleGroupBox)
interpolationOptionsLayout.setFieldGrowthPolicy(qt.QFormLayout().ExpandingFieldsGrow)
interpolationOptionsLayout.setRowWrapPolicy(qt.QFormLayout().WrapLongRows)
# Isotropic
self.isotropicCheckBox = qt.QCheckBox()
self.isotropicCheckBox.checked = True
interpolationOptionsLayout.addRow("Isotropic output voxel", self.isotropicCheckBox)
# Input spacing scaling constant
self.inputSpacingScaling = qt.QDoubleSpinBox()
self.inputSpacingScaling.setToolTip(
"In not equal to 1, this will result in upsampling (<1) or downlsampling (>1) relative to the voxel spacing of the input volume."
)
self.inputSpacingScaling.value = 1.000000
interpolationOptionsLayout.addRow("Input spacing scaling constant: ", self.inputSpacingScaling)
# Interpolator technique
interpolatorWidget = qt.QWidget()
sizep = qt.QSizePolicy()
sizep.setHorizontalPolicy(qt.QSizePolicy().Expanding)
sizep.setVerticalPolicy(qt.QSizePolicy().Preferred)
sizep.setHorizontalStretch(0)
sizep.setVerticalStretch(0)
interpolatorWidget.setSizePolicy(sizep)
interpolatorLayout = qt.QGridLayout(interpolatorWidget)
interpolationOptionsLayout.addRow("Technique: ", interpolatorWidget)
self.iNNButton = qt.QRadioButton("Nearest Neighbor")
self.iLinearButton = qt.QRadioButton("Linear")
self.iWindowedSincButton = qt.QRadioButton("WindowedSinc")
self.iBSplineButton = qt.QRadioButton("B-spline")
self.iNNButton.setSizePolicy(qt.QSizePolicy().Minimum, qt.QSizePolicy().Preferred)
self.iLinearButton.setSizePolicy(qt.QSizePolicy().MinimumExpanding, qt.QSizePolicy().Preferred)
self.iWindowedSincButton.setSizePolicy(qt.QSizePolicy().Minimum, qt.QSizePolicy().Preferred)
self.iBSplineButton.setSizePolicy(qt.QSizePolicy().MinimumExpanding, qt.QSizePolicy().Preferred)
self.iLinearButton.setChecked(True)
interpolatorLayout.addWidget(self.iNNButton, 0, 0)
interpolatorLayout.addWidget(self.iLinearButton, 0, 1)
interpolatorLayout.addWidget(self.iWindowedSincButton, 1, 0)
interpolatorLayout.addWidget(self.iBSplineButton, 1, 1)
#
# Crop Button
#
self.cropButton = qt.QPushButton("Crop")
self.cropButton.toolTip = "Crop the fixed volume."
self.cropButton.enabled = False
self.layout.addWidget(self.cropButton)
# Align and crop
self.alignAndCropButton = qt.QPushButton("Align and Crop")
self.alignAndCropButton.toolTip = "Align moving volumes with fixed volume and crop all the images"
self.alignAndCropButton.enabled = False
self.layout.addWidget(self.alignAndCropButton)
self.layout.addStretch(1)
self.cropParametersNode = slicer.modulemrml.vtkMRMLCropVolumeParametersNode()
self.onFixedVolumeSelect()
self.onMovingVolumeSelect()
self.onAnnotationROIChanged()
self.onROIVisibilityChanged()
# connections
self.cropButton.connect("clicked(bool)", self.onCrop)
self.alignAndCropButton.connect("clicked(bool)", self.onAlignAndCrop)
self.fixedVolumeSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onFixedVolumeSelect)
self.movingVolumeSelector.connect("checkedNodesChanged(void)", self.onMovingVolumeSelect)
self.annotationROISelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onAnnotationROIChanged)
self.ROIVisibilityButton.connect("toggled(bool)", self.onROIVisibilityChanged)
self.voxelBasedButton.connect("clicked(bool)", self.onVoxelBasedButtonClicked)
self.interpolationButton.connect("clicked(bool)", self.onInterpolationButtonClicked)
# Display current fixed node
self.displayFixedVolume()
self.updateCropParameters()
self.outputNodes = dict()
self.nreg_completed = 0
def setup(self):
self.pointRecorderLogic = PointRecorderLogic()
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
# Icons stuff
self.moduleDirectoryPath = slicer.modules.pointrecorder.path.replace("PointRecorder.py","")
self.playIcon = qt.QIcon(self.moduleDirectoryPath + '/Resources/Icons/playIcon.png')
self.stopIcon = qt.QIcon(self.moduleDirectoryPath + '/Resources/Icons/stopIcon.png')
self.recordIcon = qt.QIcon(self.moduleDirectoryPath + '/Resources/Icons/recordIcon.png')
self.restartIcon = qt.QIcon(self.moduleDirectoryPath + '/Resources/Icons/restartIcon.png')
self.saveIcon = qt.QIcon(self.moduleDirectoryPath + '/Resources/Icons/saveIcon.png')
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# input transform selector
#
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = ["vtkMRMLLinearTransformNode"]
self.inputSelector.selectNodeUponCreation = True
self.inputSelector.addEnabled = False
self.inputSelector.removeEnabled = False
self.inputSelector.noneEnabled = False
self.inputSelector.showChildNodeTypes = False
self.inputSelector.setMRMLScene( slicer.mrmlScene )
self.inputSelector.setToolTip( "Pick the input to the algorithm." )
parametersFormLayout.addRow("Modified Transform: ", self.inputSelector)
#
# input transform selector
#
self.fixedSelector = slicer.qMRMLNodeComboBox()
self.fixedSelector.nodeTypes = ["vtkMRMLLinearTransformNode"]
self.fixedSelector.selectNodeUponCreation = True
self.fixedSelector.addEnabled = False
self.fixedSelector.removeEnabled = False
self.fixedSelector.noneEnabled = False
self.fixedSelector.showChildNodeTypes = False
self.fixedSelector.setMRMLScene( slicer.mrmlScene )
self.fixedSelector.setToolTip( "Pick the input to the algorithm." )
parametersFormLayout.addRow("Spatial Transform: ", self.fixedSelector)
# Controls
self.controlsGroupBox = ctk.ctkCollapsibleGroupBox()
self.controlsGroupBox.setTitle("Controls")
controlsFormLayout = qt.QFormLayout(self.controlsGroupBox)
parametersFormLayout.addRow(self.controlsGroupBox)
hBoxLayoutControls = qt.QHBoxLayout()
controlsFormLayout.addRow(hBoxLayoutControls)
self.recordButton = qt.QPushButton(" Record")
self.recordButton.setIcon(self.recordIcon)
self.recordButton.setSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
self.recordButton.enabled = False
self.recordButton.checkable = True
hBoxLayoutControls.addWidget(self.recordButton)
self.saveButton = qt.QPushButton(" Save")
self.saveButton.setIcon(self.saveIcon)
self.saveButton.setSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
self.saveButton.enabled = False
hBoxLayoutControls.addWidget(self.saveButton)
self.resetButton = qt.QPushButton(" Reset")
self.resetButton.setIcon(self.restartIcon)
self.resetButton.setSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
self.resetButton.enabled = False
hBoxLayoutControls.addWidget(self.resetButton)
hBoxCheckBoxes = qt.QHBoxLayout()
controlsFormLayout.addRow(hBoxCheckBoxes)
self.singlePointCheckBox = qt.QCheckBox('Single Measurements')
self.singlePointCheckBox.checked = False
self.singlePointCheckBox.enabled = False
hBoxCheckBoxes.addWidget(self.singlePointCheckBox)
# connections
self.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.recordButton.connect('clicked(bool)', self.onRecordClicked)
self.resetButton.connect('clicked(bool)', self.onResetClicked)
self.saveButton.connect('clicked(bool)', self.onSaveClicked)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onSelect()
self.pointRecorderLogic.setLayout()
def setupNavigationPanel(self):
logging.debug('setupNavigationPanel')
self.sliderTranslationDefaultMm = 0
self.sliderTranslationMinMm = -500
self.sliderTranslationMaxMm = 500
self.sliderViewAngleDefaultDeg = 30
self.cameraViewAngleMinDeg = 5.0 # maximum magnification
self.cameraViewAngleMaxDeg = 150.0 # minimum magnification
self.sliderSingleStepValue = 1
self.sliderPageStepValue = 10
self.navigationCollapsibleButton.setProperty('collapsedHeight', 20)
setButtonStyle(self.navigationCollapsibleButton, 2.0)
self.navigationCollapsibleButton.text = "Navigation"
self.sliceletPanelLayout.addWidget(self.navigationCollapsibleButton)
self.navigationCollapsibleLayout = qt.QFormLayout(
self.navigationCollapsibleButton)
self.navigationCollapsibleLayout.setContentsMargins(12, 4, 4, 4)
self.navigationCollapsibleLayout.setSpacing(4)
self.rightCameraButton = qt.QPushButton("Setup right camera")
self.rightCameraButton.setCheckable(True)
setButtonStyle(self.rightCameraButton)
self.leftCameraButton = qt.QPushButton("Setup left camera")
self.leftCameraButton.setCheckable(True)
setButtonStyle(self.leftCameraButton)
hbox = qt.QHBoxLayout()
hbox.addWidget(self.leftCameraButton)
hbox.addWidget(self.rightCameraButton)
self.navigationCollapsibleLayout.addRow(hbox)
# "Camera Control" Collapsible
self.zoomCollapsibleButton = ctk.ctkCollapsibleGroupBox()
self.zoomCollapsibleButton.collapsed = True
self.zoomCollapsibleButton.title = "Zoom"
self.navigationCollapsibleLayout.addRow(self.zoomCollapsibleButton)
# Layout within the collapsible button
self.zoomFormLayout = qt.QFormLayout(self.zoomCollapsibleButton)
# Camera distance to focal point slider
self.cameraViewAngleLabel = qt.QLabel(qt.Qt.Horizontal, None)
self.cameraViewAngleLabel.setText("Field of view [degrees]: ")
self.cameraViewAngleSlider = slicer.qMRMLSliderWidget()
self.cameraViewAngleSlider.minimum = self.cameraViewAngleMinDeg
self.cameraViewAngleSlider.maximum = self.cameraViewAngleMaxDeg
self.cameraViewAngleSlider.value = self.sliderViewAngleDefaultDeg
self.cameraViewAngleSlider.singleStep = self.sliderSingleStepValue
self.cameraViewAngleSlider.pageStep = self.sliderPageStepValue
self.cameraViewAngleSlider.setDisabled(True)
self.zoomFormLayout.addRow(self.cameraViewAngleLabel,
self.cameraViewAngleSlider)
# "Camera Control" Collapsible
self.translationCollapsibleButton = ctk.ctkCollapsibleGroupBox()
self.translationCollapsibleButton.title = "Translation"
self.translationCollapsibleButton.collapsed = True
self.navigationCollapsibleLayout.addRow(
self.translationCollapsibleButton)
# Layout within the collapsible button
self.translationFormLayout = qt.QFormLayout(
self.translationCollapsibleButton)
self.cameraXPosLabel = qt.QLabel(qt.Qt.Horizontal, None)
self.cameraXPosLabel.text = "Left/Right [mm]: "
self.cameraXPosSlider = slicer.qMRMLSliderWidget()
setButtonStyle(self.cameraXPosSlider)
self.cameraXPosSlider.minimum = self.sliderTranslationMinMm
self.cameraXPosSlider.maximum = self.sliderTranslationMaxMm
self.cameraXPosSlider.value = self.sliderTranslationDefaultMm
self.cameraXPosSlider.singleStep = self.sliderSingleStepValue
self.cameraXPosSlider.pageStep = self.sliderPageStepValue
self.cameraXPosSlider.setDisabled(True)
self.translationFormLayout.addRow(self.cameraXPosLabel,
self.cameraXPosSlider)
self.cameraYPosLabel = qt.QLabel(qt.Qt.Horizontal, None)
self.cameraYPosLabel.setText("Down/Up [mm]: ")
self.cameraYPosSlider = slicer.qMRMLSliderWidget()
setButtonStyle(self.cameraYPosSlider)
self.cameraYPosSlider.minimum = self.sliderTranslationMinMm
self.cameraYPosSlider.maximum = self.sliderTranslationMaxMm
self.cameraYPosSlider.value = self.sliderTranslationDefaultMm
self.cameraYPosSlider.singleStep = self.sliderSingleStepValue
self.cameraYPosSlider.pageStep = self.sliderPageStepValue
self.cameraYPosSlider.setDisabled(True)
self.translationFormLayout.addRow(self.cameraYPosLabel,
self.cameraYPosSlider)
self.cameraZPosLabel = qt.QLabel(qt.Qt.Horizontal, None)
self.cameraZPosLabel.setText("Front/Back [mm]: ")
self.cameraZPosSlider = slicer.qMRMLSliderWidget()
setButtonStyle(self.cameraZPosSlider)
self.cameraZPosSlider.minimum = self.sliderTranslationMinMm
self.cameraZPosSlider.maximum = self.sliderTranslationMaxMm
self.cameraZPosSlider.value = self.sliderTranslationDefaultMm
self.cameraZPosSlider.singleStep = self.sliderSingleStepValue
self.cameraZPosSlider.pageStep = self.sliderPageStepValue
self.cameraZPosSlider.setDisabled(True)
self.translationFormLayout.addRow(self.cameraZPosLabel,
self.cameraZPosSlider)
# "Contour adjustment" Collapsible
self.contourAdjustmentCollapsibleButton = ctk.ctkCollapsibleGroupBox()
self.contourAdjustmentCollapsibleButton.title = "Contour adjustment"
self.contourAdjustmentCollapsibleButton.collapsed = True
self.navigationCollapsibleLayout.addRow(
self.contourAdjustmentCollapsibleButton)
# Layout within the collapsible button
self.contourAdjustmentFormLayout = qt.QFormLayout(
self.contourAdjustmentCollapsibleButton)
self.placeTumorPointAtCauteryTipButton = qt.QPushButton(
"Mark point at cautery tip")
setButtonStyle(self.placeTumorPointAtCauteryTipButton)
self.contourAdjustmentFormLayout.addRow(
self.placeTumorPointAtCauteryTipButton)
self.deleteLastFiducialDuringNavigationButton = qt.QPushButton(
"Delete last")
self.deleteLastFiducialDuringNavigationButton.setIcon(
qt.QIcon(":/Icons/MarkupsDelete.png"))
setButtonStyle(self.deleteLastFiducialDuringNavigationButton)
self.deleteLastFiducialDuringNavigationButton.setEnabled(False)
self.contourAdjustmentFormLayout.addRow(
self.deleteLastFiducialDuringNavigationButton)
def setup(self):
self.logic = BoneEnhancerPyLogic()
ScriptedLoadableModuleWidget.setup(self)
############################################################ Define algorithms
self.example = AlgorithmParams("Example Algorithm",
{"1st Parameter" : (1, 1, 1, 1, 0.5, "1st parameter toolTip"),
"2nd Parameter" : (0, 1, 0, 10, 5, "2nd parameter toolTip"),
"3rd Parameter" : (1, 1, 1, 100, 50, "3rd parameter toolTip")})
self.foroughi2007 = AlgorithmParams("Foroughi2007 (with minor modifications)",
{"Smoothing Sigma" : (1, 1, 1, 10, 5.0, "Smoothing Sigma ToolTip"),
"Transducer Margin" : (0, 1, 0, 300, 60, "Transducer Margin ToolTip"),
"Shadow Sigma" : (1, 1, 1, 10, 6.0, "Shadow Sigma ToolTip"),
"Bone Threshold" : (1, 0.1, 0, 1, 0.4, "Bone Threshold ToolTip"),
"Blurred vs. BLoG" : (1, 0.1, 0, 10, 3, "Blurred vs. BLoG ToolTip"),
"Shadow vs. Intensity" : (1, 0.1, 0, 10, 5, "Shadow vs. Intensity ToolTip")})
self.algorithms = (self.example, self.foroughi2007)
# Set default algorithm
self.defaultAlgorithm = self.foroughi2007
############################################################ BoneEnhancer
boneEnhancerCollapsibleButton = ctk.ctkCollapsibleButton()
boneEnhancerCollapsibleButton.text = "BoneEnhancer"
self.layout.addWidget(boneEnhancerCollapsibleButton)
boneEnhancerFormLayout = qt.QFormLayout(boneEnhancerCollapsibleButton)
self.ultrasoundImageSelector = slicer.qMRMLNodeComboBox()
self.ultrasoundImageSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.ultrasoundImageSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", 0 )
self.ultrasoundImageSelector.selectNodeUponCreation = True
self.ultrasoundImageSelector.addEnabled = False
self.ultrasoundImageSelector.removeEnabled = False
self.ultrasoundImageSelector.noneEnabled = False
self.ultrasoundImageSelector.showHidden = False
self.ultrasoundImageSelector.showChildNodeTypes = False
self.ultrasoundImageSelector.setMRMLScene( slicer.mrmlScene )
self.ultrasoundImageSelector.setToolTip( "Pick the input to the algorithm." )
boneEnhancerFormLayout.addRow("Ultrasound Image: ", self.ultrasoundImageSelector)
# Select algorithm
self.algorithmGroupBox = ctk.ctkCollapsibleGroupBox()
self.algorithmGroupBox.setTitle("Select Algorithm")
algorithmFormLayout = qt.QFormLayout(self.algorithmGroupBox)
boneEnhancerFormLayout.addRow(self.algorithmGroupBox)
for algorithm in self.algorithms:
algorithmFormLayout.addRow(algorithm.GetRadioButton())
algorithm.GetRadioButton().connect("toggled(bool)", self.onRadioButtonPressed)
# Parameters
self.parametersGroupBox = ctk.ctkCollapsibleGroupBox()
self.parametersGroupBox.setTitle("Parameters")
self.parametersFormLayout = qt.QFormLayout(self.parametersGroupBox)
boneEnhancerFormLayout.addRow(self.parametersGroupBox)
for algorithm in self.algorithms:
self.parametersFormLayout.addWidget(algorithm.getSliderWidget())
algorithm.paramChangedCallback = self.onParameterChanged
# Runtime
self.runtimeGroupBox = ctk.ctkCollapsibleGroupBox()
self.runtimeGroupBox.setTitle("Runtime")
runtimeFormLayout = qt.QFormLayout(self.runtimeGroupBox)
boneEnhancerFormLayout.addRow(self.runtimeGroupBox)
self.runtimeLabel = qt.QLabel()
self.runtimeLabel.setText("... s.")
self.runtimeLabel.setWordWrap(True)
self.runtimeLabel.setStyleSheet("QLabel { background-color : black; \
color : #66FF00; \
height : 60px; \
border-style: outset; \
border-width: 5px; \
border-radius: 10px; \
font: bold 14px; \
padding: 0px;\
font-family : SimSun; \
qproperty-alignment: AlignCenter}")
runtimeFormLayout.addRow(self.runtimeLabel)
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = False
self.applyButton.checkable = True
boneEnhancerFormLayout.addRow(self.applyButton)
############################################################ Connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.ultrasoundImageSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.layout.addStretch(1)
self.defaultAlgorithm.GetRadioButton().checked = True
self.onSelect()
self.ModuleLayoutID = -1
self.setModuleLayout()
def setup(self):
#Instantiate and Connect Widgets
#################################################
#HeterogeneityCAD Inputs Collapsible Button
self.inputHeterogeneityCADCollapsibleButton = ctk.ctkCollapsibleButton(
)
self.inputHeterogeneityCADCollapsibleButton.text = "HeterogeneityCAD Input"
self.layout.addWidget(self.inputHeterogeneityCADCollapsibleButton)
self.inputHeterogeneityCADLayout = qt.QFormLayout(
self.inputHeterogeneityCADCollapsibleButton)
##Input Volume as a PET/CT/MRI image or parameter map converted to a volume
self.inputVolHetFrame = qt.QFrame(
self.inputHeterogeneityCADCollapsibleButton)
self.inputVolHetFrame.setLayout(qt.QHBoxLayout())
self.inputHeterogeneityCADLayout.addRow(self.inputVolHetFrame)
# label for selecting individual node
self.inputVolHet = qt.QLabel("Input Node: ", self.inputVolHetFrame)
self.inputVolHetFrame.layout().addWidget(self.inputVolHet)
# select individual nodes
self.inputSelectorVolHet = slicer.qMRMLNodeComboBox(
self.inputVolHetFrame)
self.inputSelectorVolHet.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.inputSelectorVolHet.selectNodeUponCreation = False
self.inputSelectorVolHet.addEnabled = False
self.inputSelectorVolHet.removeEnabled = False
self.inputSelectorVolHet.setMRMLScene(slicer.mrmlScene)
self.inputVolHetFrame.layout().addWidget(self.inputSelectorVolHet)
# add Data Node button
self.addDataNodeButton = qt.QPushButton("Add Node",
self.inputVolHetFrame)
self.addDataNodeButton.objectName = 'AddDataNodeButton'
self.addDataNodeButton.setToolTip("Add a Node to Queue")
self.addDataNodeButton.connect('clicked()',
self.onAddDataNodeButtonClicked)
self.inputVolHetFrame.layout().addWidget(self.addDataNodeButton)
## data nodes Frame
self.dataNodesFrame = ctk.ctkCollapsibleGroupBox(
self.inputHeterogeneityCADCollapsibleButton)
self.dataNodesFrame.title = "Nodes List"
self.dataNodesFrame.collapsed = False
self.dataNodesFrame.setLayout(qt.QVBoxLayout())
# all buttons frame
self.allButtonsFrame = qt.QFrame(
self.inputHeterogeneityCADCollapsibleButton)
self.allButtonsFrame.objectName = 'AllButtonsFrameButton'
self.allButtonsFrame.setLayout(qt.QVBoxLayout())
self.inputHeterogeneityCADLayout.addRow(self.dataNodesFrame,
self.allButtonsFrame)
# Data Nodes view
# Use list view here with scroll area widget.
self.dataScrollArea = qt.QScrollArea()
self.dataNodesListWidget = qt.QListWidget()
self.dataNodesListWidget.name = 'dataNodesListWidget'
self.dataScrollArea.setWidget(self.dataNodesListWidget)
self.dataNodesListWidget.resize(350, 100)
self.dataNodesFrame.layout().addWidget(self.dataScrollArea)
#self.listWidget.setProperty('SH_ItemView_ActivateItemOnSingleClick', 1)
#self.listWidget.connect('activated(QModelIndex)', self.onActivated)
# add all Data Nodes from scene button
self.addAllDataNodesButton = qt.QPushButton("Add All Nodes From Scene",
self.allButtonsFrame)
self.addAllDataNodesButton.objectName = 'AddAllDataNodesButton'
self.addAllDataNodesButton.setToolTip(
"Add all Nodes from the Scene to Queue")
self.addAllDataNodesButton.connect('clicked()',
self.onAddAllDataNodesButtonClicked)
self.allButtonsFrame.layout().addWidget(self.addAllDataNodesButton)
# remove single Data Node
self.removeDataNodeButton = qt.QPushButton("Remove Node",
self.allButtonsFrame)
self.removeDataNodeButton.objectName = 'RemoveDataNodeButton'
self.removeDataNodeButton.setToolTip(
"Removes Selected Node from the Queue.")
self.removeDataNodeButton.connect('clicked()',
self.onRemoveDataNodeButtonClicked)
self.allButtonsFrame.layout().addWidget(self.removeDataNodeButton)
# remove all Data Nodes button
self.removeAllDataNodesButton = qt.QPushButton("Remove All Nodes",
self.allButtonsFrame)
self.removeAllDataNodesButton.objectName = 'RemoveAllDataNodesButton'
self.removeAllDataNodesButton.setToolTip(
"Removes All Nodes from the Queue.")
self.removeAllDataNodesButton.connect(
'clicked()', self.onRemoveAllDataNodesButtonClicked)
self.allButtonsFrame.layout().addWidget(self.removeAllDataNodesButton)
# Use Label Map as ROI(segmentation output or user-selected ROI)
self.inputLabelROIFrame = qt.QFrame(
self.inputHeterogeneityCADCollapsibleButton)
self.inputLabelROIFrame.setLayout(qt.QHBoxLayout())
self.inputHeterogeneityCADLayout.addRow(self.inputLabelROIFrame)
# Enable Input Label Map as ROI
self.inputLabelROI = qt.QLabel("Label Map ROI: ",
self.inputLabelROIFrame)
self.inputLabelROIFrame.layout().addWidget(self.inputLabelROI)
# Select Input Label Map as ROI
self.inputSelectorLabel = slicer.qMRMLNodeComboBox(
self.inputLabelROIFrame)
self.inputSelectorLabel.nodeTypes = (("vtkMRMLLabelMapVolumeNode"), "")
self.inputSelectorLabel.selectNodeUponCreation = False
self.inputSelectorLabel.renameEnabled = True
self.inputSelectorLabel.removeEnabled = False
self.inputSelectorLabel.noneEnabled = True
self.inputSelectorLabel.addEnabled = False
self.inputSelectorLabel.setMRMLScene(slicer.mrmlScene)
self.inputLabelROIFrame.layout().addWidget(self.inputSelectorLabel)
#End HeterogeneityCAD Inputs Collapsible Button
#################################################
#HeterogeneityCAD Features Collapsible Button
self.HeterogeneityCADCollapsibleButton = ctk.ctkCollapsibleButton()
self.HeterogeneityCADCollapsibleButton.text = "HeterogeneityCAD Features Selection"
self.layout.addWidget(self.HeterogeneityCADCollapsibleButton)
self.featuresHeterogeneityCADLayout = qt.QFormLayout(
self.HeterogeneityCADCollapsibleButton)
# auto-generate QTabWidget Tabs and QCheckBoxes (subclassed in FeatureWidgetHelperLib)
self.tabsFeatureClasses = FeatureWidgetHelperLib.CheckableTabWidget()
self.featuresHeterogeneityCADLayout.addRow(self.tabsFeatureClasses)
gridWidth, gridHeight = 3, 9
for featureClass in self.featureClassKeys:
# by default, features from the following features classes are checked:
if featureClass in [
"Node Information", "First-Order Statistics",
"Morphology and Shape", "Texture: GLCM", "Texture: GLRL"
]:
check = True
else:
check = False
tabFeatureClass = qt.QWidget()
tabFeatureClass.setLayout(qt.QGridLayout())
#featureList = (feature for feature in self.featureClassKeys[featureClass])
gridLayoutCoordinates = ((row, col) for col in range(gridWidth)
for row in range(gridHeight))
for featureName in self.featureClassKeys[featureClass]:
row, col = next(gridLayoutCoordinates, None)
if featureName is None or row is None or col is None:
break
featureCheckboxWidget = FeatureWidgetHelperLib.FeatureWidget()
featureCheckboxWidget.Setup(featureName=featureName,
checkStatus=check)
tabFeatureClass.layout().addWidget(featureCheckboxWidget, row,
col)
self.featureWidgets[featureClass].append(featureCheckboxWidget)
self.tabsFeatureClasses.addTab(tabFeatureClass,
featureClass,
self.featureWidgets[featureClass],
checkStatus=check)
self.tabsFeatureClasses.setCurrentIndex(1)
# note: try using itertools list merging with lists of GLRL diagonal
self.heterogeneityFeatureWidgets = list(
itertools.chain.from_iterable(self.featureWidgets.values()))
self.classes = list(self.featureWidgets.keys())
# or reduce(lambda x,y: x+y, self.featureWidgets.values())
########## Parameter options
# add parameters for top-level feature classes
self.tabsFeatureClasses.addParameter("Geometrical Measures",
"Extrusion Parameter 1")
self.tabsFeatureClasses.addParameter("Texture: GLCM",
"GLCM Matrix Parameter 1")
self.tabsFeatureClasses.addParameter("Texture: GLRL",
"GLRL Matrix Parameter 1")
# compile dict of feature classes with parameter names and values
self.featureClassParametersDict = collections.OrderedDict()
for featureClassWidget in self.tabsFeatureClasses.getFeatureClassWidgets(
):
featureClassName = featureClassWidget.getName()
self.featureClassParametersDict[
featureClassName] = collections.OrderedDict()
self.updateFeatureClassParameterDict(0, featureClassWidget)
for parameterName in featureClassWidget.widgetMenu.parameters:
featureClassWidget.getParameterEditWindow(
parameterName).connect(
'intValueChanged(int)',
lambda intValue, featureClassWidget=featureClassWidget:
self.updateFeatureClassParameterDict(
intValue, featureClassWidget))
# add parameters for individual features
for featureWidget in self.heterogeneityFeatureWidgets:
if featureWidget.getName() == "Voxel Count":
featureWidget.addParameter("Example Parameter 1")
featureWidget.addParameter("Example Parameter 2")
if featureWidget.getName() == "Gray Levels":
featureWidget.addParameter("Example Parameter 1-GL")
featureWidget.addParameter("Example Parameter 2-GL")
# compile dict of features with parameter names and values
self.featureParametersDict = collections.OrderedDict()
for featureWidget in self.heterogeneityFeatureWidgets:
featureName = featureWidget.getName()
self.featureParametersDict[featureName] = collections.OrderedDict()
self.updateFeatureParameterDict(0, featureWidget)
for parameterName in featureWidget.widgetMenu.parameters:
featureWidget.getParameterEditWindow(parameterName).connect(
'intValueChanged(int)',
lambda intValue, featureWidget=featureWidget: self.
updateFeatureParameterDict(intValue, featureWidget)
) #connect intvaluechanged signals to updateParamaterDict function
##########
# Feature Buttons Frame and Layout
self.featureButtonFrame = qt.QFrame(
self.HeterogeneityCADCollapsibleButton)
self.featureButtonFrame.setLayout(qt.QHBoxLayout())
self.featuresHeterogeneityCADLayout.addRow(self.featureButtonFrame)
# HeterogeneityCAD Apply Button
self.HeterogeneityCADButton = qt.QPushButton("Apply HeterogeneityCAD",
self.featureButtonFrame)
self.HeterogeneityCADButton.toolTip = "Analyze input volume using selected Heterogeneity Features."
self.featureButtonFrame.layout().addWidget(self.HeterogeneityCADButton)
self.HeterogeneityCADButton.connect(
'clicked()', self.onHeterogeneityCADButtonClicked)
# Save Button
self.saveButton = qt.QPushButton("Save to File",
self.featureButtonFrame)
self.saveButton.toolTip = "Save analyses to CSV file"
self.saveButton.enabled = False
self.featureButtonFrame.layout().addWidget(self.saveButton)
self.saveButton.connect('clicked()', self.onSave)
#End HeterogeneityCAD Features Collapsible Button
#################################################
#Feature Summary Chart
#Complete chart options, export list of user-selected options identified via connections to labelstatistics module
self.chartOptions = ("Count", "Volume mm^3", "Volume cc", "Min", "Max",
"Mean", "StdDev")
self.StatisticsChartCollapsibleButton = ctk.ctkCollapsibleButton()
self.StatisticsChartCollapsibleButton.text = "HeterogeneityCAD Features Summary"
self.layout.addWidget(self.StatisticsChartCollapsibleButton)
self.StatisticsChartLayout = qt.QFormLayout(
self.StatisticsChartCollapsibleButton)
self.StatisticsChartCollapsibleButton.collapsed = False
#Table View to display Label statistics
self.view = qt.QTableView(self.StatisticsChartCollapsibleButton)
self.view.sortingEnabled = True
self.StatisticsChartLayout.addWidget(self.view)
self.view.minimumHeight = 175
def setup(self):
# reload button
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "HeterogeneityCAD Reload"
self.layout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
# Tumor Segmentation Collapsible Button
self.TumorSegmentationCollapsibleButton = ctk.ctkCollapsibleButton()
self.TumorSegmentationCollapsibleButton.text = "SegmentCAD Segmentation"
self.layout.addWidget(self.TumorSegmentationCollapsibleButton)
self.TumorSegmentationLayout = qt.QFormLayout(
self.TumorSegmentationCollapsibleButton)
# Select Volumes Collapsible Button
self.selectionsCollapsibleButton = ctk.ctkCollapsibleButton()
self.selectionsCollapsibleButton.text = "Select DCE-MRI Volumes for Segmentation"
self.TumorSegmentationLayout.addWidget(
self.selectionsCollapsibleButton)
# Layout within the collapsible button
self.volumesLayout = qt.QFormLayout(self.selectionsCollapsibleButton)
# Use Multivolume Node as input
self.enableMultiVolume = qt.QCheckBox(self.selectionsCollapsibleButton)
self.enableMultiVolume.setText('Input Multi-Volume Node')
self.enableMultiVolume.checked = True
self.enableMultiVolume.setToolTip(
'Use Multi-Volume Node, with volumes imported in the correct order'
)
self.inputSelectorMultiVolume = slicer.qMRMLNodeComboBox(
self.selectionsCollapsibleButton)
self.inputSelectorMultiVolume.nodeTypes = (("vtkMRMLMultiVolumeNode"),
"")
self.inputSelectorMultiVolume.selectNodeUponCreation = False
self.inputSelectorMultiVolume.renameEnabled = True
self.inputSelectorMultiVolume.removeEnabled = False
self.inputSelectorMultiVolume.noneEnabled = True
self.inputSelectorMultiVolume.addEnabled = False
self.inputSelectorMultiVolume.setMRMLScene(slicer.mrmlScene)
self.inputSelectorMultiVolume.setToolTip(
'Use Multi-Volume Node, with volumes imported in the correct order'
)
self.volumesLayout.addRow(self.enableMultiVolume,
self.inputSelectorMultiVolume)
self.nodeInputFrame = ctk.ctkCollapsibleGroupBox(
self.selectionsCollapsibleButton)
self.nodeInputFrame.title = "Input Scalar Volume Nodes"
self.nodeInputFrame.collapsed = True
self.nodeInputFrame.enabled = False
self.nodeInputFrame.setLayout(qt.QFormLayout())
self.volumesLayout.addRow(self.nodeInputFrame)
# Select Pre Node
self.inputPre = qt.QLabel("Pre-contrast Volume", self.nodeInputFrame)
self.inputPre.setToolTip(
'Select the initial pre-contrast volume node.')
self.inputSelectorPre = slicer.qMRMLNodeComboBox(self.nodeInputFrame)
self.inputSelectorPre.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.inputSelectorPre.selectNodeUponCreation = False
self.inputSelectorPre.addEnabled = False
self.inputSelectorPre.removeEnabled = False
self.inputSelectorPre.noneEnabled = True
self.inputSelectorPre.noneDisplay = 'Please Select Volume'
self.inputSelectorPre.setMRMLScene(slicer.mrmlScene)
self.inputSelectorPre.setToolTip(
'Select the initial pre-contrast volume node.')
#self.volumesLayout.addRow(self.inputPre, self.inputSelectorPre)
self.nodeInputFrame.layout().addRow(self.inputPre,
self.inputSelectorPre)
# Select First Node
self.inputFirst = qt.QLabel("First Post-contrast Volume",
self.nodeInputFrame)
self.inputFirst.setToolTip(
'Select the first post-contrast volume node to calculate intitial enhancement and curve type.'
)
self.inputSelectorFirst = slicer.qMRMLNodeComboBox(self.nodeInputFrame)
self.inputSelectorFirst.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.inputSelectorFirst.selectNodeUponCreation = False
self.inputSelectorFirst.addEnabled = False
self.inputSelectorFirst.removeEnabled = False
self.inputSelectorFirst.noneEnabled = True
self.inputSelectorFirst.noneDisplay = 'Please Select Volume'
self.inputSelectorFirst.setMRMLScene(slicer.mrmlScene)
self.inputSelectorFirst.setToolTip(
'Select the first post-contrast volume node to calculate intitial enhancement and curve type.'
)
#self.volumesLayout.addRow(self.inputFirst, self.inputSelectorFirst)
self.nodeInputFrame.layout().addRow(self.inputFirst,
self.inputSelectorFirst)
# Select Second Node
self.inputSecond = qt.QLabel("Second Post-contrast Volume",
self.nodeInputFrame)
self.inputSecond.setToolTip(
'Select a second post-contrast volume node (not required).')
self.inputSelectorSecond = slicer.qMRMLNodeComboBox(
self.nodeInputFrame)
self.inputSelectorSecond.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.inputSelectorSecond.selectNodeUponCreation = False
self.inputSelectorSecond.addEnabled = False
self.inputSelectorSecond.removeEnabled = False
self.inputSelectorSecond.noneEnabled = True
self.inputSelectorSecond.noneDisplay = 'Please Select Volume'
self.inputSelectorSecond.setMRMLScene(slicer.mrmlScene)
self.inputSelectorSecond.setToolTip(
'Select a second post-contrast volume node (not required).')
#self.volumesLayout.addRow(self.inputSecond, self.inputSelectorSecond)
self.nodeInputFrame.layout().addRow(self.inputSecond,
self.inputSelectorSecond)
# Select Third Node
self.inputThird = qt.QLabel("Third Post-contrast Volume",
self.nodeInputFrame)
self.inputThird.setToolTip(
'Select a third post-contrast volume node (not required).')
self.inputSelectorThird = slicer.qMRMLNodeComboBox(self.nodeInputFrame)
self.inputSelectorThird.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.inputSelectorThird.selectNodeUponCreation = False
self.inputSelectorThird.addEnabled = False
self.inputSelectorThird.removeEnabled = False
self.inputSelectorThird.noneEnabled = True
self.inputSelectorThird.noneDisplay = 'Please Select Volume'
self.inputSelectorThird.setMRMLScene(slicer.mrmlScene)
self.inputSelectorThird.setToolTip(
'Select a third post-contrast volume node (not required).')
#self.volumesLayout.addRow(self.inputThird, self.inputSelectorThird)
self.nodeInputFrame.layout().addRow(self.inputThird,
self.inputSelectorThird)
# Select Fourth Node
self.inputFourth = qt.QLabel("Fourth Post-contrast Volume",
self.nodeInputFrame)
self.inputFourth.setToolTip(
'Select the fourth or final post-contrast volume node to calculate curve type based on the delayed curve slope.'
)
self.inputSelectorFourth = slicer.qMRMLNodeComboBox(
self.nodeInputFrame)
self.inputSelectorFourth.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.inputSelectorFourth.selectNodeUponCreation = False
self.inputSelectorFourth.addEnabled = False
self.inputSelectorFourth.removeEnabled = False
self.inputSelectorFourth.noneEnabled = True
self.inputSelectorFourth.noneDisplay = 'Please Select Volume'
self.inputSelectorFourth.setMRMLScene(slicer.mrmlScene)
self.inputSelectorFourth.setToolTip(
'Select the fourth or final post-contrast volume node to calculate curve type based on the delayed curve slope.'
)
#self.volumesLayout.addRow(self.inputFourth, self.inputSelectorFourth)
self.nodeInputFrame.layout().addRow(self.inputFourth,
self.inputSelectorFourth)
# Enable and Select Input Label Map as ROI
self.enableLabel = qt.QCheckBox(self.selectionsCollapsibleButton)
self.enableLabel.setText('Use Label Map as ROI')
self.enableLabel.checked = True
self.enableLabel.setToolTip(
'Select and identify a custom label map node to define an ROI over the input volumes for faster segmentation.'
)
self.inputSelectorLabel = slicer.qMRMLNodeComboBox(
self.selectionsCollapsibleButton)
self.inputSelectorLabel.nodeTypes = (("vtkMRMLLabelMapVolumeNode"), "")
self.inputSelectorLabel.selectNodeUponCreation = False
self.inputSelectorLabel.renameEnabled = True
self.inputSelectorLabel.removeEnabled = False
self.inputSelectorLabel.noneEnabled = True
self.inputSelectorLabel.addEnabled = False
self.inputSelectorLabel.setMRMLScene(slicer.mrmlScene)
self.inputSelectorLabel.setToolTip(
'Select and identify a custom label map node to define an ROI over the input volumes for faster segmentation.'
)
self.volumesLayout.addRow(self.enableLabel, self.inputSelectorLabel)
# Select output SegmentCAD Label collapsible button
self.outlabelCollapsibleButton = ctk.ctkCollapsibleButton()
self.outlabelCollapsibleButton.text = "Select or Create Output SegmentCAD Label Map"
self.TumorSegmentationLayout.addWidget(self.outlabelCollapsibleButton)
# Layout within the collapsible button
self.outlabelLayout = qt.QFormLayout(self.outlabelCollapsibleButton)
# Select or create output SegmentCAD Label Map
self.outputLabel = qt.QLabel("Output SegmentCAD Label Map",
self.outlabelCollapsibleButton)
self.outputLabel.setToolTip(
'Select or create a label map volume node as the SegmentCAD segmentation output.'
)
self.outputSelectorLabel = slicer.qMRMLNodeComboBox(
self.outlabelCollapsibleButton)
self.outputSelectorLabel.nodeTypes = (("vtkMRMLLabelMapVolumeNode"),
"")
self.outputSelectorLabel.baseName = "SegmentCAD Label Map"
self.outputSelectorLabel.selectNodeUponCreation = True
self.outputSelectorLabel.renameEnabled = True
self.outputSelectorLabel.removeEnabled = True
self.outputSelectorLabel.noneEnabled = False
self.outputSelectorLabel.addEnabled = True
self.outputSelectorLabel.setMRMLScene(slicer.mrmlScene)
self.outputSelectorLabel.setToolTip(
'Select or create a label map volume node as the SegmentCAD segmentation output.'
)
self.outlabelLayout.addRow(self.outputLabel, self.outputSelectorLabel)
# SegmentCAD Label Map Legend
self.outputLegend = qt.QLabel(
"| Type I Persistent: Blue | Type II Plateau: Yellow | Type III Washout: Red |",
self.outlabelCollapsibleButton)
self.outputLegend.setToolTip(
'SegmentCAD Label Map Legend | Blue: Type I Persistent curve | Yellow: Type II Plateau curve | Red: Type III Washout curve |'
)
self.outlabelLayout.addRow(self.outputLegend)
# Enable Volume Rendering of the SegmentCAD label map
self.enableVolumeRendering = qt.QCheckBox(
self.selectionsCollapsibleButton)
self.enableVolumeRendering.setText('Display Volume Rendering')
self.enableVolumeRendering.checked = True
self.enableVolumeRendering.setToolTip(
'Display volume rendering of the SegmentCAD Label Map in the 3D View'
)
self.outlabelLayout.addRow(self.enableVolumeRendering)
# Enable Label Statistics Table and Data
self.enableStats = qt.QCheckBox(self.selectionsCollapsibleButton)
self.enableStats.setText('Calculate SegmentCAD Label statistics')
self.enableStats.checked = False
self.enableStats.setToolTip(
'Use logic from Label Statistics Module to calculate statistics for first post-contrast voxels within the SegmentCAD Label Map.'
)
self.outlabelLayout.addRow(self.enableStats)
# Set Advanced Parameters Collapsible Button
self.parametersCollapsibleButton = ctk.ctkCollapsibleButton()
self.parametersCollapsibleButton.text = "Set Advanced Segmentation Parameters"
self.TumorSegmentationLayout.addWidget(
self.parametersCollapsibleButton)
self.parametersCollapsibleButton.collapsed = True
# Layout within the collapsible button
self.parametersLayout = qt.QFormLayout(
self.parametersCollapsibleButton)
# Set Minimum Threshold of Percentage Increase to First Post-Contrast Image
self.inputMinimumThreshold = qt.QLabel(
"Minimum Threshold of Increase", self.parametersCollapsibleButton)
self.inputMinimumThreshold.setToolTip(
'Minimum Threshold of Percentage Increase (Pre- to First Post-contrast (Range: 10% to 150%)'
)
self.inputSelectorMinimumThreshold = qt.QDoubleSpinBox(
self.parametersCollapsibleButton)
self.inputSelectorMinimumThreshold.setSuffix("%")
self.inputSelectorMinimumThreshold.singleStep = (1)
self.inputSelectorMinimumThreshold.minimum = (10)
self.inputSelectorMinimumThreshold.maximum = (150)
self.inputSelectorMinimumThreshold.value = (75)
self.inputSelectorMinimumThreshold.setToolTip(
'Minimum Threshold of Percentage Increase (Pre- to First Post-contrast (Range: 10% to 150%)'
)
self.parametersLayout.addRow(self.inputMinimumThreshold,
self.inputSelectorMinimumThreshold)
# Curve 1 Type Parameters (Slopes from First to Fourth Post-Contrast Images)
self.inputCurve1 = qt.QLabel("Type 1 (Persistent) Curve Minimum Slope",
self.parametersCollapsibleButton)
self.inputCurve1.setToolTip(
'Minimum Slope of Delayed Curve to classify as Persistent (Range: 0.02 to 0.3)'
)
self.inputSelectorCurve1 = qt.QDoubleSpinBox(
self.parametersCollapsibleButton)
self.inputSelectorCurve1.singleStep = (0.02)
self.inputSelectorCurve1.minimum = (0.02)
self.inputSelectorCurve1.maximum = (0.3)
self.inputSelectorCurve1.value = (0.20)
self.inputSelectorCurve1.setToolTip(
'Minimum Slope of Delayed Curve to classify as Persistent (Range: 0.02 to 0.3)'
)
self.parametersLayout.addRow(self.inputCurve1,
self.inputSelectorCurve1)
# Curve 3 Type Parameters (Slopes from First to Fourth Post-Contrast Images)
self.inputCurve3 = qt.QLabel("Type 3 (Washout) Curve Maximum Slope",
self.parametersCollapsibleButton)
self.inputCurve3.setToolTip(
'Maximum Slope of Delayed Curve to classify as Washout (Range: -0.02 to -0.3)'
)
self.inputSelectorCurve3 = qt.QDoubleSpinBox(
self.parametersCollapsibleButton)
self.inputSelectorCurve3.singleStep = (0.02)
self.inputSelectorCurve3.setPrefix("-")
self.inputSelectorCurve3.minimum = (0.02)
self.inputSelectorCurve3.maximum = (0.30)
self.inputSelectorCurve3.value = (0.20)
self.inputSelectorCurve3.setToolTip(
'Maximum Slope of Delayed Curve to classify as Washout (Range: -0.02 to -0.3)'
)
self.parametersLayout.addRow(self.inputCurve3,
self.inputSelectorCurve3)
# Apply Tumor Adaptive Segmentation button
self.SegmentCADButton = qt.QPushButton("Apply SegmentCAD")
self.SegmentCADButton.toolTip = "Apply SegmentCAD segmentation to selected volumes."
self.TumorSegmentationLayout.addWidget(self.SegmentCADButton)
# LabelStatistics Table Collapsible Button
self.labelstatisticsCollapsibleButton = ctk.ctkCollapsibleButton()
self.labelstatisticsCollapsibleButton.text = "SegmentCAD Label Statistics"
self.layout.addWidget(self.labelstatisticsCollapsibleButton)
self.labelstatisticsCollapsibleButton.collapsed = True
# Layout within the collapsible button
self.labelstatisticsLayout = qt.QFormLayout(
self.labelstatisticsCollapsibleButton)
# Table View to display Label statistics
self.labelStatisticsTableView = qt.QTableView()
self.labelStatisticsTableView.sortingEnabled = True
self.labelstatisticsLayout.addWidget(self.labelStatisticsTableView)
self.labelStatisticsTableView.minimumHeight = 200
# Charting Statistics Button
self.chartOptions = ("Volume", "Curve Type", "Voxel Count",
"Volume mm^3", "Volume cc", "Minimum Intensity",
"Maximum Intensity", "Mean Intensity",
"Standard Deviation")
self.chartFrame = qt.QFrame()
self.chartFrame.setLayout(qt.QHBoxLayout())
self.labelstatisticsLayout.addWidget(self.chartFrame)
self.chartButton = qt.QPushButton(
"Chart Statistics", self.labelstatisticsCollapsibleButton)
self.chartButton.toolTip = "Make a chart from the current statistics."
self.chartFrame.layout().addWidget(self.chartButton)
self.chartOption = qt.QComboBox(self.labelstatisticsCollapsibleButton)
self.chartOption.addItems(self.chartOptions)
self.chartFrame.layout().addWidget(self.chartOption)
self.chartIgnoreZero = qt.QCheckBox(
self.labelstatisticsCollapsibleButton)
self.chartIgnoreZero.setText('Ignore Zero Label')
self.chartIgnoreZero.checked = False
self.chartIgnoreZero.setToolTip(
'Do not include the zero index in the chart to avoid dwarfing other bars'
)
self.chartFrame.layout().addWidget(self.chartIgnoreZero)
self.chartButton.enabled = False
# Interactive Charting Settings Collapsible Button
self.iChartingCollapsibleButton = ctk.ctkCollapsibleButton()
self.iChartingCollapsibleButton.text = "Interactive Charting Settings"
self.iChartingCollapsibleButton.collapsed = True
self.layout.addWidget(self.iChartingCollapsibleButton)
# Layout within the collapsible button
self.iChartingLayout = qt.QFormLayout(self.iChartingCollapsibleButton)
# iCharting toggle button
self.iCharting = qt.QPushButton("Enable Interactive Charting")
self.iCharting.checkable = True
self.iCharting.setChecked(False)
self.iCharting.enabled = False
self.iCharting.toolTip = "Toggle the real-time charting of the %increase from baseline of the selected voxel from each input volume."
self.iChartingLayout.addRow(self.iCharting)
# Initialize slice observers (from DataProbe.py)
# Keep list of pairs: [observee,tag] so they can be removed easily
self.styleObserverTags = []
# Keep a map of interactor styles to sliceWidgets so we can easily get sliceLogic
self.sliceWidgetsPerStyle = {}
self.refreshObservers()
# Connections
self.SegmentCADButton.connect('clicked()',
self.onSegmentCADButtonClicked)
self.enableLabel.connect('stateChanged(int)', self.onEnableLabel)
self.enableMultiVolume.connect('stateChanged(int)',
self.onEnableMultiVolume)
self.chartButton.connect('clicked()', self.onChart)
self.iCharting.connect('toggled(bool)',
self.onInteractiveChartingChanged)
def create(self):
"""create the segmentation helper box"""
#
# Master Frame
#
self.masterFrame = qt.QFrame(self.parent)
self.masterFrame.setLayout(qt.QVBoxLayout())
self.parent.layout().addWidget(self.masterFrame)
#
# the master volume selector
#
self.masterSelectorFrame = qt.QFrame(self.parent)
self.masterSelectorFrame.objectName = 'MasterVolumeFrame'
self.masterSelectorFrame.setLayout(qt.QHBoxLayout())
self.masterFrame.layout().addWidget(self.masterSelectorFrame)
self.masterSelectorLabel = qt.QLabel("Master Volume: ",
self.masterSelectorFrame)
self.masterSelectorLabel.setToolTip(
"Select the master volume (background grayscale scalar volume node)"
)
self.masterSelectorFrame.layout().addWidget(self.masterSelectorLabel)
self.masterSelector = slicer.qMRMLNodeComboBox(
self.masterSelectorFrame)
self.masterSelector.objectName = 'MasterVolumeNodeSelector'
# TODO
self.masterSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.masterSelector.selectNodeUponCreation = False
self.masterSelector.addEnabled = False
self.masterSelector.removeEnabled = False
self.masterSelector.noneEnabled = True
self.masterSelector.showHidden = False
self.masterSelector.showChildNodeTypes = False
self.masterSelector.setMRMLScene(slicer.mrmlScene)
# TODO: need to add a QLabel
# self.masterSelector.SetLabelText( "Master Volume:" )
self.masterSelector.setToolTip(
"Pick the master structural volume to define the segmentation. A label volume with the with \"%s\" appended to the name will be created if it doesn't already exist."
% self.mergeVolumePostfix)
self.masterSelectorFrame.layout().addWidget(self.masterSelector)
#
# merge label name and set button
#
self.mergeSelectorFrame = qt.QFrame(self.masterFrame)
self.mergeSelectorFrame.objectName = 'MergeVolumeFrame'
self.mergeSelectorFrame.setLayout(qt.QHBoxLayout())
self.masterFrame.layout().addWidget(self.mergeSelectorFrame)
mergeNameToolTip = "Composite label map containing the merged structures (be aware that merge operations will overwrite any edits applied to this volume)"
self.mergeNameLabel = qt.QLabel("Merge Volume: ",
self.mergeSelectorFrame)
self.mergeNameLabel.setToolTip(mergeNameToolTip)
self.mergeSelectorFrame.layout().addWidget(self.mergeNameLabel)
self.mergeSelector = slicer.qMRMLNodeComboBox(self.mergeSelectorFrame)
self.mergeSelector.objectName = 'MergeVolumeNodeSelector'
self.mergeSelector.setToolTip(mergeNameToolTip)
self.mergeSelector.nodeTypes = ["vtkMRMLLabelMapVolumeNode"]
self.mergeSelector.addEnabled = False
self.mergeSelector.removeEnabled = False
self.mergeSelector.noneEnabled = False
self.mergeSelector.showHidden = False
self.mergeSelector.showChildNodeTypes = False
self.mergeSelector.setMRMLScene(slicer.mrmlScene)
self.mergeSelectorFrame.layout().addWidget(self.mergeSelector)
self.newMergeVolumeAction = qt.QAction("Create new LabelMapVolume",
self.mergeSelector)
self.newMergeVolumeAction.connect("triggered()", self.newMerge)
self.mergeSelector.addMenuAction(self.newMergeVolumeAction)
#
# Structures Frame
#
self.structuresFrame = ctk.ctkCollapsibleGroupBox(self.masterFrame)
self.structuresFrame.objectName = 'PerStructureVolumesFrame'
self.structuresFrame.title = "Per-Structure Volumes"
self.structuresFrame.collapsed = True
self.structuresFrame.setLayout(qt.QVBoxLayout())
self.masterFrame.layout().addWidget(self.structuresFrame)
self.structureListWidget = LabelStructureListWidget()
self.structureListWidget.mergeVolumePostfix = self.mergeVolumePostfix
self.structuresFrame.layout().addWidget(self.structureListWidget)
#
# signals, slots, and observers
#
# signals/slots on qt widgets are automatically when
# this class destructs, but observers of the scene must be explicitly
# removed in the destuctor
# node selected
self.masterSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
self.mergeSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onMergeSelect)
# so buttons will initially be disabled
self.master = None
self.structureListWidget.updateStructures()
def setup(self):
self.conoProbeConnectorLogic = ConoProbeConnectorLogic()
self.firstInitColouring = True
ScriptedLoadableModuleWidget.setup(self)
# Icons stuff
self.conoProbeConnectorModuleDirectoryPath = slicer.modules.conoprobeconnector.path.replace("ConoProbeConnector.py","")
self.playIcon = qt.QIcon(self.conoProbeConnectorModuleDirectoryPath + '/Resources/Icons/playIcon.png')
self.stopIcon = qt.QIcon(self.conoProbeConnectorModuleDirectoryPath + '/Resources/Icons/stopIcon.png')
self.recordIcon = qt.QIcon(self.conoProbeConnectorModuleDirectoryPath + '/Resources/Icons/recordIcon.png')
self.restartIcon = qt.QIcon(self.conoProbeConnectorModuleDirectoryPath + '/Resources/Icons/restartIcon.png')
self.saveIcon = qt.QIcon(self.conoProbeConnectorModuleDirectoryPath + '/Resources/Icons/saveIcon.png')
self.errorStyleSheet = "QLabel { color : #FF0000; \
font: bold 14px}"
self.defaultStyleSheet = "QLabel { color : #000000; \
font: bold 14px}"
######################################################## Recorder
recorderCollapsibleButton = ctk.ctkCollapsibleButton()
recorderCollapsibleButton.text = "ConoProbe Connector"
recorderCollapsibleButton.collapsed = False
self.layout.addWidget(recorderCollapsibleButton)
recorderFormLayout = qt.QFormLayout(recorderCollapsibleButton)
# Output
self.recorderOutputGroupBox = ctk.ctkCollapsibleGroupBox()
self.recorderOutputGroupBox.setTitle("Output")
recorderOutputFormLayout = qt.QFormLayout(self.recorderOutputGroupBox)
recorderFormLayout.addRow(self.recorderOutputGroupBox)
self.lensMinLabel = qt.QLabel('-')
self.lensMinLabel.setStyleSheet(self.defaultStyleSheet)
self.QFormLayoutLeftLabel10 = qt.QLabel('Lens Min. Dist. (mm): ')
self.QFormLayoutLeftLabel10.setStyleSheet(self.defaultStyleSheet)
recorderOutputFormLayout.addRow(self.QFormLayoutLeftLabel10, self.lensMinLabel)
self.distanceLabel = qt.QLabel('-')
self.distanceLabel.setStyleSheet(self.defaultStyleSheet)
self.QFormLayoutLeftLabel1 = qt.QLabel('Distance (mm): ')
self.QFormLayoutLeftLabel1.setStyleSheet(self.defaultStyleSheet)
recorderOutputFormLayout.addRow(self.QFormLayoutLeftLabel1, self.distanceLabel)
self.lensMaxLabel = qt.QLabel('-')
self.lensMaxLabel.setStyleSheet(self.defaultStyleSheet)
self.QFormLayoutLeftLabel11 = qt.QLabel('Lens Max. Dist. (mm): ')
self.QFormLayoutLeftLabel11.setStyleSheet(self.defaultStyleSheet)
recorderOutputFormLayout.addRow(self.QFormLayoutLeftLabel11, self.lensMaxLabel)
dummyLabel1 = qt.QLabel('')
recorderOutputFormLayout.addRow('', dummyLabel1)
self.powerLabel = qt.QLabel('-')
self.powerLabel.setStyleSheet(self.defaultStyleSheet)
self.QFormLayoutLeftLabel8 = qt.QLabel('Laser Power (arb. unit): ')
self.QFormLayoutLeftLabel8.setStyleSheet(self.defaultStyleSheet)
recorderOutputFormLayout.addRow(self.QFormLayoutLeftLabel8, self.powerLabel)
self.frequencyLabel = qt.QLabel('-')
self.frequencyLabel.setStyleSheet(self.defaultStyleSheet)
self.QFormLayoutLeftLabel9 = qt.QLabel('Laser Frequency (Hz): ')
self.QFormLayoutLeftLabel9.setStyleSheet(self.defaultStyleSheet)
recorderOutputFormLayout.addRow(self.QFormLayoutLeftLabel9, self.frequencyLabel)
self.nbrOfPointsRecordedLabel = qt.QLabel('0')
self.nbrOfPointsRecordedLabel.setStyleSheet(self.defaultStyleSheet)
self.QFormLayoutLeftLabel2 = qt.QLabel('Nbr. of Points Recorded: ')
self.QFormLayoutLeftLabel2.setStyleSheet(self.defaultStyleSheet)
recorderOutputFormLayout.addRow(self.QFormLayoutLeftLabel2, self.nbrOfPointsRecordedLabel)
self.positionLabel = qt.QLabel('-')
self.positionLabel.setStyleSheet(self.defaultStyleSheet)
self.QFormLayoutLeftLabel3 = qt.QLabel('Position ([r, a, s]): ')
self.QFormLayoutLeftLabel3.setStyleSheet(self.defaultStyleSheet)
recorderOutputFormLayout.addRow(self.QFormLayoutLeftLabel3, self.positionLabel)
self.timeLabel = qt.QLabel('-')
self.timeLabel.setStyleSheet(self.defaultStyleSheet)
self.QFormLayoutLeftLabel4 = qt.QLabel('Recording Time (s): ')
self.QFormLayoutLeftLabel4.setStyleSheet(self.defaultStyleSheet)
recorderOutputFormLayout.addRow(self.QFormLayoutLeftLabel4, self.timeLabel)
self.snrLabel = qt.QLabel('-')
self.snrLabel.setStyleSheet(self.defaultStyleSheet)
self.QFormLayoutLeftLabel5 = qt.QLabel('SNR (%): ')
self.QFormLayoutLeftLabel5.setStyleSheet(self.defaultStyleSheet)
recorderOutputFormLayout.addRow(self.QFormLayoutLeftLabel5, self.snrLabel)
self.totalLabel = qt.QLabel('-')
self.totalLabel.setStyleSheet(self.defaultStyleSheet)
self.QFormLayoutLeftLabel6 = qt.QLabel('Total: ')
self.QFormLayoutLeftLabel6.setStyleSheet(self.defaultStyleSheet)
recorderOutputFormLayout.addRow(self.QFormLayoutLeftLabel6, self.totalLabel)
dummyLabel2 = qt.QLabel('')
recorderOutputFormLayout.addRow('', dummyLabel2)
self.infoLabel = qt.QLabel('Make sure Plus is running')
self.infoLabel.setWordWrap(True)
self.infoLabel.setStyleSheet(self.errorStyleSheet)
self.QFormLayoutLeftLabel7 = qt.QLabel('INFO: ')
self.QFormLayoutLeftLabel7.setStyleSheet(self.defaultStyleSheet)
recorderOutputFormLayout.addRow(self.QFormLayoutLeftLabel7, self.infoLabel)
# Live Filtering
self.recorderFilteringGroupBox = ctk.ctkCollapsibleGroupBox()
self.recorderFilteringGroupBox.setTitle("Live Filtering")
recorderFilteringFormLayout = qt.QFormLayout(self.recorderFilteringGroupBox)
recorderFormLayout.addRow(self.recorderFilteringGroupBox)
self.snrFilteringSlider = ctk.ctkSliderWidget()
self.snrFilteringSlider.setDecimals(0)
self.snrFilteringSlider.singleStep = 1
self.snrFilteringSlider.minimum = 0
self.snrFilteringSlider.maximum = 100
self.snrFilteringSlider.value = 40
recorderFilteringFormLayout.addRow('SNR (%): ', self.snrFilteringSlider)
self.distanceFilteringSlider = ctk.ctkRangeWidget()
self.distanceFilteringSlider.minimum = 0
self.distanceFilteringSlider.maximum = 500
self.distanceFilteringSlider.setValues(0, 500)
recorderFilteringFormLayout.addRow('Distance (mm): ', self.distanceFilteringSlider)
# Intuitive Colouring
self.colouringGroupBox = ctk.ctkCollapsibleGroupBox()
self.colouringGroupBox.setTitle("Intuitive Colouring")
colouringFormLayout = qt.QFormLayout(self.colouringGroupBox)
recorderFormLayout.addRow(self.colouringGroupBox)
hBoxLayoutColouring = qt.QHBoxLayout()
colouringFormLayout.addRow(hBoxLayoutColouring)
self.rasLabel = qt.QLabel('Direction: ')
hBoxLayoutColouring.addWidget(self.rasLabel)
self.rasComboBox = qt.QComboBox()
self.rasComboBox.addItem('R')
self.rasComboBox.addItem('A')
self.rasComboBox.addItem('S')
hBoxLayoutColouring.addWidget(self.rasComboBox)
self.minLabel = qt.QLabel(' Minimum: ')
hBoxLayoutColouring.addWidget(self.minLabel)
self.minSpinBox = qt.QDoubleSpinBox ()
self.minSpinBox.setMinimum(-500)
self.minSpinBox.setMaximum(500)
self.minSpinBox.setSingleStep(0.1)
self.minSpinBox.setValue(0.0)
hBoxLayoutColouring.addWidget(self.minSpinBox)
self.maxLabel = qt.QLabel(' Maximum: ')
hBoxLayoutColouring.addWidget(self.maxLabel)
self.maxSpinBox = qt.QDoubleSpinBox ()
self.maxSpinBox.setMinimum(-500)
self.maxSpinBox.setMaximum(500)
self.maxSpinBox.setSingleStep(0.1)
self.maxSpinBox.setValue(0.0)
hBoxLayoutColouring.addWidget(self.maxSpinBox)
hBoxLayoutColouring.addStretch()
# Controls
self.controlsGroupBox = ctk.ctkCollapsibleGroupBox()
self.controlsGroupBox.setTitle("Controls")
controlsFormLayout = qt.QFormLayout(self.controlsGroupBox)
recorderFormLayout.addRow(self.controlsGroupBox)
hBoxLayoutControls = qt.QHBoxLayout()
controlsFormLayout.addRow(hBoxLayoutControls)
self.initButton = qt.QPushButton(" Init")
self.initButton.setIcon(self.playIcon)
self.initButton.setSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
self.initButton.enabled = True
hBoxLayoutControls.addWidget(self.initButton)
self.recordButton = qt.QPushButton(" Record")
self.recordButton.setIcon(self.recordIcon)
self.recordButton.setSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
self.recordButton.enabled = False
self.recordButton.checkable = True
hBoxLayoutControls.addWidget(self.recordButton)
self.probeDialogButton = qt.QPushButton("ProbeDialog")
self.probeDialogButton.setSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
self.probeDialogButton.enabled = False
hBoxLayoutControls.addWidget(self.probeDialogButton)
self.saveButton = qt.QPushButton(" Save")
self.saveButton.setIcon(self.saveIcon)
self.saveButton.setSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
self.saveButton.enabled = False
hBoxLayoutControls.addWidget(self.saveButton)
self.resetButton = qt.QPushButton(" Reset")
self.resetButton.setIcon(self.restartIcon)
self.resetButton.setSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
self.resetButton.enabled = False
hBoxLayoutControls.addWidget(self.resetButton)
hBoxCheckBoxes = qt.QHBoxLayout()
controlsFormLayout.addRow(hBoxCheckBoxes)
self.viewpointCheckBox = qt.QCheckBox('Enable Viewpoint')
self.viewpointCheckBox.checked = True
self.viewpointCheckBox.enabled = False
hBoxCheckBoxes.addWidget(self.viewpointCheckBox)
self.singlePointCheckBox = qt.QCheckBox('Single Measurements')
self.singlePointCheckBox.checked = False
self.singlePointCheckBox.enabled = False
hBoxCheckBoxes.addWidget(self.singlePointCheckBox)
self.plusRemoteCheckBox = qt.QCheckBox('Record PLUS Data Stream')
self.plusRemoteCheckBox.checked = False
self.plusRemoteCheckBox.enabled = False
hBoxCheckBoxes.addWidget(self.plusRemoteCheckBox)
# Post-Processing
self.postProcessingGroupBox = ctk.ctkCollapsibleGroupBox()
self.postProcessingGroupBox.setTitle("Post-Processing")
postProcessingFormLayout = qt.QFormLayout(self.postProcessingGroupBox)
recorderFormLayout.addRow(self.postProcessingGroupBox)
self.snrPostProcessingSlider = ctk.ctkSliderWidget()
self.snrPostProcessingSlider.setDecimals(0)
self.snrPostProcessingSlider.singleStep = 1
self.snrPostProcessingSlider.minimum = 0
self.snrPostProcessingSlider.maximum = 100
self.snrPostProcessingSlider.value = 0
postProcessingFormLayout.addRow('SNR (%): ', self.snrPostProcessingSlider)
self.distancePostProcessingSlider = ctk.ctkRangeWidget()
self.distancePostProcessingSlider.minimum = 0
self.distancePostProcessingSlider.maximum = 500
self.distancePostProcessingSlider.setValues(0, 500)
postProcessingFormLayout.addRow('Distance (mm): ', self.distancePostProcessingSlider)
hBoxLayoutPostProcessing = qt.QHBoxLayout()
postProcessingFormLayout.addRow(hBoxLayoutPostProcessing)
self.undoButton = qt.QPushButton("Undo")
self.undoButton.setSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
self.undoButton.enabled = False
hBoxLayoutPostProcessing.addWidget(self.undoButton)
self.applyButton = qt.QPushButton("Apply")
self.applyButton.setSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
self.applyButton.enabled = False
hBoxLayoutPostProcessing.addWidget(self.applyButton)
######################################################## Connections
self.snrFilteringSlider.connect('valueChanged(double)', self.onSnrFilteringValueChanged)
self.distanceFilteringSlider.connect('maximumValueChanged(double)', self.onDistanceFilteringMaximumValueChanged)
self.distanceFilteringSlider.connect('minimumValueChanged(double)', self.onDistanceFilteringMinimumValueChanged)
self.initButton.connect('clicked(bool)', self.onInitClicked)
self.recordButton.connect('clicked(bool)', self.onRecordClicked)
self.resetButton.connect('clicked(bool)', self.onResetClicked)
self.probeDialogButton.connect('clicked(bool)', self.onProbeDialogClicked)
self.saveButton.connect('clicked(bool)', self.onSaveClicked)
self.undoButton.connect('clicked(bool)', self.onUndoClicked)
self.applyButton.connect('clicked(bool)', self.onApplyClicked)
self.viewpointCheckBox.connect('stateChanged(int)', self.onViewpointChecked)
self.plusRemoteCheckBox.connect('stateChanged(int)', self.onPlusRemoteChecked)
# Add vertical spacer
self.layout.addStretch(1)
# Create Plus connector and activate it
self.conoProbeConnectorLogic.setupPlus()
def setup(self):
self.dir = os.path.dirname(os.path.realpath(__file__))
#
# Setup
#
setupWindow = ctk.ctkCollapsibleButton()
setupWindow.text = 'Setup'
self.layout.addWidget(setupWindow)
self.setupLayout = qt.QFormLayout(setupWindow)
# Input box
inputBox = ctk.ctkCollapsibleGroupBox()
inputBox.setTitle('Input:')
self.setupLayout.addRow(inputBox)
self.inputBoxLayout = qt.QFormLayout(inputBox)
# Bevel angle slider
self.bevelAngleSlider = ctk.ctkSliderWidget()
self.bevelAngleSlider.connect('valueChanged(double)', self.bevel_angle_changed)
self.bevelAngleSlider.decimals = 0
self.bevelAngleSlider.minimum = 0
self.bevelAngleSlider.maximum = 360
self.inputBoxLayout.addRow("Bevel Angle:", self.bevelAngleSlider)
# R-Axis Entry Error
self.entryErrR = qt.QLineEdit()
self.entryErrR.setPlaceholderText("Enter length (mm)")
self.inputBoxLayout.addRow("R-Axis Entry Error:", self.entryErrR)
# A-Axis Entry Error
self.entryErrA = qt.QLineEdit()
self.entryErrA.setPlaceholderText("Enter length (mm)")
self.inputBoxLayout.addRow("A-Axis Entry Error:", self.entryErrA)
# S-Axis Entry Error
self.entryErrS = qt.QLineEdit()
self.entryErrS.setPlaceholderText("Enter length (mm)")
self.inputBoxLayout.addRow("S-Axis Entry Error:", self.entryErrS)
# Curve Radius
self.curveRadius = qt.QLineEdit()
self.curveRadius.setPlaceholderText("Enter length (mm)")
self.inputBoxLayout.addRow("Curve Radius:", self.curveRadius)
# Insertion Length
self.insertionLength = qt.QLineEdit()
self.insertionLength.setPlaceholderText("Enter length (mm)")
self.inputBoxLayout.addRow("Insertion Length:", self.insertionLength)
# Needle length in prostate
self.len1 = qt.QLineEdit()
self.len1.setPlaceholderText("Enter length (mm)")
self.inputBoxLayout.addRow("Needle length in prostate:", self.len1)
# Needle Length in pelvic diaphragm
self.len2 = qt.QLineEdit()
self.len2.setPlaceholderText("Enter length (mm)")
self.inputBoxLayout.addRow("Needle length in pelvic diaphragm:", self.len2)
# Needle length in bulbospongiosus
self.len3 = qt.QLineEdit()
self.len3.setPlaceholderText("Enter length (mm)")
self.inputBoxLayout.addRow("Needle length in bulbospongiousus:", self.len3)
# Needle length in ischiocavernosus
self.len4 = qt.QLineEdit()
self.len4.setPlaceholderText("Enter length (mm)")
self.inputBoxLayout.addRow("Needle length in ischiocavernosus:", self.len4)
# Needle length in unsegmented tissue
self.len5 = qt.QLineEdit()
self.len5.setPlaceholderText("Enter length (mm)")
self.inputBoxLayout.addRow("Needle length in unsegmented tissue:", self.len5)
# Calculate Error
self.calculateError = qt.QPushButton("Calculate Error")
self.calculateError.clicked.connect(self.run_regressions)
self.setupLayout.addWidget(self.calculateError)
# Disable calculation until data is entered
self.calculateError.setEnabled(0)
self.calculateError.setText('Enter all data first!')
#
# Output
#
outputWindow = ctk.ctkCollapsibleButton()
outputWindow.text = 'Output'
self.layout.addWidget(outputWindow)
self.outputLayout = qt.QFormLayout(outputWindow)
# Output box
outputBoxCollapsible = ctk.ctkCollapsibleGroupBox()
outputBoxCollapsible.setTitle('Output')
self.outputLayout.addRow(outputBoxCollapsible)
self.outputBox = qt.QFormLayout(outputBoxCollapsible)
# Initial output text
self.outputLabel = qt.QLabel("")
self.outputBox.addRow(self.outputLabel)
self.outputLabel.setText("The needle has a probability of 00.00% to hit the \ntarget, a probability of 00.00% "
"to deflect to the right,\nand a probability of 00.00% to deflect to the top.")
# Initial visual output
image = qt.QPixmap(self.dir + "/NeedleDeviationPredictor GUI/empty.png")
self.label1 = qt.QLabel("")
# Scaling and sizing
self.label1.setScaledContents(True)
self.label1.setMargin(0)
self.label1.setPixmap(image)
qSize = qt.QSizePolicy()
self.label1.setSizePolicy(qSize)
self.outputBox.addRow(self.label1)
# Vertical spacer
self.layout.addStretch(1)
# Check all entered values are floats
values = [self.entryErrR, self.entryErrA, self.entryErrS, self.curveRadius,
self.insertionLength, self.len1, self.len2, self.len3, self.len4, self.len5]
for value in values:
value.textChanged.connect(self.check_inputs)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
############################################################ Playground
playgroundCollapsibleButton = ctk.ctkCollapsibleButton()
playgroundCollapsibleButton.text = "Playground"
playgroundCollapsibleButton.collapsed = False
self.layout.addWidget(playgroundCollapsibleButton)
playgroundFormLayout = qt.QFormLayout(playgroundCollapsibleButton)
# Load for testing
self.loadTestModelButton = qt.QPushButton("Load Test Model")
playgroundFormLayout.addRow(self.loadTestModelButton)
# ModelTipToToolCreator
self.modelTipToToolCreatorGroupBox = ctk.ctkCollapsibleGroupBox()
self.modelTipToToolCreatorGroupBox.setTitle("ModelTipToToolCreator")
self.modelTipToToolCreatorGroupBox.collapsed = True
modelTipToToolCreatorFormLayout = qt.QFormLayout(self.modelTipToToolCreatorGroupBox)
playgroundFormLayout.addRow(self.modelTipToToolCreatorGroupBox)
self.modeldistanceToModelToolTipToToolSelector = slicer.qMRMLNodeComboBox()
self.modeldistanceToModelToolTipToToolSelector.nodeTypes = ["vtkMRMLLinearTransformNode"]
self.modeldistanceToModelToolTipToToolSelector.selectNodeUponCreation = True
self.modeldistanceToModelToolTipToToolSelector.addEnabled = True
self.modeldistanceToModelToolTipToToolSelector.editEnabled = False
self.modeldistanceToModelToolTipToToolSelector.removeEnabled = True
self.modeldistanceToModelToolTipToToolSelector.renameEnabled = True
self.modeldistanceToModelToolTipToToolSelector.noneEnabled = False
self.modeldistanceToModelToolTipToToolSelector.showHidden = False
self.modeldistanceToModelToolTipToToolSelector.showChildNodeTypes = False
self.modeldistanceToModelToolTipToToolSelector.setMRMLScene( slicer.mrmlScene )
modelTipToToolCreatorFormLayout.addRow("ModelTipToTool: ", self.modeldistanceToModelToolTipToToolSelector)
self.modelTipToToolCreatorByTransformsGroupBox = ctk.ctkCollapsibleGroupBox()
self.modelTipToToolCreatorByTransformsGroupBox.setTitle("By Transforms")
self.modelTipToToolCreatorByTransformsGroupBox.collapsed = False
modelTipToToolCreatorByTransformsFormLayout = qt.QFormLayout(self.modelTipToToolCreatorByTransformsGroupBox)
modelTipToToolCreatorFormLayout.addRow(self.modelTipToToolCreatorByTransformsGroupBox)
self.tooldistanceToModelToolTipToToolSelector = slicer.qMRMLNodeComboBox()
self.tooldistanceToModelToolTipToToolSelector.nodeTypes = ["vtkMRMLLinearTransformNode"]
self.tooldistanceToModelToolTipToToolSelector.selectNodeUponCreation = False
self.tooldistanceToModelToolTipToToolSelector.addEnabled = False
self.tooldistanceToModelToolTipToToolSelector.removeEnabled = False
self.tooldistanceToModelToolTipToToolSelector.noneEnabled = False
self.tooldistanceToModelToolTipToToolSelector.showHidden = False
self.tooldistanceToModelToolTipToToolSelector.showChildNodeTypes = False
self.tooldistanceToModelToolTipToToolSelector.setMRMLScene( slicer.mrmlScene )
modelTipToToolCreatorByTransformsFormLayout.addRow("ToolTipToTool: ", self.tooldistanceToModelToolTipToToolSelector)
self.modelTipToToolTipSelector = slicer.qMRMLNodeComboBox()
self.modelTipToToolTipSelector.nodeTypes = ["vtkMRMLLinearTransformNode"]
self.modelTipToToolTipSelector.selectNodeUponCreation = False
self.modelTipToToolTipSelector.addEnabled = False
self.modelTipToToolTipSelector.removeEnabled = False
self.modelTipToToolTipSelector.noneEnabled = False
self.modelTipToToolTipSelector.showHidden = False
self.modelTipToToolTipSelector.showChildNodeTypes = False
self.modelTipToToolTipSelector.setMRMLScene( slicer.mrmlScene )
modelTipToToolCreatorByTransformsFormLayout.addRow("ModelTipToToolTip: ", self.modelTipToToolTipSelector)
self.toolToReferenceSelector = slicer.qMRMLNodeComboBox()
self.toolToReferenceSelector.nodeTypes = ["vtkMRMLLinearTransformNode"]
self.toolToReferenceSelector.selectNodeUponCreation = False
self.toolToReferenceSelector.addEnabled = False
self.toolToReferenceSelector.removeEnabled = False
self.toolToReferenceSelector.noneEnabled = False
self.toolToReferenceSelector.showHidden = False
self.toolToReferenceSelector.showChildNodeTypes = False
self.toolToReferenceSelector.setMRMLScene( slicer.mrmlScene )
modelTipToToolCreatorByTransformsFormLayout.addRow("ToolToReference: ", self.toolToReferenceSelector)
self.applyModelTipToReferenceCreatorByTransformsButton = qt.QPushButton("Apply")
self.applyModelTipToReferenceCreatorByTransformsButton.enabled = False
modelTipToToolCreatorByTransformsFormLayout.addRow(self.applyModelTipToReferenceCreatorByTransformsButton)
self.modelTipToToolCreatorByFiducialsGroupBox = ctk.ctkCollapsibleGroupBox()
self.modelTipToToolCreatorByFiducialsGroupBox.setTitle("By Fiducials")
self.modelTipToToolCreatorByFiducialsGroupBox.collapsed = False
modelTipToToolCreatorByFiducialsFormLayout = qt.QFormLayout(self.modelTipToToolCreatorByFiducialsGroupBox)
modelTipToToolCreatorFormLayout.addRow(self.modelTipToToolCreatorByFiducialsGroupBox)
self.originFiducialSelector = slicer.qMRMLNodeComboBox()
self.originFiducialSelector.nodeTypes = ["vtkMRMLMarkupsFiducialNode"]
self.originFiducialSelector.selectNodeUponCreation = False
self.originFiducialSelector.addEnabled = False
self.originFiducialSelector.removeEnabled = False
self.originFiducialSelector.noneEnabled = False
self.originFiducialSelector.showHidden = False
self.originFiducialSelector.showChildNodeTypes = False
self.originFiducialSelector.setMRMLScene( slicer.mrmlScene )
modelTipToToolCreatorByFiducialsFormLayout.addRow("Origin Fiducial: ", self.originFiducialSelector)
self.fromFiducialSelector = slicer.qMRMLNodeComboBox()
self.fromFiducialSelector.nodeTypes = ["vtkMRMLMarkupsFiducialNode"]
self.fromFiducialSelector.selectNodeUponCreation = False
self.fromFiducialSelector.addEnabled = False
self.fromFiducialSelector.removeEnabled = False
self.fromFiducialSelector.noneEnabled = False
self.fromFiducialSelector.showHidden = False
self.fromFiducialSelector.showChildNodeTypes = False
self.fromFiducialSelector.setMRMLScene( slicer.mrmlScene )
modelTipToToolCreatorByFiducialsFormLayout.addRow("From Fiducial: ", self.fromFiducialSelector)
self.toFiducialSelector = slicer.qMRMLNodeComboBox()
self.toFiducialSelector.nodeTypes = ["vtkMRMLMarkupsFiducialNode"]
self.toFiducialSelector.selectNodeUponCreation = False
self.toFiducialSelector.addEnabled = False
self.toFiducialSelector.removeEnabled = False
self.toFiducialSelector.noneEnabled = False
self.toFiducialSelector.showHidden = False
self.toFiducialSelector.showChildNodeTypes = False
self.toFiducialSelector.setMRMLScene( slicer.mrmlScene )
modelTipToToolCreatorByFiducialsFormLayout.addRow("To Fiducial: ", self.toFiducialSelector)
self.applyModelTipToToolCreatorByFiducialsButton = qt.QPushButton("Apply")
self.applyModelTipToToolCreatorByFiducialsButton.enabled = False
modelTipToToolCreatorByFiducialsFormLayout.addRow(self.applyModelTipToToolCreatorByFiducialsButton)
# FirstPersonView
self.firstPersonViewGroupBox = ctk.ctkCollapsibleGroupBox()
self.firstPersonViewGroupBox.setTitle("FirstPersonView")
self.firstPersonViewGroupBox.collapsed = True
firstPersonViewFormLayout = qt.QFormLayout(self.firstPersonViewGroupBox)
playgroundFormLayout.addRow(self.firstPersonViewGroupBox)
self.stylusTipSelector = slicer.qMRMLNodeComboBox()
self.stylusTipSelector.nodeTypes = ["vtkMRMLLinearTransformNode"]
self.stylusTipSelector.selectNodeUponCreation = False
self.stylusTipSelector.addEnabled = False
self.stylusTipSelector.removeEnabled = False
self.stylusTipSelector.noneEnabled = False
self.stylusTipSelector.showHidden = False
self.stylusTipSelector.showChildNodeTypes = False
self.stylusTipSelector.setMRMLScene( slicer.mrmlScene )
firstPersonViewFormLayout.addRow("StylusTip: ", self.stylusTipSelector)
self.movingLRS_FiducialSelector = slicer.qMRMLNodeComboBox()
self.movingLRS_FiducialSelector.nodeTypes = ["vtkMRMLMarkupsFiducialNode"]
self.movingLRS_FiducialSelector.selectNodeUponCreation = True
self.movingLRS_FiducialSelector.addEnabled = True
self.movingLRS_FiducialSelector.editEnabled = False
self.movingLRS_FiducialSelector.removeEnabled = True
self.movingLRS_FiducialSelector.renameEnabled = True
self.movingLRS_FiducialSelector.noneEnabled = False
self.movingLRS_FiducialSelector.showHidden = False
self.movingLRS_FiducialSelector.showChildNodeTypes = False
self.movingLRS_FiducialSelector.setMRMLScene( slicer.mrmlScene )
firstPersonViewFormLayout.addRow("Moving LRS Fiducials List: ", self.movingLRS_FiducialSelector)
self.recordFirstPersonViewPointButton = qt.QPushButton(" Record Point")
self.recordFirstPersonViewPointButton.enabled = False
firstPersonViewFormLayout.addRow(self.recordFirstPersonViewPointButton)
self.createFirstPersonViewButton = qt.QPushButton("Create First Person View")
self.createFirstPersonViewButton.setSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
self.createFirstPersonViewButton.enabled = False
firstPersonViewFormLayout.addRow(self.createFirstPersonViewButton)
# Record points
self.pointRecorderGroupBox = ctk.ctkCollapsibleGroupBox()
self.pointRecorderGroupBox.setTitle("PointRecorder")
self.pointRecorderGroupBox.collapsed = True
pointRecorderFormLayout = qt.QFormLayout(self.pointRecorderGroupBox)
playgroundFormLayout.addRow(self.pointRecorderGroupBox)
self.pointerTransformSelector = slicer.qMRMLNodeComboBox()
self.pointerTransformSelector.nodeTypes = ["vtkMRMLLinearTransformNode"]
self.pointerTransformSelector.selectNodeUponCreation = True
self.pointerTransformSelector.addEnabled = True
self.pointerTransformSelector.editEnabled = False
self.pointerTransformSelector.removeEnabled = True
self.pointerTransformSelector.renameEnabled = True
self.pointerTransformSelector.noneEnabled = False
self.pointerTransformSelector.showHidden = False
self.pointerTransformSelector.showChildNodeTypes = False
self.pointerTransformSelector.setMRMLScene( slicer.mrmlScene )
pointRecorderFormLayout.addRow("Pointer Transform: ", self.pointerTransformSelector)
self.pointerFiducialsSelector = slicer.qMRMLNodeComboBox()
self.pointerFiducialsSelector.nodeTypes = ["vtkMRMLMarkupsFiducialNode"]
self.pointerFiducialsSelector.selectNodeUponCreation = True
self.pointerFiducialsSelector.addEnabled = True
self.pointerFiducialsSelector.editEnabled = False
self.pointerFiducialsSelector.removeEnabled = True
self.pointerFiducialsSelector.renameEnabled = True
self.pointerFiducialsSelector.noneEnabled = False
self.pointerFiducialsSelector.showHidden = False
self.pointerFiducialsSelector.showChildNodeTypes = False
self.pointerFiducialsSelector.setMRMLScene( slicer.mrmlScene )
pointRecorderFormLayout.addRow("Pointer Fiducials: ", self.pointerFiducialsSelector)
self.pointRecorderApplyButton = qt.QPushButton("Record Point")
self.pointRecorderApplyButton.enabled = False
pointRecorderFormLayout.addRow(self.pointRecorderApplyButton)
# Texture Mapping
self.textureMappingGroupBox = ctk.ctkCollapsibleGroupBox()
self.textureMappingGroupBox.setTitle("TextureMapping")
self.textureMappingGroupBox.collapsed = True
textureMappingFormLayout = qt.QFormLayout(self.textureMappingGroupBox)
playgroundFormLayout.addRow(self.textureMappingGroupBox)
self.inputTextureSelector = slicer.qMRMLNodeComboBox()
self.inputTextureSelector.nodeTypes = ["vtkMRMLVectorVolumeNode"]
self.inputTextureSelector.selectNodeUponCreation = True
self.inputTextureSelector.addEnabled = False
self.inputTextureSelector.removeEnabled = False
self.inputTextureSelector.noneEnabled = False
self.inputTextureSelector.showHidden = False
self.inputTextureSelector.showChildNodeTypes = False
self.inputTextureSelector.setMRMLScene( slicer.mrmlScene )
textureMappingFormLayout.addRow("Input Texture: ", self.inputTextureSelector)
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 )
textureMappingFormLayout.addRow("Input Model: ", self.inputModelSelector)
self.textureMappingApplyButton = qt.QPushButton("Apply")
self.textureMappingApplyButton.enabled = False
textureMappingFormLayout.addRow(self.textureMappingApplyButton)
# Fiducial registration
self.registrationGroupBox = ctk.ctkCollapsibleGroupBox()
self.registrationGroupBox.setTitle("Fiducial Registration")
self.registrationGroupBox.collapsed = True
registrationFormLayout = qt.QFormLayout(self.registrationGroupBox)
playgroundFormLayout.addRow(self.registrationGroupBox)
self.registrationOutputSelector = slicer.qMRMLNodeComboBox()
self.registrationOutputSelector.nodeTypes = ["vtkMRMLLinearTransformNode"]
self.registrationOutputSelector.selectNodeUponCreation = True
self.registrationOutputSelector.addEnabled = True
self.registrationOutputSelector.editEnabled = False
self.registrationOutputSelector.removeEnabled = True
self.registrationOutputSelector.renameEnabled = True
self.registrationOutputSelector.noneEnabled = False
self.registrationOutputSelector.showHidden = False
self.registrationOutputSelector.showChildNodeTypes = False
self.registrationOutputSelector.setMRMLScene( slicer.mrmlScene )
registrationFormLayout.addRow("Output Transform: ", self.registrationOutputSelector)
self.movingFiducialsSelector = slicer.qMRMLNodeComboBox()
self.movingFiducialsSelector.nodeTypes = ["vtkMRMLMarkupsFiducialNode"]
self.movingFiducialsSelector.selectNodeUponCreation = True
self.movingFiducialsSelector.addEnabled = True
self.movingFiducialsSelector.editEnabled = False
self.movingFiducialsSelector.removeEnabled = True
self.movingFiducialsSelector.renameEnabled = True
self.movingFiducialsSelector.noneEnabled = False
self.movingFiducialsSelector.showHidden = False
self.movingFiducialsSelector.showChildNodeTypes = False
self.movingFiducialsSelector.setMRMLScene( slicer.mrmlScene )
registrationFormLayout.addRow("Moving Fiducials: ", self.movingFiducialsSelector)
self.fixedFiducialsSelector = slicer.qMRMLNodeComboBox()
self.fixedFiducialsSelector.nodeTypes = ["vtkMRMLMarkupsFiducialNode"]
self.fixedFiducialsSelector.selectNodeUponCreation = True
self.fixedFiducialsSelector.addEnabled = True
self.fixedFiducialsSelector.editEnabled = False
self.fixedFiducialsSelector.removeEnabled = True
self.fixedFiducialsSelector.renameEnabled = True
self.fixedFiducialsSelector.noneEnabled = False
self.fixedFiducialsSelector.showHidden = False
self.fixedFiducialsSelector.showChildNodeTypes = False
self.fixedFiducialsSelector.setMRMLScene( slicer.mrmlScene )
registrationFormLayout.addRow("Fixed Fiducials: ", self.fixedFiducialsSelector)
self.errorLabel = qt.QLabel('0.0')
registrationFormLayout.addRow("RMS Error: ", self.errorLabel)
self.registrationApplyButton = qt.QPushButton("Apply")
self.registrationApplyButton.enabled = False
registrationFormLayout.addRow(self.registrationApplyButton)
# PreviousToNextCalculator
self.previousToNextCalculatorGroupBox = ctk.ctkCollapsibleGroupBox()
self.previousToNextCalculatorGroupBox.setTitle("PreviousToNextCalculator")
self.previousToNextCalculatorGroupBox.collapsed = True
previousToNextCalculatorFormLayout = qt.QFormLayout(self.previousToNextCalculatorGroupBox)
playgroundFormLayout.addRow(self.previousToNextCalculatorGroupBox)
self.previousTransformSelector = slicer.qMRMLNodeComboBox()
self.previousTransformSelector.nodeTypes = ["vtkMRMLLinearTransformNode"]
self.previousTransformSelector.selectNodeUponCreation = False
self.previousTransformSelector.addEnabled = False
self.previousTransformSelector.removeEnabled = False
self.previousTransformSelector.noneEnabled = False
self.previousTransformSelector.showHidden = False
self.previousTransformSelector.showChildNodeTypes = False
self.previousTransformSelector.setMRMLScene( slicer.mrmlScene )
previousToNextCalculatorFormLayout.addRow("Select Previous: ", self.previousTransformSelector)
self.nextTransformSelector = slicer.qMRMLNodeComboBox()
self.nextTransformSelector.nodeTypes = ["vtkMRMLLinearTransformNode"]
self.nextTransformSelector.selectNodeUponCreation = False
self.nextTransformSelector.addEnabled = False
self.nextTransformSelector.removeEnabled = False
self.nextTransformSelector.noneEnabled = False
self.nextTransformSelector.showHidden = False
self.nextTransformSelector.showChildNodeTypes = False
self.nextTransformSelector.setMRMLScene( slicer.mrmlScene )
previousToNextCalculatorFormLayout.addRow("Select Next: ", self.nextTransformSelector)
self.previousToNextTransformSelector = slicer.qMRMLNodeComboBox()
self.previousToNextTransformSelector.nodeTypes = ["vtkMRMLLinearTransformNode"]
self.previousToNextTransformSelector.selectNodeUponCreation = True
self.previousToNextTransformSelector.addEnabled = True
self.previousToNextTransformSelector.editEnabled = False
self.previousToNextTransformSelector.removeEnabled = True
self.previousToNextTransformSelector.renameEnabled = True
self.previousToNextTransformSelector.noneEnabled = False
self.previousToNextTransformSelector.showHidden = False
self.previousToNextTransformSelector.showChildNodeTypes = False
self.previousToNextTransformSelector.setMRMLScene( slicer.mrmlScene )
previousToNextCalculatorFormLayout.addRow("Select PreviousToNext: ", self.previousToNextTransformSelector)
self.calculatePreviousToNextButton = qt.QPushButton("Calculate")
self.calculatePreviousToNextButton.enabled = False
previousToNextCalculatorFormLayout.addRow(self.calculatePreviousToNextButton)
# TransformPolyData
self.transformPolyDataGroupBox = ctk.ctkCollapsibleGroupBox()
self.transformPolyDataGroupBox.setTitle("TransformPolyData")
self.transformPolyDataGroupBox.collapsed = True
transformPolyDataFormLayout = qt.QFormLayout(self.transformPolyDataGroupBox)
playgroundFormLayout.addRow(self.transformPolyDataGroupBox)
self.transformPolyDataModelSelector = slicer.qMRMLNodeComboBox()
self.transformPolyDataModelSelector.nodeTypes = ["vtkMRMLModelNode"]
self.transformPolyDataModelSelector.selectNodeUponCreation = False
self.transformPolyDataModelSelector.addEnabled = False
self.transformPolyDataModelSelector.removeEnabled = False
self.transformPolyDataModelSelector.noneEnabled = False
self.transformPolyDataModelSelector.showHidden = False
self.transformPolyDataModelSelector.showChildNodeTypes = False
self.transformPolyDataModelSelector.setMRMLScene( slicer.mrmlScene )
transformPolyDataFormLayout.addRow("Select Model: ", self.transformPolyDataModelSelector)
self.transformPolyDataSelector = slicer.qMRMLNodeComboBox()
self.transformPolyDataSelector.nodeTypes = ["vtkMRMLLinearTransformNode"]
self.transformPolyDataSelector.selectNodeUponCreation = True
self.transformPolyDataSelector.addEnabled = True
self.transformPolyDataSelector.editEnabled = False
self.transformPolyDataSelector.removeEnabled = True
self.transformPolyDataSelector.renameEnabled = True
self.transformPolyDataSelector.noneEnabled = False
self.transformPolyDataSelector.showHidden = False
self.transformPolyDataSelector.showChildNodeTypes = False
self.transformPolyDataSelector.setMRMLScene( slicer.mrmlScene )
transformPolyDataFormLayout.addRow("Select Transform: ", self.transformPolyDataSelector)
self.applyTransformPolyDataButton = qt.QPushButton("Apply")
self.applyTransformPolyDataButton.enabled = False
transformPolyDataFormLayout.addRow(self.applyTransformPolyDataButton)
# FiducialToModelDistance
self.fiducialTestingGroupBox = ctk.ctkCollapsibleGroupBox()
self.fiducialTestingGroupBox.setTitle("FiducialToModelDistance")
self.fiducialTestingGroupBox.collapsed = True
fiducialTestingFormLayout = qt.QFormLayout(self.fiducialTestingGroupBox)
playgroundFormLayout.addRow(self.fiducialTestingGroupBox)
self.fiducialTestingModelSelector = slicer.qMRMLNodeComboBox()
self.fiducialTestingModelSelector.nodeTypes = ["vtkMRMLModelNode"]
self.fiducialTestingModelSelector.selectNodeUponCreation = False
self.fiducialTestingModelSelector.addEnabled = False
self.fiducialTestingModelSelector.removeEnabled = False
self.fiducialTestingModelSelector.noneEnabled = False
self.fiducialTestingModelSelector.showHidden = False
self.fiducialTestingModelSelector.showChildNodeTypes = False
self.fiducialTestingModelSelector.setMRMLScene( slicer.mrmlScene )
fiducialTestingFormLayout.addRow("Select Model: ", self.fiducialTestingModelSelector)
self.outerPointSelector = slicer.qMRMLNodeComboBox()
self.outerPointSelector.nodeTypes = ["vtkMRMLMarkupsFiducialNode"]
self.outerPointSelector.selectNodeUponCreation = True
self.outerPointSelector.addEnabled = True
self.outerPointSelector.editEnabled = False
self.outerPointSelector.removeEnabled = True
self.outerPointSelector.renameEnabled = True
self.outerPointSelector.noneEnabled = False
self.outerPointSelector.showHidden = False
self.outerPointSelector.showChildNodeTypes = False
self.outerPointSelector.setMRMLScene( slicer.mrmlScene )
fiducialTestingFormLayout.addRow("Select Point: ", self.outerPointSelector)
self.calculateFiducialDistanceButton = qt.QPushButton("Calculate Distance")
self.calculateFiducialDistanceButton.enabled = False
fiducialTestingFormLayout.addRow(self.calculateFiducialDistanceButton)
# CastToDouble
self.castToDoubleGroupBox = ctk.ctkCollapsibleGroupBox()
self.castToDoubleGroupBox.setTitle("CastToDouble")
self.castToDoubleGroupBox.collapsed = True
castToDoubleFormLayout = qt.QFormLayout(self.castToDoubleGroupBox)
playgroundFormLayout.addRow(self.castToDoubleGroupBox)
self.castToDoubleSelector = slicer.qMRMLNodeComboBox()
self.castToDoubleSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.castToDoubleSelector.selectNodeUponCreation = False
self.castToDoubleSelector.addEnabled = False
self.castToDoubleSelector.removeEnabled = False
self.castToDoubleSelector.noneEnabled = False
self.castToDoubleSelector.showHidden = False
self.castToDoubleSelector.showChildNodeTypes = False
self.castToDoubleSelector.setMRMLScene( slicer.mrmlScene )
castToDoubleFormLayout.addRow("Select Volume: ", self.castToDoubleSelector)
self.castToDoubleButton = qt.QPushButton("Apply")
self.castToDoubleButton.enabled = False
castToDoubleFormLayout.addRow(self.castToDoubleButton)
############################################### Connnections
# Load for testing
self.loadTestModelButton.connect('clicked(bool)', self.onLoadTestModelButton)
# FirstPersonView
self.stylusTipSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.recordFirstPersonViewPointButton.connect('clicked(bool)', self.onRecordFirstPersonViewPointButton)
self.createFirstPersonViewButton.connect('clicked(bool)', self.onCreateFirstPersonViewButton)
self.movingLRS_FiducialSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
# ModelTipToReferenceCreator
self.modeldistanceToModelToolTipToToolSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.applyModelTipToReferenceCreatorByTransformsButton.connect('clicked(bool)', self.onApplyModelTipToReferenceCreatorByTransformsButton)
self.applyModelTipToToolCreatorByFiducialsButton.connect('clicked(bool)', self.onApplymodelTipToToolCreatorByFiducialsButton)
self.tooldistanceToModelToolTipToToolSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.toolToReferenceSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.modelTipToToolTipSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.originFiducialSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.fromFiducialSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.toFiducialSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
# Record points
self.pointerTransformSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.pointerFiducialsSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.pointRecorderApplyButton.connect('clicked(bool)', self.onPointRecorderApplyButton)
# Texture Mapping
self.textureMappingApplyButton.connect('clicked(bool)', self.onTextureMappingApplyButton)
self.inputModelSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.inputTextureSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
# Fiducial registration
self.registrationApplyButton.connect('clicked(bool)', self.onRegistrationApplyButton)
self.registrationOutputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.movingFiducialsSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.fixedFiducialsSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
# PreviousToNextCalculator
self.calculatePreviousToNextButton.connect('clicked(bool)', self.onCalculatePreviousToNextClicked)
self.previousTransformSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.nextTransformSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.previousToNextTransformSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
# TransformPolyData
self.applyTransformPolyDataButton.connect('clicked(bool)', self.onApplyTransformPolyDataClicked)
self.transformPolyDataSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.transformPolyDataModelSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
# FiducialToModelDistance
self.outerPointSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.fiducialTestingModelSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.calculateFiducialDistanceButton.connect('clicked(bool)', self.onCalculateFiducialDistanceClicked)
# CastToDouble
self.castToDoubleSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.castToDoubleButton.connect('clicked(bool)', self.onCastToDoubleClicked)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onSelect()
def setup(self):
self.logic = BoneEnhancerPyLogic()
ScriptedLoadableModuleWidget.setup(self)
# Add default algorithm parameters to Slicer.ini
self.settings = slicer.app.userSettings()
self.settings.beginGroup(self.moduleName + '/Foroughi2007')
if not self.settings.allKeys(): # If no keys
self.settings.setValue('SmoothingSigma', 5.0)
self.settings.setValue('TransducerMargin', 60)
self.settings.setValue('ShadowSigma', 6.0)
self.settings.setValue('BoneThreshold', 0.4)
self.settings.setValue('BlurredVsBLoG', 3)
self.settings.setValue('ShadowVsIntensity', 5)
smoothingSigma = float(self.settings.value('SmoothingSigma'))
transducerMargin = float(self.settings.value('TransducerMargin'))
shadowSigma = float(self.settings.value('ShadowSigma'))
boneThreshold = float(self.settings.value('BoneThreshold'))
blurredVsBLoG = float(self.settings.value('BlurredVsBLoG'))
shadowVsIntensity = float(self.settings.value('ShadowVsIntensity'))
self.settings.endGroup()
############################################################# Define algorithms
self.foroughi2007 = AlgorithmParams("Foroughi2007 (with minor modifications)",
{"Smoothing Sigma" : (1, 1, 1, 10, smoothingSigma, "Smoothing Sigma ToolTip"),
"Transducer Margin" : (0, 1, 0, 300, transducerMargin, "Transducer Margin ToolTip"),
"Shadow Sigma" : (1, 1, 1, 10, shadowSigma, "Shadow Sigma ToolTip"),
"Bone Threshold" : (1, 0.1, 0, 1, boneThreshold, "Bone Threshold ToolTip"),
"Blurred vs. BLoG" : (1, 0.1, 0, 10, blurredVsBLoG, "Blurred vs. BLoG ToolTip"),
"Shadow vs. Intensity" : (1, 0.1, 0, 10, shadowVsIntensity, "Shadow vs. Intensity ToolTip")})
self.algorithms = [self.foroughi2007]
# Set default algorithm
self.defaultAlgorithm = self.foroughi2007
############################################################ BoneEnhancer
boneEnhancerCollapsibleButton = ctk.ctkCollapsibleButton()
boneEnhancerCollapsibleButton.text = "BoneEnhancer"
self.layout.addWidget(boneEnhancerCollapsibleButton)
boneEnhancerFormLayout = qt.QFormLayout(boneEnhancerCollapsibleButton)
self.ultrasoundImageSelector = slicer.qMRMLNodeComboBox()
self.ultrasoundImageSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.ultrasoundImageSelector.selectNodeUponCreation = True
self.ultrasoundImageSelector.addEnabled = False
self.ultrasoundImageSelector.removeEnabled = False
self.ultrasoundImageSelector.noneEnabled = False
self.ultrasoundImageSelector.showHidden = False
self.ultrasoundImageSelector.showChildNodeTypes = False
self.ultrasoundImageSelector.setMRMLScene( slicer.mrmlScene )
self.ultrasoundImageSelector.setToolTip( "Pick the input to the algorithm." )
boneEnhancerFormLayout.addRow("Ultrasound Image: ", self.ultrasoundImageSelector)
# Select algorithm
self.algorithmGroupBox = ctk.ctkCollapsibleGroupBox()
self.algorithmGroupBox.setTitle("Select Algorithm")
algorithmFormLayout = qt.QFormLayout(self.algorithmGroupBox)
boneEnhancerFormLayout.addRow(self.algorithmGroupBox)
for algorithm in self.algorithms:
algorithmFormLayout.addRow(algorithm.GetRadioButton())
algorithm.GetRadioButton().connect("toggled(bool)", self.onRadioButtonPressed)
# Parameters
self.parametersGroupBox = ctk.ctkCollapsibleGroupBox()
self.parametersGroupBox.setTitle("Parameters")
self.parametersFormLayout = qt.QFormLayout(self.parametersGroupBox)
boneEnhancerFormLayout.addRow(self.parametersGroupBox)
for algorithm in self.algorithms:
self.parametersFormLayout.addWidget(algorithm.getSliderWidget())
algorithm.paramChangedCallback = self.onParameterChanged
# Runtime
self.runtimeGroupBox = ctk.ctkCollapsibleGroupBox()
self.runtimeGroupBox.setTitle("Runtime")
runtimeFormLayout = qt.QFormLayout(self.runtimeGroupBox)
boneEnhancerFormLayout.addRow(self.runtimeGroupBox)
self.runtimeLabel = qt.QLabel()
self.runtimeLabel.setText("... s.")
self.runtimeLabel.setWordWrap(True)
self.runtimeLabel.setStyleSheet("QLabel { background-color : black; \
color : #66FF00; \
height : 60px; \
border-style: outset; \
border-width: 5px; \
border-radius: 10px; \
font: bold 14px; \
padding: 0px;\
font-family : SimSun; \
qproperty-alignment: AlignCenter}")
runtimeFormLayout.addRow(self.runtimeLabel)
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = False
self.applyButton.checkable = True
boneEnhancerFormLayout.addRow(self.applyButton)
############################################################ Connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.ultrasoundImageSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.layout.addStretch(1)
self.defaultAlgorithm.GetRadioButton().checked = True
self.onSelect()
def create(self):
"""create the segmentation helper box"""
#
# Master Frame
#
self.masterFrame = qt.QFrame(self.parent)
self.masterFrame.setLayout(qt.QVBoxLayout())
self.parent.layout().addWidget(self.masterFrame)
#
# the master volume selector
#
self.masterSelectorFrame = qt.QFrame(self.parent)
self.masterSelectorFrame.setLayout(qt.QHBoxLayout())
self.masterFrame.layout().addWidget(self.masterSelectorFrame)
self.masterSelectorLabel = qt.QLabel("Master Volume: ",
self.masterSelectorFrame)
self.masterSelectorLabel.setToolTip(
"Select the master volume (background grayscale scalar volume node)"
)
self.masterSelectorFrame.layout().addWidget(self.masterSelectorLabel)
self.masterSelector = slicer.qMRMLNodeComboBox(
self.masterSelectorFrame)
# TODO
self.masterSelector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.masterSelector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap",
0)
self.masterSelector.selectNodeUponCreation = False
self.masterSelector.addEnabled = False
self.masterSelector.removeEnabled = False
self.masterSelector.noneEnabled = True
self.masterSelector.showHidden = False
self.masterSelector.showChildNodeTypes = False
self.masterSelector.setMRMLScene(slicer.mrmlScene)
# TODO: need to add a QLabel
# self.masterSelector.SetLabelText( "Master Volume:" )
self.masterSelector.setToolTip(
"Pick the master structural volume to define the segmentation. A label volume with the with \"-label\" appended to the name will be created if it doesn't already exist."
)
self.masterSelectorFrame.layout().addWidget(self.masterSelector)
#
# merge label name and set button
#
self.mergeFrame = qt.QFrame(self.masterFrame)
self.mergeFrame.setLayout(qt.QHBoxLayout())
self.masterFrame.layout().addWidget(self.mergeFrame)
mergeNameToolTip = "Composite label map containing the merged structures (be aware that merge operations will overwrite any edits applied to this volume)"
self.mergeNameLabel = qt.QLabel("Merge Volume: ", self.mergeFrame)
self.mergeNameLabel.setToolTip(mergeNameToolTip)
self.mergeFrame.layout().addWidget(self.mergeNameLabel)
self.mergeName = qt.QLabel("", self.mergeFrame)
self.mergeName.setToolTip(mergeNameToolTip)
self.mergeFrame.layout().addWidget(self.mergeName)
self.setMergeButton = qt.QPushButton("Set...", self.mergeFrame)
self.setMergeButton.setToolTip(
"Set the merge volume to use with this master.")
self.mergeFrame.layout().addWidget(self.setMergeButton)
#
# Structures Frame
#
self.structuresFrame = ctk.ctkCollapsibleGroupBox(self.masterFrame)
self.structuresFrame.title = "Per-Structure Volumes"
self.structuresFrame.collapsed = True
self.structuresFrame.setLayout(qt.QVBoxLayout())
self.masterFrame.layout().addWidget(self.structuresFrame)
# buttons frame
self.structureButtonsFrame = qt.QFrame(self.structuresFrame)
self.structureButtonsFrame.setLayout(qt.QHBoxLayout())
self.structuresFrame.layout().addWidget(self.structureButtonsFrame)
# add button
self.addStructureButton = qt.QPushButton("Add Structure",
self.structureButtonsFrame)
self.addStructureButton.setToolTip(
"Add a label volume for a structure to edit")
self.structureButtonsFrame.layout().addWidget(self.addStructureButton)
# split button
self.splitButton = qt.QPushButton("Split Merge Volume",
self.structuresFrame)
self.splitButton.setToolTip(
"Split distinct labels from merge volume into new volumes")
self.structureButtonsFrame.layout().addWidget(self.splitButton)
# structures view
self.structuresView = qt.QTreeView()
self.structuresView.sortingEnabled = True
self.structuresFrame.layout().addWidget(self.structuresView)
# all buttons frame
self.allButtonsFrame = qt.QFrame(self.structuresFrame)
self.allButtonsFrame.setLayout(qt.QHBoxLayout())
self.structuresFrame.layout().addWidget(self.allButtonsFrame)
# delete structures button
self.deleteStructuresButton = qt.QPushButton("Delete Structures",
self.allButtonsFrame)
self.deleteStructuresButton.setToolTip(
"Delete all the structure volumes from the scene.\n\nNote: to delete individual structure volumes, use the Data Module."
)
self.allButtonsFrame.layout().addWidget(self.deleteStructuresButton)
# merge button
self.mergeButton = qt.QPushButton("Merge All", self.allButtonsFrame)
self.mergeButton.setToolTip("Merge all structures into Merge Volume")
self.allButtonsFrame.layout().addWidget(self.mergeButton)
# merge and build button
self.mergeAndBuildButton = qt.QPushButton("Merge And Build",
self.allButtonsFrame)
self.mergeAndBuildButton.setToolTip(
"Merge all structures into Merge Volume and build models from all structures"
)
self.allButtonsFrame.layout().addWidget(self.mergeAndBuildButton)
# options frame
self.optionsFrame = qt.QFrame(self.structuresFrame)
self.optionsFrame.setLayout(qt.QHBoxLayout())
self.structuresFrame.layout().addWidget(self.optionsFrame)
# replace models button
self.replaceModels = qt.QCheckBox("Replace Models", self.optionsFrame)
self.replaceModels.setToolTip(
"Replace any existing models when building")
self.replaceModels.setChecked(1)
self.optionsFrame.layout().addWidget(self.replaceModels)
#
# signals, slots, and observers
#
# signals/slots on qt widgets are automatically when
# this class destructs, but observers of the scene must be explicitly
# removed in the destuctor
# node selected
self.masterSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
# buttons pressed
self.addStructureButton.connect("clicked()", self.addStructure)
self.deleteStructuresButton.connect("clicked()", self.deleteStructures)
# selection changed event
self.structuresView.connect("clicked(QModelIndex)",
self.onStructuresClicked)
# invoked event
self.splitButton.connect("clicked()", self.split)
self.mergeButton.connect("clicked()", self.mergeStructures)
self.mergeAndBuildButton.connect("clicked()", self.onMergeAndBuild)
self.setMergeButton.connect("clicked()", self.labelSelectDialog)
# new scene, node added or removed events
# TODO: allow observers on speific events: 66000, 66001, 66002
tag = slicer.mrmlScene.AddObserver("ModifiedEvent",
self.updateStructures)
self.observerTags.append((slicer.mrmlScene, tag))
# so buttons will initially be disabled
self.master = None
self.updateStructures()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
pointSetProcessingCollapsibleButton = ctk.ctkCollapsibleButton()
pointSetProcessingCollapsibleButton.text = "Surface Reconstruction from Unorganized Points"
self.layout.addWidget(pointSetProcessingCollapsibleButton)
pointSetProcessingFormLayout = qt.QFormLayout(pointSetProcessingCollapsibleButton)
# Input
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = ( ("vtkMRMLModelNode"), "" )
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." )
pointSetProcessingFormLayout.addRow("Input Model: ", self.inputSelector)
self.nbrOfPointsLabel = qt.QLabel('Number of Points in Input Model: - ')
pointSetProcessingFormLayout.addRow(self.nbrOfPointsLabel)
self.inputPointSizeSlider = ctk.ctkSliderWidget()
self.inputPointSizeSlider.setDecimals(0)
self.inputPointSizeSlider.singleStep = 1
self.inputPointSizeSlider.minimum = 1
self.inputPointSizeSlider.maximum = 10
self.inputPointSizeSlider.value = 1
pointSetProcessingFormLayout.addRow('Input Model Point Size: ', self.inputPointSizeSlider)
# Runtime
self.runtimeGroupBox = qt.QGroupBox('Runtime')
runtimeFormLayout = qt.QFormLayout(self.runtimeGroupBox)
pointSetProcessingFormLayout.addRow(self.runtimeGroupBox)
self.runtimeLabel = qt.QLabel()
self.runtimeLabel.setText("... s.")
self.runtimeLabel.setWordWrap(True)
self.runtimeLabel.setStyleSheet("QLabel { background-color : black; \
color : #66FF00; \
height : 60px; \
border-style: outset; \
border-width: 5px; \
border-radius: 10px; \
font: bold 14px; \
padding: 0px;\
font-family : SimSun; \
qproperty-alignment: AlignCenter}")
runtimeFormLayout.addRow(self.runtimeLabel)
# Downsample
self.downSampleGroupBox = ctk.ctkCollapsibleGroupBox()
self.downSampleGroupBox.setTitle("Downsample Input Model")
downSampleFormLayout = qt.QFormLayout(self.downSampleGroupBox)
pointSetProcessingFormLayout.addRow(self.downSampleGroupBox)
self.toleranceCleanSlider = ctk.ctkSliderWidget()
self.toleranceCleanSlider.setDecimals(2)
self.toleranceCleanSlider.singleStep = 0.01
self.toleranceCleanSlider.minimum = 0.0
self.toleranceCleanSlider.maximum = 1.0
self.toleranceCleanSlider.value = 0.01
self.toleranceCleanSlider.setToolTip('')
self.toleranceCleanSlider.enabled = True
downSampleFormLayout.addRow('Tolerance: ', self.toleranceCleanSlider)
self.vtkCleanPolyDataButton = qt.QPushButton("Apply")
self.vtkCleanPolyDataButton.enabled = False
self.vtkCleanPolyDataButton.checkable = True
downSampleFormLayout.addRow(self.vtkCleanPolyDataButton)
# Outlier Removal
self.outlierRemovalGroupBox = ctk.ctkCollapsibleGroupBox()
self.outlierRemovalGroupBox.setTitle("Outlier Removal")
outlierRemovalFormLayout = qt.QFormLayout(self.outlierRemovalGroupBox)
pointSetProcessingFormLayout.addRow(self.outlierRemovalGroupBox)
self.percentToRemoveSlider = ctk.ctkSliderWidget()
self.percentToRemoveSlider.setDecimals(2)
self.percentToRemoveSlider.singleStep = 0.01
self.percentToRemoveSlider.minimum = 0.0
self.percentToRemoveSlider.maximum = 1.0
self.percentToRemoveSlider.value = 0.01
self.percentToRemoveSlider.setToolTip('')
self.percentToRemoveSlider.enabled = True
outlierRemovalFormLayout.addRow('Percent to Remove: ', self.percentToRemoveSlider)
self.vtkPointSetOutlierRemovalButton = qt.QPushButton("Apply")
self.vtkPointSetOutlierRemovalButton.enabled = False
self.vtkPointSetOutlierRemovalButton.checkable = True
outlierRemovalFormLayout.addRow(self.vtkPointSetOutlierRemovalButton)
# Compute Normals
self.normalsGroupBox = ctk.ctkCollapsibleGroupBox()
self.normalsGroupBox.setTitle("Compute Normals")
normalsFormLayout = qt.QFormLayout(self.normalsGroupBox)
pointSetProcessingFormLayout.addRow(self.normalsGroupBox)
self.normalsTabWidget = qt.QTabWidget()
normalsFormLayout.addRow(self.normalsTabWidget)
# vtkPointSetNormalEstimationAndOrientation
self.vtkPointSetNormalEstimationWidget = qt.QWidget()
vtkPointSetNormalEstimationFormLayout = qt.QFormLayout(self.vtkPointSetNormalEstimationWidget)
normalsFormLayout.addRow(self.vtkPointSetNormalEstimationWidget)
self.normalsTabWidget.addTab(self.vtkPointSetNormalEstimationWidget, "vtkPointSetNormalEstimationAndOrientation")
self.modeTypeComboBox = qt.QComboBox()
self.modeTypeComboBox.addItem('Fixed')
self.modeTypeComboBox.addItem('Radius')
self.modeTypeComboBox.setCurrentIndex(1)
self.modeTypeComboBox.setToolTip('')
vtkPointSetNormalEstimationFormLayout.addRow('Mode Type: ', self.modeTypeComboBox)
self.numberOfNeighborsSlider = ctk.ctkSliderWidget()
self.numberOfNeighborsSlider.setDecimals(0)
self.numberOfNeighborsSlider.singleStep = 1
self.numberOfNeighborsSlider.minimum = 1
self.numberOfNeighborsSlider.maximum = 20
self.numberOfNeighborsSlider.value = 4
self.numberOfNeighborsSlider.setToolTip('')
self.numberOfNeighborsSlider.enabled = False
vtkPointSetNormalEstimationFormLayout.addRow('Fixed Neighbors: ', self.numberOfNeighborsSlider)
self.radiusSlider = ctk.ctkSliderWidget()
self.radiusSlider.setDecimals(2)
self.radiusSlider.singleStep = 0.01
self.radiusSlider.minimum = 0
self.radiusSlider.maximum = 50
self.radiusSlider.value = 1.0
self.radiusSlider.setToolTip('')
vtkPointSetNormalEstimationFormLayout.addRow('Radius: ', self.radiusSlider)
self.graphTypeComboBox = qt.QComboBox()
self.graphTypeComboBox.addItem('Riemann')
self.graphTypeComboBox.addItem('KNN')
self.graphTypeComboBox.setCurrentIndex(1)
self.graphTypeComboBox.setToolTip('')
vtkPointSetNormalEstimationFormLayout.addRow('Graph Type: ', self.graphTypeComboBox)
self.knnSlider = ctk.ctkSliderWidget()
self.knnSlider.setDecimals(0)
self.knnSlider.singleStep = 1
self.knnSlider.minimum = 1
self.knnSlider.maximum = 100
self.knnSlider.value = 5
self.knnSlider.setToolTip('')
vtkPointSetNormalEstimationFormLayout.addRow('K-Nearest Neighbors: ', self.knnSlider)
self.vtkPointSetNormalEstimationButton = qt.QPushButton("Apply")
self.vtkPointSetNormalEstimationButton.enabled = False
self.vtkPointSetNormalEstimationButton.checkable = True
vtkPointSetNormalEstimationFormLayout.addRow(self.vtkPointSetNormalEstimationButton)
# vtkPolyDataNormals
self.vtkPolyDataNormalsWidget = qt.QWidget()
vtkPolyDataNormalsFormLayout = qt.QFormLayout(self.vtkPolyDataNormalsWidget)
normalsFormLayout.addRow(self.vtkPolyDataNormalsWidget)
self.normalsTabWidget.addTab(self.vtkPolyDataNormalsWidget, "vtkPolyDataNormals")
self.featureAngleSlider = ctk.ctkSliderWidget()
self.featureAngleSlider.setDecimals(2)
self.featureAngleSlider.singleStep = 0.01
self.featureAngleSlider.minimum = 0
self.featureAngleSlider.maximum = 360
self.featureAngleSlider.value = 0.1
self.featureAngleSlider.setToolTip('')
vtkPolyDataNormalsFormLayout.addRow('Feature Angle: ', self.featureAngleSlider)
self.splittingComboBox = qt.QComboBox()
self.splittingComboBox.addItem('False')
self.splittingComboBox.addItem('True')
self.splittingComboBox.setCurrentIndex(1)
self.splittingComboBox.setToolTip('')
vtkPolyDataNormalsFormLayout.addRow('Splitting: ', self.splittingComboBox)
self.consistencyComboBox = qt.QComboBox()
self.consistencyComboBox.addItem('False')
self.consistencyComboBox.addItem('True')
self.consistencyComboBox.setCurrentIndex(0)
self.consistencyComboBox.setToolTip('')
vtkPolyDataNormalsFormLayout.addRow('Consistency: ', self.consistencyComboBox)
self.autoOrientNormalsComboBox = qt.QComboBox()
self.autoOrientNormalsComboBox.addItem('False')
self.autoOrientNormalsComboBox.addItem('True')
self.autoOrientNormalsComboBox.setCurrentIndex(0)
self.autoOrientNormalsComboBox.setToolTip('')
vtkPolyDataNormalsFormLayout.addRow('Auto-Orient Normals: ', self.autoOrientNormalsComboBox)
self.computePointNormalsComboBox = qt.QComboBox()
self.computePointNormalsComboBox.addItem('False')
self.computePointNormalsComboBox.addItem('True')
self.computePointNormalsComboBox.setCurrentIndex(1)
self.computePointNormalsComboBox.setToolTip('')
vtkPolyDataNormalsFormLayout.addRow('Compute Point Normals: ', self.computePointNormalsComboBox)
self.computeCellNormalsComboBox = qt.QComboBox()
self.computeCellNormalsComboBox.addItem('False')
self.computeCellNormalsComboBox.addItem('True')
self.computeCellNormalsComboBox.setCurrentIndex(0)
self.computeCellNormalsComboBox.setToolTip('')
vtkPolyDataNormalsFormLayout.addRow('Compute Cell Normals: ', self.computeCellNormalsComboBox)
self.flipNormalsComboBox = qt.QComboBox()
self.flipNormalsComboBox.addItem('False')
self.flipNormalsComboBox.addItem('True')
self.flipNormalsComboBox.setCurrentIndex(0)
self.flipNormalsComboBox.setToolTip('')
vtkPolyDataNormalsFormLayout.addRow('Flip Normals: ', self.flipNormalsComboBox)
self.nonManifoldTraversalComboBox = qt.QComboBox()
self.nonManifoldTraversalComboBox.addItem('False')
self.nonManifoldTraversalComboBox.addItem('True')
self.nonManifoldTraversalComboBox.setCurrentIndex(1)
self.nonManifoldTraversalComboBox.setToolTip('')
vtkPolyDataNormalsFormLayout.addRow('Non-Manifold Traversal: ', self.nonManifoldTraversalComboBox)
self.vtkPolyDataNormalsButton = qt.QPushButton("Apply")
self.vtkPolyDataNormalsButton.enabled = False
self.vtkPolyDataNormalsButton.checkable = True
vtkPolyDataNormalsFormLayout.addRow(self.vtkPolyDataNormalsButton)
self.normalsVisibleCheckBox = qt.QCheckBox('Arrows Visibility: ')
self.normalsVisibleCheckBox.checked = True
self.normalsVisibleCheckBox.enabled = True
self.normalsVisibleCheckBox.setLayoutDirection(1)
normalsFormLayout.addRow(self.normalsVisibleCheckBox)
# Compute Surface
self.surfaceGroupBox = ctk.ctkCollapsibleGroupBox()
self.surfaceGroupBox.setTitle("Compute Surface")
surfaceFormLayout = qt.QFormLayout(self.surfaceGroupBox)
pointSetProcessingFormLayout.addRow(self.surfaceGroupBox)
self.surfaceTabWidget = qt.QTabWidget()
surfaceFormLayout.addRow(self.surfaceTabWidget)
# vtkPoissionReconstruction
self.vtkPoissionReconstructionWidget = qt.QWidget()
vtkPoissionReconstructionFormLayout = qt.QFormLayout(self.vtkPoissionReconstructionWidget)
surfaceFormLayout.addRow(self.vtkPoissionReconstructionWidget)
self.surfaceTabWidget.addTab(self.vtkPoissionReconstructionWidget, "vtkPoissionReconstruction")
self.depthSlider = ctk.ctkSliderWidget()
self.depthSlider.setDecimals(0)
self.depthSlider.singleStep = 1
self.depthSlider.minimum = 1
self.depthSlider.maximum = 14
self.depthSlider.value = 8
self.depthSlider.setToolTip('This integer controls the reconstruction depth; the maximum depth of the tree that will be used for surface reconstruction. Running at depth d corresponds to solving on a voxel grid whose resolution is no larger than 2^d x 2^d x 2^d. Note that since the reconstructor adapts the octree to the sampling density, the specified reconstruction depth is only an upper bound.')
vtkPoissionReconstructionFormLayout.addRow('Depth: ', self.depthSlider)
self.scaleSlider = ctk.ctkSliderWidget()
self.scaleSlider.setDecimals(2)
self.scaleSlider.singleStep = 0.01
self.scaleSlider.minimum = 0
self.scaleSlider.maximum = 10
self.scaleSlider.value = 1.25
self.scaleSlider.setToolTip('This floating point value specifies the ratio between the diameter of the cube used for reconstruction and the diameter of the samples bounding cube.')
vtkPoissionReconstructionFormLayout.addRow('Scale: ', self.scaleSlider)
self.solverDivideSlider = ctk.ctkSliderWidget()
self.solverDivideSlider.setDecimals(0)
self.solverDivideSlider.singleStep = 1
self.solverDivideSlider.minimum = 1
self.solverDivideSlider.maximum = 20
self.solverDivideSlider.value = 8
self.solverDivideSlider.setToolTip('Solver subdivision depth; This integer argument specifies the depth at which a block Gauss-Seidel solver is used to solve the Laplacian equation. Using this parameter helps reduce the memory overhead at the cost of a small increase in reconstruction time. (In practice, we have found that for reconstructions of depth 9 or higher a subdivide depth of 7 or 8 can greatly reduce the memory usage.)')
vtkPoissionReconstructionFormLayout.addRow('Solver Divide: ', self.solverDivideSlider)
self.isoDivideSlider = ctk.ctkSliderWidget()
self.isoDivideSlider.setDecimals(0)
self.isoDivideSlider.singleStep = 1
self.isoDivideSlider.minimum = 1
self.isoDivideSlider.maximum = 20
self.isoDivideSlider.value = 8
self.isoDivideSlider.setToolTip('Iso-surface extraction subdivision depth; This integer argument specifies the depth at which a block isosurface extractor should be used to extract the iso-surface. Using this parameter helps reduce the memory overhead at the cost of a small increase in extraction time. (In practice, we have found that for reconstructions of depth 9 or higher a subdivide depth of 7 or 8 can greatly reduce the memory usage.)')
vtkPoissionReconstructionFormLayout.addRow('Iso Divide: ', self.isoDivideSlider)
self.samplesPerNodeSlider = ctk.ctkSliderWidget()
self.samplesPerNodeSlider.setDecimals(2)
self.samplesPerNodeSlider.singleStep = 0.1
self.samplesPerNodeSlider.minimum = 1
self.samplesPerNodeSlider.maximum = 30
self.samplesPerNodeSlider.value = 1.0
self.samplesPerNodeSlider.setToolTip('Minimum number of samples; This floating point value specifies the minimum number of sample points that should fall within an octree node as the octree construction is adapted to sampling density. For noise-free samples, small values in the range [1.0 - 5.0] can be used. For more noisy samples, larger values in the range [15.0 - 20.0] may be needed to provide a smoother, noise-reduced, reconstruction.')
vtkPoissionReconstructionFormLayout.addRow('Samples per Node: ', self.samplesPerNodeSlider)
self.confidenceComboBox = qt.QComboBox()
self.confidenceComboBox.addItem('False')
self.confidenceComboBox.addItem('True')
self.confidenceComboBox.setToolTip('Enabling tells the reconstructor to use the size of the normals as confidence information. When the flag is not enabled, all normals are normalized to have unit-length prior to reconstruction.')
vtkPoissionReconstructionFormLayout.addRow('Confidence: ', self.confidenceComboBox)
self.verboseComboBox = qt.QComboBox()
self.verboseComboBox.addItem('False')
self.verboseComboBox.addItem('True')
self.verboseComboBox.setToolTip('Enabling this flag provides a more verbose description of the running times and memory usages of individual components of the surface reconstructor.')
vtkPoissionReconstructionFormLayout.addRow('Verbose: ', self.verboseComboBox)
self.vtkPoissionReconstructionButton = qt.QPushButton("Apply")
self.vtkPoissionReconstructionButton.enabled = False
self.vtkPoissionReconstructionButton.checkable = True
vtkPoissionReconstructionFormLayout.addRow(self.vtkPoissionReconstructionButton)
# vtkDelaunay3D
self.vtkDelaunay3DWidget = qt.QWidget()
vtkDelaunay3DFormLayout = qt.QFormLayout(self.vtkDelaunay3DWidget)
surfaceFormLayout.addRow(self.vtkDelaunay3DWidget)
self.surfaceTabWidget.addTab(self.vtkDelaunay3DWidget, "vtkDelaunay3D")
self.alphaSlider = ctk.ctkSliderWidget()
self.alphaSlider.setDecimals(1)
self.alphaSlider.singleStep = 0.1
self.alphaSlider.minimum = 0.0
self.alphaSlider.maximum = 100.0
self.alphaSlider.value = 0.0
self.alphaSlider.setToolTip('')
vtkDelaunay3DFormLayout.addRow('Alpha: ', self.alphaSlider)
self.toleranceSlider = ctk.ctkSliderWidget()
self.toleranceSlider.setDecimals(2)
self.toleranceSlider.singleStep = 0.01
self.toleranceSlider.minimum = 0.0
self.toleranceSlider.maximum = 1.0
self.toleranceSlider.value = 0.0
self.toleranceSlider.setToolTip('')
vtkDelaunay3DFormLayout.addRow('Tolerance: ', self.toleranceSlider)
self.offsetSlider = ctk.ctkSliderWidget()
self.offsetSlider.setDecimals(1)
self.offsetSlider.singleStep = 0.1
self.offsetSlider.minimum = 0.0
self.offsetSlider.maximum = 10.0
self.offsetSlider.value = 2.5
self.offsetSlider.setToolTip('')
vtkDelaunay3DFormLayout.addRow('Offset: ', self.offsetSlider)
self.boundingComboBox = qt.QComboBox()
self.boundingComboBox.addItem('False')
self.boundingComboBox.addItem('True')
self.boundingComboBox.setCurrentIndex(0)
self.boundingComboBox.setToolTip('')
vtkDelaunay3DFormLayout.addRow('Bounding Triangulations: ', self.boundingComboBox)
self.vtkDelaunay3DButton = qt.QPushButton("Apply")
self.vtkDelaunay3DButton.enabled = False
self.vtkDelaunay3DButton.checkable = True
vtkDelaunay3DFormLayout.addRow(self.vtkDelaunay3DButton)
self.surfaceVisibleCheckBox = qt.QCheckBox('Surface Visibility: ')
self.surfaceVisibleCheckBox.checked = True
self.surfaceVisibleCheckBox.enabled = True
self.surfaceVisibleCheckBox.setLayoutDirection(1)
surfaceFormLayout.addRow(self.surfaceVisibleCheckBox)
# connections
self.vtkCleanPolyDataButton.connect('clicked(bool)', self.vtkCleanPolyDataClicked)
self.vtkPointSetOutlierRemovalButton.connect('clicked(bool)', self.vtkPointSetOutlierRemovalClicked)
self.vtkPointSetNormalEstimationButton.connect('clicked(bool)', self.vtkPointSetNormalEstimationClicked)
self.vtkPolyDataNormalsButton.connect('clicked(bool)', self.vtkPolyDataNormalsClicked)
self.vtkPoissionReconstructionButton.connect('clicked(bool)', self.vtkPoissionReconstructionClicked)
self.vtkDelaunay3DButton.connect('clicked(bool)', self.vtkDelaunay3DClicked)
self.inputSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onSelect)
self.graphTypeComboBox.connect('currentIndexChanged(const QString &)', self.onGraphTypeChanged)
self.modeTypeComboBox.connect('currentIndexChanged(const QString &)', self.onModeChanged)
self.surfaceVisibleCheckBox.connect('stateChanged(int)', self.onSurfaceVisible)
self.normalsVisibleCheckBox.connect('stateChanged(int)', self.onNormalsVisible)
self.inputPointSizeSlider.connect('valueChanged (double)', self.onInputPointSliderModified)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh
self.onSelect()
lm=slicer.app.layoutManager()
lm.setLayout(4) # One 3D-view
def setup(self):
# # Instantiate and connect widgets
# ---------------------------- Window Settings -----------------------------
initializationCollapsibleButton = ctk.ctkCollapsibleButton()
initializationCollapsibleButton.text = "Window Initialization"
self.layout.addWidget(initializationCollapsibleButton)
initializationLayout = qt.QFormLayout(initializationCollapsibleButton)
self.stereoCheckBox = qt.QCheckBox()
initializationLayout.addRow("Stereoscopic mode:", self.stereoCheckBox)
self.startButton = qt.QPushButton("Create Windows")
initializationLayout.addRow(self.startButton)
self.showButton = qt.QPushButton("Show Windows")
initializationLayout.addRow(self.showButton)
self.hideButton = qt.QPushButton("Hide Windows")
initializationLayout.addRow(self.hideButton)
# ---------------------------- Stereo Settings -----------------------------
stereoCollapsibleButton = ctk.ctkCollapsibleButton()
stereoCollapsibleButton.text = "Stereoscopic Settings"
self.layout.addWidget(stereoCollapsibleButton)
stereoSettingsLayout = qt.QFormLayout(stereoCollapsibleButton)
self.upViewAngleButton = qt.QPushButton("Increase View Angle")
stereoSettingsLayout.addWidget(self.upViewAngleButton)
self.downViewAngleButton = qt.QPushButton("Decrease View Angle")
stereoSettingsLayout.addWidget(self.downViewAngleButton)
# ------------------- Transform and Tracking Settings ----------------------
trackingCollapsibleButton = ctk.ctkCollapsibleButton()
trackingCollapsibleButton.text = "Update Settings"
self.layout.addWidget(trackingCollapsibleButton)
trackingSettingsLayout = qt.QFormLayout(trackingCollapsibleButton)
self.followNodeSelector = slicer.qMRMLNodeComboBox()
self.followNodeSelector.nodeTypes = ["vtkMRMLMarkupsFiducialNode", "vtkMRMLLinearTransformNode"]
self.followNodeSelector.selectNodeUponCreation = False
self.followNodeSelector.noneEnabled = False
self.followNodeSelector.addEnabled = True
self.followNodeSelector.showHidden = False
self.followNodeSelector.setMRMLScene( slicer.mrmlScene )
self.followNodeSelector.setToolTip( "Pick Fiducial Node or Linear Transform to follow" )
trackingSettingsLayout.addRow("Path node (transform or fiducial)", self.followNodeSelector)
self.oculusNodeSelector = slicer.qMRMLNodeComboBox()
self.oculusNodeSelector.nodeTypes = ["vtkMRMLLinearTransformNode"]
self.oculusNodeSelector.selectNodeUponCreation = False
self.oculusNodeSelector.noneEnabled = False
self.oculusNodeSelector.addEnabled = True
self.oculusNodeSelector.showHidden = False
self.oculusNodeSelector.setMRMLScene( slicer.mrmlScene )
self.oculusNodeSelector.setToolTip( "Pick Transform for Oculus Rift" )
trackingSettingsLayout.addRow("Oculus Transform", self.oculusNodeSelector)
self.updateTrackingButton = qt.QPushButton("Update Tracking")
trackingSettingsLayout.addWidget(self.updateTrackingButton)
# ---------------------------- Update Export Image Settings -----------------------------
updatesCollapsibleButton = ctk.ctkCollapsibleButton()
updatesCollapsibleButton.text = "Update Settings"
self.layout.addWidget(updatesCollapsibleButton)
updateSettingsLayout = qt.QFormLayout(updatesCollapsibleButton)
self.createButton = qt.QPushButton("Create Image")
updateSettingsLayout.addWidget(self.createButton)
self.startRepeatButton = qt.QPushButton("Continually Create Images")
updateSettingsLayout.addWidget(self.startRepeatButton)
self.stopRepeatButton = qt.QPushButton("Stop Creating Images")
updateSettingsLayout.addWidget(self.stopRepeatButton)
# ---------------------------- Lighting Settings -----------------------------
lightingCollapsibleButton = ctk.ctkCollapsibleButton()
lightingCollapsibleButton.text = "Lighting Settings"
self.layout.addWidget(lightingCollapsibleButton)
lightingSettingsLayout = qt.QFormLayout(lightingCollapsibleButton)
# ----- Manual Lighting Control ------
manualLightingGroupBox = ctk.ctkCollapsibleGroupBox()
lightingSettingsLayout.addWidget(manualLightingGroupBox)
manualLightingLayout = qt.QFormLayout(manualLightingGroupBox)
self.lightSliderX = ctk.ctkSliderWidget()
self.lightSliderX.maximum = 500
self.lightSliderX.minimum = -500
self.lightSliderX.value = 0
self.lightSliderX.tracking = True
manualLightingLayout.addRow("X", self.lightSliderX)
self.lightSliderY = ctk.ctkSliderWidget()
self.lightSliderY.maximum = 500
self.lightSliderY.minimum = -500
self.lightSliderY.value = 0
self.lightSliderY.tracking = True
manualLightingLayout.addRow("Y", self.lightSliderY)
self.lightSliderZ = ctk.ctkSliderWidget()
self.lightSliderZ.maximum = 500
self.lightSliderZ.minimum = -500
self.lightSliderZ.value = 300
self.lightSliderZ.tracking = True
manualLightingLayout.addRow("Z", self.lightSliderZ)
# # Connections
self.startButton.connect('clicked(bool)', self.createWindows)
self.showButton.connect('clicked(bool)', self.showWindows)
self.hideButton.connect('clicked(bool)', self.hideWindows)
self.upViewAngleButton.connect('clicked(bool)', self.upViewAngle)
self.downViewAngleButton.connect('clicked(bool)', self.downViewAngle)
self.createButton.connect('clicked(bool)', self.createWindowImages)
self.startRepeatButton.connect('clicked(bool)', self.startCreatingImages)
self.stopRepeatButton.connect('clicked(bool)', self.stopCreatingImages)
self.followNodeSelector.connect('currentNodeChanged(bool)', self.setFollowNode)
self.updateTrackingButton.connect('clicked(bool)', self.updateTracking)
self.lightSliderX.connect('valueChanged(double)', self.onLightSliderChanged)
self.lightSliderY.connect('valueChanged(double)', self.onLightSliderChanged)
self.lightSliderZ.connect('valueChanged(double)', self.onLightSliderChanged)
self.timer = qt.QTimer()
self.timer.timeout.connect(self.createWindowImages)
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
self.logic = NeedleTrackingLogic(None)
self.logic.setWidget(self)
#--------------------------------------------------
# For debugging
#
# Reload and Test area
reloadCollapsibleButton = ctk.ctkCollapsibleButton()
reloadCollapsibleButton.text = "Reload && Test"
self.layout.addWidget(reloadCollapsibleButton)
reloadFormLayout = qt.QFormLayout(reloadCollapsibleButton)
reloadCollapsibleButton.collapsed = True
# reload button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "Reload"
reloadFormLayout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
#
#--------------------------------------------------
self.nCath = 1 # Number of catheters
#--------------------------------------------------
# GUI components
#
# Connection Area
#
connectionCollapsibleButton = ctk.ctkCollapsibleButton()
connectionCollapsibleButton.text = "Connection (OpenIGTLink)"
self.layout.addWidget(connectionCollapsibleButton)
# Layout within the dummy collapsible button
connectionFormLayout = qt.QFormLayout(connectionCollapsibleButton)
#--------------------------------------------------
# Connector Selector
#--------------------------------------------------
self.igtlConnector1 = NeedleTrackingIGTLConnector("Connector 1")
self.igtlConnector1.port = 18944
self.igtlConnector1.buildGUI(connectionFormLayout)
#--------------------------------------------------
# Catheter
#--------------------------------------------------
catheterCollapsibleButton = ctk.ctkCollapsibleButton()
catheterCollapsibleButton.text = "Tracking Node"
self.layout.addWidget(catheterCollapsibleButton)
catheterFormLayout = qt.QFormLayout(catheterCollapsibleButton)
#--------------------------------------------------
# Tracking node selector
trackingNodeGroupBox = ctk.ctkCollapsibleGroupBox()
trackingNodeGroupBox.title = "Tracking Node"
catheterFormLayout.addWidget(trackingNodeGroupBox)
trackingNodeFormLayout = qt.QFormLayout(trackingNodeGroupBox)
self.trackingDataSelector = slicer.qMRMLNodeComboBox()
self.trackingDataSelector.nodeTypes = ((
"vtkMRMLIGTLTrackingDataBundleNode"), "")
self.trackingDataSelector.selectNodeUponCreation = True
self.trackingDataSelector.addEnabled = True
self.trackingDataSelector.removeEnabled = False
self.trackingDataSelector.noneEnabled = False
self.trackingDataSelector.showHidden = True
self.trackingDataSelector.showChildNodeTypes = False
self.trackingDataSelector.setMRMLScene(slicer.mrmlScene)
self.trackingDataSelector.setToolTip("Incoming tracking data")
trackingNodeFormLayout.addRow("TrackingData: ",
self.trackingDataSelector)
#
# check box to trigger transform conversion
#
self.activeTrackingCheckBox = qt.QCheckBox()
self.activeTrackingCheckBox.checked = 0
self.activeTrackingCheckBox.enabled = 1
self.activeTrackingCheckBox.setToolTip("Activate Tracking")
trackingNodeFormLayout.addRow("Active: ", self.activeTrackingCheckBox)
#--------------------------------------------------
# Catheter Configuration
configGroupBox = ctk.ctkCollapsibleGroupBox()
configGroupBox.title = "Catheter Configuration"
configGroupBox.collapsed = True
catheterFormLayout.addWidget(configGroupBox)
configFormLayout = qt.QFormLayout(configGroupBox)
self.tipLengthSliderWidget = [None] * self.nCath
self.catheterDiameterSliderWidget = [None] * self.nCath
self.catheterOpacitySliderWidget = [None] * self.nCath
for cath in range(self.nCath):
#
# Tip Length (legnth between the catheter tip and the first coil)
#
self.tipLengthSliderWidget[cath] = ctk.ctkSliderWidget()
self.tipLengthSliderWidget[cath].singleStep = 0.5
self.tipLengthSliderWidget[cath].minimum = 0.0
self.tipLengthSliderWidget[cath].maximum = 100.0
self.tipLengthSliderWidget[cath].value = 10.0
self.tipLengthSliderWidget[cath].setToolTip(
"Set the length of the catheter tip.")
configFormLayout.addRow("Cath %d Tip Length (mm): " % cath,
self.tipLengthSliderWidget[cath])
#
# Catheter #1 Catheter diameter
#
self.catheterDiameterSliderWidget[cath] = ctk.ctkSliderWidget()
self.catheterDiameterSliderWidget[cath].singleStep = 0.1
self.catheterDiameterSliderWidget[cath].minimum = 0.1
self.catheterDiameterSliderWidget[cath].maximum = 10.0
self.catheterDiameterSliderWidget[cath].value = 1.0
self.catheterDiameterSliderWidget[cath].setToolTip(
"Set the diameter of the catheter")
configFormLayout.addRow("Cath %d Diameter (mm): " % cath,
self.catheterDiameterSliderWidget[cath])
#
# Catheter #1 Catheter opacity
#
self.catheterOpacitySliderWidget[cath] = ctk.ctkSliderWidget()
self.catheterOpacitySliderWidget[cath].singleStep = 0.1
self.catheterOpacitySliderWidget[cath].minimum = 0.0
self.catheterOpacitySliderWidget[cath].maximum = 1.0
self.catheterOpacitySliderWidget[cath].value = 1.0
self.catheterOpacitySliderWidget[cath].setToolTip(
"Set the opacity of the catheter")
configFormLayout.addRow("Cath %d Opacity: " % cath,
self.catheterOpacitySliderWidget[cath])
#
# Check box to show/hide coil labels
#
self.showCoilLabelCheckBox = qt.QCheckBox()
self.showCoilLabelCheckBox.checked = 0
self.showCoilLabelCheckBox.setToolTip("Show/hide coil labels")
configFormLayout.addRow("Show Coil Labels: ",
self.showCoilLabelCheckBox)
#--------------------------------------------------
# Coordinate System
#
coordinateGroupBox = ctk.ctkCollapsibleGroupBox()
coordinateGroupBox.title = "Coordinate System"
coordinateGroupBox.collapsed = True
catheterFormLayout.addWidget(coordinateGroupBox)
coordinateLayout = qt.QFormLayout(coordinateGroupBox)
self.coordinateRPlusRadioButton = qt.QRadioButton("+X")
self.coordinateRMinusRadioButton = qt.QRadioButton("-X")
self.coordinateRPlusRadioButton.checked = 1
self.coordinateRBoxLayout = qt.QHBoxLayout()
self.coordinateRBoxLayout.addWidget(self.coordinateRPlusRadioButton)
self.coordinateRBoxLayout.addWidget(self.coordinateRMinusRadioButton)
self.coordinateRGroup = qt.QButtonGroup()
self.coordinateRGroup.addButton(self.coordinateRPlusRadioButton)
self.coordinateRGroup.addButton(self.coordinateRMinusRadioButton)
coordinateLayout.addRow("Right:", self.coordinateRBoxLayout)
self.coordinateAPlusRadioButton = qt.QRadioButton("+Y")
self.coordinateAMinusRadioButton = qt.QRadioButton("-Y")
self.coordinateAPlusRadioButton.checked = 1
self.coordinateABoxLayout = qt.QHBoxLayout()
self.coordinateABoxLayout.addWidget(self.coordinateAPlusRadioButton)
self.coordinateABoxLayout.addWidget(self.coordinateAMinusRadioButton)
self.coordinateAGroup = qt.QButtonGroup()
self.coordinateAGroup.addButton(self.coordinateAPlusRadioButton)
self.coordinateAGroup.addButton(self.coordinateAMinusRadioButton)
coordinateLayout.addRow("Anterior:", self.coordinateABoxLayout)
self.coordinateSPlusRadioButton = qt.QRadioButton("+Z")
self.coordinateSMinusRadioButton = qt.QRadioButton("-Z")
self.coordinateSPlusRadioButton.checked = 1
self.coordinateSBoxLayout = qt.QHBoxLayout()
self.coordinateSBoxLayout.addWidget(self.coordinateSPlusRadioButton)
self.coordinateSBoxLayout.addWidget(self.coordinateSMinusRadioButton)
self.coordinateSGroup = qt.QButtonGroup()
self.coordinateSGroup.addButton(self.coordinateSPlusRadioButton)
self.coordinateSGroup.addButton(self.coordinateSMinusRadioButton)
coordinateLayout.addRow("Superior:", self.coordinateSBoxLayout)
#--------------------------------------------------
# Reslice
#
resliceCollapsibleButton = ctk.ctkCollapsibleButton()
resliceCollapsibleButton.text = "Image Reslice"
self.layout.addWidget(resliceCollapsibleButton)
#resliceLayout = qt.QFormLayout(resliceCollapsibleButton)
self.reslice = NeedleTrackingReslice("Image Reslice")
self.reslice.nCath = self.nCath
self.reslice.buildGUI(resliceCollapsibleButton)
#--------------------------------------------------
# Connections
#--------------------------------------------------
self.trackingDataSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onTrackingDataSelected)
self.activeTrackingCheckBox.connect('toggled(bool)',
self.onActiveTracking)
for cath in range(self.nCath):
self.tipLengthSliderWidget[cath].connect(
"valueChanged(double)",
functools.partial(self.onTipLengthChanged, cath))
self.catheterDiameterSliderWidget[cath].connect(
"valueChanged(double)",
functools.partial(self.onCatheterDiameterChanged, cath))
self.catheterOpacitySliderWidget[cath].connect(
"valueChanged(double)",
functools.partial(self.onCatheterOpacityChanged, cath))
self.showCoilLabelCheckBox.connect('toggled(bool)',
self.onCoilLabelChecked)
self.coordinateRPlusRadioButton.connect('clicked(bool)',
self.onSelectCoordinate)
self.coordinateRMinusRadioButton.connect('clicked(bool)',
self.onSelectCoordinate)
self.coordinateAPlusRadioButton.connect('clicked(bool)',
self.onSelectCoordinate)
self.coordinateAMinusRadioButton.connect('clicked(bool)',
self.onSelectCoordinate)
self.coordinateSPlusRadioButton.connect('clicked(bool)',
self.onSelectCoordinate)
self.coordinateSMinusRadioButton.connect('clicked(bool)',
self.onSelectCoordinate)
# Add vertical spacer
self.layout.addStretch(1)
def initMainPanel(self):
# Create main collapsible Button
self.mainCollapsibleBtn = ctk.ctkCollapsibleButton()
self.mainCollapsibleBtn.setStyleSheet(
"ctkCollapsibleButton { background-color: DarkSeaGreen }")
self.mainCollapsibleBtn.text = "Remeshing Tools Selection"
#self.mainCollapsibleBtn.collapsible = True
self.layout.addWidget(self.mainCollapsibleBtn)
self.mainFormLayout = qt.QFormLayout(self.mainCollapsibleBtn)
# Create input Segmentation Selector
self.inputSelectorCoBx = slicer.qMRMLNodeComboBox()
self.inputSelectorCoBx.nodeTypes = ["vtkMRMLModelNode"]
self.inputSelectorCoBx.setFixedWidth(200)
self.inputSelectorCoBx.selectNodeUponCreation = True
self.inputSelectorCoBx.addEnabled = False
self.inputSelectorCoBx.removeEnabled = False
self.inputSelectorCoBx.noneEnabled = False
self.inputSelectorCoBx.showHidden = False
self.inputSelectorCoBx.showChildNodeTypes = False
self.inputSelectorCoBx.setMRMLScene(slicer.mrmlScene)
self.inputSelectorCoBx.setToolTip(
"select an .stl file as the input segmentation")
self.mainFormLayout.addRow("Input segmentation: ",
self.inputSelectorCoBx)
# Create button to show mesh of InputNode
self.showMeshBtn = qt.QPushButton("Show Mesh")
self.showMeshBtn.setFixedHeight(20)
self.showMeshBtn.setFixedWidth(100)
self.showMeshBtn.setStyleSheet(
"QPushButton{ background-color: DarkSeaGreen }")
self.showMeshBtn.toolTip = (
'How to use:'
' Click the Show Mesh Button to show mesh of Input Segmentation ')
self.showMeshBtn.connect('clicked(bool)', self.onShowBtnClick)
self.mainFormLayout.addRow("Input Segmentation: ", self.showMeshBtn)
# Create button to set visibility to 1 of inputNode
self.showBtn = qt.QPushButton("Show Input")
self.showBtn.setFixedHeight(20)
self.showBtn.setFixedWidth(100)
self.showBtn.setStyleSheet(
"QPushButton{ background-color: DarkSeaGreen }")
self.showBtn.toolTip = (
'How to use:'
' Click the Show Mesh Button to show Input Segmentation ')
self.showBtn.connect('clicked(bool)', self.onInputBtnClick)
self.mainFormLayout.addRow("Input Segmentation: ", self.showBtn)
# ---------------------------------------INSTANT MESHING--------------------------------------------
# Create collapsible Button for Instant-Meshing options
self.instantCollapsibleBtn = ctk.ctkCollapsibleButton()
self.instantCollapsibleBtn.text = "Instant-Meshing"
self.layout.addWidget(self.instantCollapsibleBtn)
self.instantFormLayout = qt.QFormLayout(self.instantCollapsibleBtn)
self.instantCollapsibleBtn.connect('clicked(bool)',
self.onInstantClick)
# Create button to run the Instant-Meshing tool
self.imBtn = qt.QPushButton("Run")
self.imBtn.setFixedHeight(40)
self.imBtn.setFixedWidth(100)
self.imBtn.setStyleSheet(
"QPushButton{ background-color: DarkSeaGreen }")
self.imBtn.toolTip = (
'How to use:'
' Click the Run Button to start instant-meshing ')
self.imBtn.connect('clicked(bool)', self.onImBtnClick)
self.instantFormLayout.addRow(self.imBtn, self.imtimeLbl)
# Create check box to display normals
self.checkshowNormals = qt.QCheckBox()
self.checkshowNormals.checked = False
self.checkshowNormals.toolTip = ('If activated:' ' shows normals ')
self.checkshowNormals.stateChanged.connect(
self.onCheckShowNormalsChkBx)
self.instantFormLayout.addRow(
" Show normals: ",
self.checkshowNormals)
# ---------------------------------------ADVANCED USER OPTIONS--------------------------------------------
# Create group box for advanced user options
self.instantCollapsiblegroupBtn = ctk.ctkCollapsibleGroupBox()
self.instantCollapsiblegroupBtn.title = "Advanced Options"
self.layout.addWidget(self.instantCollapsiblegroupBtn)
self.instantCollapsiblegroupBtn.collapsed = True
self.instantFormLayout.addRow(self.instantCollapsiblegroupBtn)
self.instantCGBFormLayout = qt.QFormLayout(
self.instantCollapsiblegroupBtn)
# Create radio buttons for triangle or quad meshing
self.checkTR = qt.QRadioButton()
self.checkTR.text = "Triangles (6/6)"
self.checkTR.checked = True # use triangle meshing by default
self.instantCGBFormLayout.addRow(
"Orientation and Position Symmetry Type: ", self.checkTR)
self.checkQD1 = qt.QRadioButton()
self.checkQD1.text = "Quads (2/4)"
self.instantCGBFormLayout.addRow(
" ", self.checkQD1)
self.checkQD2 = qt.QRadioButton()
self.checkQD2.text = "Quads (4/4)"
self.instantCGBFormLayout.addRow(
" ", self.checkQD2)
# Create check boxes for boolean values
self.checkintrinsic = qt.QCheckBox()
self.checkintrinsic.checked = False # use extrinsic by default
self.checkintrinsic.toolTip = (
'If activated:'
' Measures smoothness directly on the surface instead of natural alignment to surface features '
)
self.checkintrinsic.stateChanged.connect(self.oncheckint)
self.instantCGBFormLayout.addRow("Intrinsic: ", self.checkintrinsic)
self.checkdominant = qt.QCheckBox()
self.checkdominant.checked = False
self.checkdominant.toolTip = (
'If activated:'
' Generates a tri/quad dominant mesh instead of a pure tri/quad mesh '
)
self.checkdominant.stateChanged.connect(self.oncheckdom)
self.instantCGBFormLayout.addRow("Dominant: ", self.checkdominant)
self.checkdetermin = qt.QCheckBox()
self.checkdetermin.checked = False
self.checkdetermin.toolTip = (
'If activated:'
' Prefers (slower) deterministic algorithms ')
self.checkdetermin.stateChanged.connect(self.oncheckdet)
self.instantCGBFormLayout.addRow("Deterministic: ", self.checkdetermin)
# Create slider widget to adjust face count (triangle), prior vertex count (to change back, change -f in cmd to -v)
self.vertSlider = ctk.ctkSliderWidget()
self.vertSlider.minimum = 1000
self.vertSlider.maximum = 10000
self.vertSlider.setFixedWidth(400)
self.vertSlider.value = 2800
self.vertSlider.toolTip = ('What it changes:'
' Desired face count of the output mesh ')
self.instantCGBFormLayout.addRow("Triangle count: ", self.vertSlider)
# Create slider widget to adjust smoothing & ray tracing reprojection steps
self.smoothraySlider = ctk.ctkSliderWidget()
self.smoothraySlider.minimum = 0
self.smoothraySlider.maximum = 10
self.smoothraySlider.setFixedWidth(400)
self.smoothraySlider.value = 2
self.smoothraySlider.toolTip = (
'What it changes:'
' Number of smoothing & ray tracing reprojection steps (default: 2) '
)
self.instantCGBFormLayout.addRow("Smoothing Steps: ",
self.smoothraySlider)
# Create slider widget to adjust Point cloud mode
self.knnSlider = ctk.ctkSliderWidget()
self.knnSlider.minimum = 5
self.knnSlider.maximum = 20
self.knnSlider.setFixedWidth(400)
self.knnSlider.value = 10
self.knnSlider.toolTip = (
'Point cloud mode:'
' Number of adjacent points to consider (default: 10) ')
self.instantCGBFormLayout.addRow("Adjacent Points: ", self.knnSlider)
# Create slider widget to adjust Dihedral angle threshold
self.angleSlider = ctk.ctkSliderWidget()
self.angleSlider.minimum = -1
self.angleSlider.maximum = 90
self.angleSlider.setFixedWidth(400)
self.angleSlider.value = -1
self.angleSlider.toolTip = (
'What it changes:'
' Dihedral angle threshold for creases, -1 means sharp creases ')
self.instantCGBFormLayout.addRow("Crease Angle: ", self.angleSlider)
# ---------------------------------------ROBUST QUAD/HEX-DOMINANT MESHING--------------------------------------------
# Create collapsible Button for robust quad/hex-dominant meshing options
self.quadhexCollapsibleBtn = ctk.ctkCollapsibleButton()
self.quadhexCollapsibleBtn.text = "Robust Quad/Hex-dominant Meshing"
self.layout.addWidget(self.quadhexCollapsibleBtn)
self.quadhexCollapsibleBtn.collapsed = True
self.quadhexFormLayout = qt.QFormLayout(self.quadhexCollapsibleBtn)
self.quadhexCollapsibleBtn.connect('clicked(bool)',
self.onQuadHexClick)
# Create button to run the tool
self.rmBtn = qt.QPushButton("Run")
self.rmBtn.setFixedHeight(40)
self.rmBtn.setFixedWidth(100)
self.rmBtn.setStyleSheet(
"QPushButton{ background-color: DarkSeaGreen }")
self.rmBtn.toolTip = (
'How to use:'
' Click the Run Button to start robust quad/hex-dominant meshing ')
self.rmBtn.connect('clicked(bool)', self.onRmBtnClick)
self.quadhexFormLayout.addRow(self.rmBtn, self.qhtimeLbl)
# ---------------------------------------ADVANCED USER OPTIONS--------------------------------------------
# Create group box for advanced user options
self.robustCollapsiblegroupBtn = ctk.ctkCollapsibleGroupBox()
self.robustCollapsiblegroupBtn.title = "Advanced Options"
self.layout.addWidget(self.robustCollapsiblegroupBtn)
self.robustCollapsiblegroupBtn.collapsed = True
self.quadhexFormLayout.addRow(self.robustCollapsiblegroupBtn)
self.robustCGBFormLayout = qt.QFormLayout(
self.robustCollapsiblegroupBtn)
# Create radio buttons to adjust dimension
self.checkdim2 = qt.QRadioButton()
self.checkdim2.checked = True # use dimension 2 by default
self.checkdim2.text = "2"
self.robustCGBFormLayout.addRow("Dimension: ", self.checkdim2)
# Create slider widget to adjust scale
self.scaleSlider = ctk.ctkSliderWidget()
self.scaleSlider.minimum = 2
self.scaleSlider.maximum = 10
self.scaleSlider.setFixedWidth(400)
self.scaleSlider.value = 3
self.robustCGBFormLayout.addRow("Scale: ", self.scaleSlider)
# Create slider widget to adjust smooth iterator
self.smoothSlider = ctk.ctkSliderWidget()
self.smoothSlider.minimum = 5
self.smoothSlider.maximum = 20
self.smoothSlider.setFixedWidth(400)
self.smoothSlider.value = 10
self.robustCGBFormLayout.addRow("Smoothing iteration count: ",
self.smoothSlider)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
pointSetProcessingCollapsibleButton = ctk.ctkCollapsibleButton()
pointSetProcessingCollapsibleButton.text = "Surface Reconstruction from Unorganized Points"
self.layout.addWidget(pointSetProcessingCollapsibleButton)
pointSetProcessingFormLayout = qt.QFormLayout(
pointSetProcessingCollapsibleButton)
# Input
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = (("vtkMRMLModelNode"), "")
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.")
pointSetProcessingFormLayout.addRow("Input Model: ",
self.inputSelector)
self.nbrOfPointsLabel = qt.QLabel(
'Number of Points in Input Model: - ')
pointSetProcessingFormLayout.addRow(self.nbrOfPointsLabel)
self.inputPointSizeSlider = ctk.ctkSliderWidget()
self.inputPointSizeSlider.setDecimals(0)
self.inputPointSizeSlider.singleStep = 1
self.inputPointSizeSlider.minimum = 1
self.inputPointSizeSlider.maximum = 10
self.inputPointSizeSlider.value = 1
pointSetProcessingFormLayout.addRow('Input Model Point Size: ',
self.inputPointSizeSlider)
# Runtime
self.runtimeGroupBox = qt.QGroupBox('Runtime')
runtimeFormLayout = qt.QFormLayout(self.runtimeGroupBox)
pointSetProcessingFormLayout.addRow(self.runtimeGroupBox)
self.runtimeLabel = qt.QLabel()
self.runtimeLabel.setText("... s.")
self.runtimeLabel.setWordWrap(True)
self.runtimeLabel.setStyleSheet("QLabel { background-color : black; \
color : #66FF00; \
height : 60px; \
border-style: outset; \
border-width: 5px; \
border-radius: 10px; \
font: bold 14px; \
padding: 0px;\
font-family : SimSun; \
qproperty-alignment: AlignCenter}")
runtimeFormLayout.addRow(self.runtimeLabel)
# Downsample
self.downSampleGroupBox = ctk.ctkCollapsibleGroupBox()
self.downSampleGroupBox.setTitle("Downsample Input Model")
downSampleFormLayout = qt.QFormLayout(self.downSampleGroupBox)
pointSetProcessingFormLayout.addRow(self.downSampleGroupBox)
self.toleranceCleanSlider = ctk.ctkSliderWidget()
self.toleranceCleanSlider.setDecimals(2)
self.toleranceCleanSlider.singleStep = 0.01
self.toleranceCleanSlider.minimum = 0.0
self.toleranceCleanSlider.maximum = 1.0
self.toleranceCleanSlider.value = 0.01
self.toleranceCleanSlider.setToolTip('')
self.toleranceCleanSlider.enabled = True
downSampleFormLayout.addRow('Tolerance: ', self.toleranceCleanSlider)
self.vtkCleanPolyDataButton = qt.QPushButton("Apply")
self.vtkCleanPolyDataButton.enabled = False
self.vtkCleanPolyDataButton.checkable = True
downSampleFormLayout.addRow(self.vtkCleanPolyDataButton)
# Outlier Removal
self.outlierRemovalGroupBox = ctk.ctkCollapsibleGroupBox()
self.outlierRemovalGroupBox.setTitle("Outlier Removal")
outlierRemovalFormLayout = qt.QFormLayout(self.outlierRemovalGroupBox)
pointSetProcessingFormLayout.addRow(self.outlierRemovalGroupBox)
self.percentToRemoveSlider = ctk.ctkSliderWidget()
self.percentToRemoveSlider.setDecimals(2)
self.percentToRemoveSlider.singleStep = 0.01
self.percentToRemoveSlider.minimum = 0.0
self.percentToRemoveSlider.maximum = 1.0
self.percentToRemoveSlider.value = 0.01
self.percentToRemoveSlider.setToolTip('')
self.percentToRemoveSlider.enabled = True
outlierRemovalFormLayout.addRow('Percent to Remove: ',
self.percentToRemoveSlider)
self.vtkPointSetOutlierRemovalButton = qt.QPushButton("Apply")
self.vtkPointSetOutlierRemovalButton.enabled = False
self.vtkPointSetOutlierRemovalButton.checkable = True
outlierRemovalFormLayout.addRow(self.vtkPointSetOutlierRemovalButton)
# Compute Normals
self.normalsGroupBox = ctk.ctkCollapsibleGroupBox()
self.normalsGroupBox.setTitle("Compute Normals")
normalsFormLayout = qt.QFormLayout(self.normalsGroupBox)
pointSetProcessingFormLayout.addRow(self.normalsGroupBox)
self.normalsTabWidget = qt.QTabWidget()
normalsFormLayout.addRow(self.normalsTabWidget)
# vtkPointSetNormalEstimationAndOrientation
self.vtkPointSetNormalEstimationWidget = qt.QWidget()
vtkPointSetNormalEstimationFormLayout = qt.QFormLayout(
self.vtkPointSetNormalEstimationWidget)
normalsFormLayout.addRow(self.vtkPointSetNormalEstimationWidget)
self.normalsTabWidget.addTab(
self.vtkPointSetNormalEstimationWidget,
"vtkPointSetNormalEstimationAndOrientation")
self.modeTypeComboBox = qt.QComboBox()
self.modeTypeComboBox.addItem('Fixed')
self.modeTypeComboBox.addItem('Radius')
self.modeTypeComboBox.setCurrentIndex(1)
self.modeTypeComboBox.setToolTip('')
vtkPointSetNormalEstimationFormLayout.addRow('Mode Type: ',
self.modeTypeComboBox)
self.numberOfNeighborsSlider = ctk.ctkSliderWidget()
self.numberOfNeighborsSlider.setDecimals(0)
self.numberOfNeighborsSlider.singleStep = 1
self.numberOfNeighborsSlider.minimum = 1
self.numberOfNeighborsSlider.maximum = 20
self.numberOfNeighborsSlider.value = 4
self.numberOfNeighborsSlider.setToolTip('')
self.numberOfNeighborsSlider.enabled = False
vtkPointSetNormalEstimationFormLayout.addRow(
'Fixed Neighbors: ', self.numberOfNeighborsSlider)
self.radiusSlider = ctk.ctkSliderWidget()
self.radiusSlider.setDecimals(2)
self.radiusSlider.singleStep = 0.01
self.radiusSlider.minimum = 0
self.radiusSlider.maximum = 50
self.radiusSlider.value = 1.0
self.radiusSlider.setToolTip('')
vtkPointSetNormalEstimationFormLayout.addRow('Radius: ',
self.radiusSlider)
self.graphTypeComboBox = qt.QComboBox()
self.graphTypeComboBox.addItem('Riemann')
self.graphTypeComboBox.addItem('KNN')
self.graphTypeComboBox.setCurrentIndex(1)
self.graphTypeComboBox.setToolTip('')
vtkPointSetNormalEstimationFormLayout.addRow('Graph Type: ',
self.graphTypeComboBox)
self.knnSlider = ctk.ctkSliderWidget()
self.knnSlider.setDecimals(0)
self.knnSlider.singleStep = 1
self.knnSlider.minimum = 1
self.knnSlider.maximum = 100
self.knnSlider.value = 5
self.knnSlider.setToolTip('')
vtkPointSetNormalEstimationFormLayout.addRow('K-Nearest Neighbors: ',
self.knnSlider)
self.vtkPointSetNormalEstimationButton = qt.QPushButton("Apply")
self.vtkPointSetNormalEstimationButton.enabled = False
self.vtkPointSetNormalEstimationButton.checkable = True
vtkPointSetNormalEstimationFormLayout.addRow(
self.vtkPointSetNormalEstimationButton)
# vtkPolyDataNormals
self.vtkPolyDataNormalsWidget = qt.QWidget()
vtkPolyDataNormalsFormLayout = qt.QFormLayout(
self.vtkPolyDataNormalsWidget)
normalsFormLayout.addRow(self.vtkPolyDataNormalsWidget)
self.normalsTabWidget.addTab(self.vtkPolyDataNormalsWidget,
"vtkPolyDataNormals")
self.featureAngleSlider = ctk.ctkSliderWidget()
self.featureAngleSlider.setDecimals(2)
self.featureAngleSlider.singleStep = 0.01
self.featureAngleSlider.minimum = 0
self.featureAngleSlider.maximum = 360
self.featureAngleSlider.value = 0.1
self.featureAngleSlider.setToolTip('')
vtkPolyDataNormalsFormLayout.addRow('Feature Angle: ',
self.featureAngleSlider)
self.splittingComboBox = qt.QComboBox()
self.splittingComboBox.addItem('False')
self.splittingComboBox.addItem('True')
self.splittingComboBox.setCurrentIndex(1)
self.splittingComboBox.setToolTip('')
vtkPolyDataNormalsFormLayout.addRow('Splitting: ',
self.splittingComboBox)
self.consistencyComboBox = qt.QComboBox()
self.consistencyComboBox.addItem('False')
self.consistencyComboBox.addItem('True')
self.consistencyComboBox.setCurrentIndex(0)
self.consistencyComboBox.setToolTip('')
vtkPolyDataNormalsFormLayout.addRow('Consistency: ',
self.consistencyComboBox)
self.autoOrientNormalsComboBox = qt.QComboBox()
self.autoOrientNormalsComboBox.addItem('False')
self.autoOrientNormalsComboBox.addItem('True')
self.autoOrientNormalsComboBox.setCurrentIndex(0)
self.autoOrientNormalsComboBox.setToolTip('')
vtkPolyDataNormalsFormLayout.addRow('Auto-Orient Normals: ',
self.autoOrientNormalsComboBox)
self.computePointNormalsComboBox = qt.QComboBox()
self.computePointNormalsComboBox.addItem('False')
self.computePointNormalsComboBox.addItem('True')
self.computePointNormalsComboBox.setCurrentIndex(1)
self.computePointNormalsComboBox.setToolTip('')
vtkPolyDataNormalsFormLayout.addRow('Compute Point Normals: ',
self.computePointNormalsComboBox)
self.computeCellNormalsComboBox = qt.QComboBox()
self.computeCellNormalsComboBox.addItem('False')
self.computeCellNormalsComboBox.addItem('True')
self.computeCellNormalsComboBox.setCurrentIndex(0)
self.computeCellNormalsComboBox.setToolTip('')
vtkPolyDataNormalsFormLayout.addRow('Compute Cell Normals: ',
self.computeCellNormalsComboBox)
self.flipNormalsComboBox = qt.QComboBox()
self.flipNormalsComboBox.addItem('False')
self.flipNormalsComboBox.addItem('True')
self.flipNormalsComboBox.setCurrentIndex(0)
self.flipNormalsComboBox.setToolTip('')
vtkPolyDataNormalsFormLayout.addRow('Flip Normals: ',
self.flipNormalsComboBox)
self.nonManifoldTraversalComboBox = qt.QComboBox()
self.nonManifoldTraversalComboBox.addItem('False')
self.nonManifoldTraversalComboBox.addItem('True')
self.nonManifoldTraversalComboBox.setCurrentIndex(1)
self.nonManifoldTraversalComboBox.setToolTip('')
vtkPolyDataNormalsFormLayout.addRow('Non-Manifold Traversal: ',
self.nonManifoldTraversalComboBox)
self.vtkPolyDataNormalsButton = qt.QPushButton("Apply")
self.vtkPolyDataNormalsButton.enabled = False
self.vtkPolyDataNormalsButton.checkable = True
vtkPolyDataNormalsFormLayout.addRow(self.vtkPolyDataNormalsButton)
self.normalsVisibleCheckBox = qt.QCheckBox('Arrows Visibility: ')
self.normalsVisibleCheckBox.checked = True
self.normalsVisibleCheckBox.enabled = True
self.normalsVisibleCheckBox.setLayoutDirection(1)
normalsFormLayout.addRow(self.normalsVisibleCheckBox)
# Compute Surface
self.surfaceGroupBox = ctk.ctkCollapsibleGroupBox()
self.surfaceGroupBox.setTitle("Compute Surface")
surfaceFormLayout = qt.QFormLayout(self.surfaceGroupBox)
pointSetProcessingFormLayout.addRow(self.surfaceGroupBox)
self.surfaceTabWidget = qt.QTabWidget()
surfaceFormLayout.addRow(self.surfaceTabWidget)
# vtkPoissionReconstruction
self.vtkPoissionReconstructionWidget = qt.QWidget()
vtkPoissionReconstructionFormLayout = qt.QFormLayout(
self.vtkPoissionReconstructionWidget)
surfaceFormLayout.addRow(self.vtkPoissionReconstructionWidget)
self.surfaceTabWidget.addTab(self.vtkPoissionReconstructionWidget,
"vtkPoissionReconstruction")
self.depthSlider = ctk.ctkSliderWidget()
self.depthSlider.setDecimals(0)
self.depthSlider.singleStep = 1
self.depthSlider.minimum = 1
self.depthSlider.maximum = 14
self.depthSlider.value = 8
self.depthSlider.setToolTip(
'This integer controls the reconstruction depth; the maximum depth of the tree that will be used for surface reconstruction. Running at depth d corresponds to solving on a voxel grid whose resolution is no larger than 2^d x 2^d x 2^d. Note that since the reconstructor adapts the octree to the sampling density, the specified reconstruction depth is only an upper bound.'
)
vtkPoissionReconstructionFormLayout.addRow('Depth: ', self.depthSlider)
self.scaleSlider = ctk.ctkSliderWidget()
self.scaleSlider.setDecimals(2)
self.scaleSlider.singleStep = 0.01
self.scaleSlider.minimum = 0
self.scaleSlider.maximum = 10
self.scaleSlider.value = 1.25
self.scaleSlider.setToolTip(
'This floating point value specifies the ratio between the diameter of the cube used for reconstruction and the diameter of the samples bounding cube.'
)
vtkPoissionReconstructionFormLayout.addRow('Scale: ', self.scaleSlider)
self.solverDivideSlider = ctk.ctkSliderWidget()
self.solverDivideSlider.setDecimals(0)
self.solverDivideSlider.singleStep = 1
self.solverDivideSlider.minimum = 1
self.solverDivideSlider.maximum = 20
self.solverDivideSlider.value = 8
self.solverDivideSlider.setToolTip(
'Solver subdivision depth; This integer argument specifies the depth at which a block Gauss-Seidel solver is used to solve the Laplacian equation. Using this parameter helps reduce the memory overhead at the cost of a small increase in reconstruction time. (In practice, we have found that for reconstructions of depth 9 or higher a subdivide depth of 7 or 8 can greatly reduce the memory usage.)'
)
vtkPoissionReconstructionFormLayout.addRow('Solver Divide: ',
self.solverDivideSlider)
self.isoDivideSlider = ctk.ctkSliderWidget()
self.isoDivideSlider.setDecimals(0)
self.isoDivideSlider.singleStep = 1
self.isoDivideSlider.minimum = 1
self.isoDivideSlider.maximum = 20
self.isoDivideSlider.value = 8
self.isoDivideSlider.setToolTip(
'Iso-surface extraction subdivision depth; This integer argument specifies the depth at which a block isosurface extractor should be used to extract the iso-surface. Using this parameter helps reduce the memory overhead at the cost of a small increase in extraction time. (In practice, we have found that for reconstructions of depth 9 or higher a subdivide depth of 7 or 8 can greatly reduce the memory usage.)'
)
vtkPoissionReconstructionFormLayout.addRow('Iso Divide: ',
self.isoDivideSlider)
self.samplesPerNodeSlider = ctk.ctkSliderWidget()
self.samplesPerNodeSlider.setDecimals(2)
self.samplesPerNodeSlider.singleStep = 0.1
self.samplesPerNodeSlider.minimum = 1
self.samplesPerNodeSlider.maximum = 30
self.samplesPerNodeSlider.value = 1.0
self.samplesPerNodeSlider.setToolTip(
'Minimum number of samples; This floating point value specifies the minimum number of sample points that should fall within an octree node as the octree construction is adapted to sampling density. For noise-free samples, small values in the range [1.0 - 5.0] can be used. For more noisy samples, larger values in the range [15.0 - 20.0] may be needed to provide a smoother, noise-reduced, reconstruction.'
)
vtkPoissionReconstructionFormLayout.addRow('Samples per Node: ',
self.samplesPerNodeSlider)
self.confidenceComboBox = qt.QComboBox()
self.confidenceComboBox.addItem('False')
self.confidenceComboBox.addItem('True')
self.confidenceComboBox.setToolTip(
'Enabling tells the reconstructor to use the size of the normals as confidence information. When the flag is not enabled, all normals are normalized to have unit-length prior to reconstruction.'
)
vtkPoissionReconstructionFormLayout.addRow('Confidence: ',
self.confidenceComboBox)
self.verboseComboBox = qt.QComboBox()
self.verboseComboBox.addItem('False')
self.verboseComboBox.addItem('True')
self.verboseComboBox.setToolTip(
'Enabling this flag provides a more verbose description of the running times and memory usages of individual components of the surface reconstructor.'
)
vtkPoissionReconstructionFormLayout.addRow('Verbose: ',
self.verboseComboBox)
self.vtkPoissionReconstructionButton = qt.QPushButton("Apply")
self.vtkPoissionReconstructionButton.enabled = False
self.vtkPoissionReconstructionButton.checkable = True
vtkPoissionReconstructionFormLayout.addRow(
self.vtkPoissionReconstructionButton)
# vtkDelaunay3D
self.vtkDelaunay3DWidget = qt.QWidget()
vtkDelaunay3DFormLayout = qt.QFormLayout(self.vtkDelaunay3DWidget)
surfaceFormLayout.addRow(self.vtkDelaunay3DWidget)
self.surfaceTabWidget.addTab(self.vtkDelaunay3DWidget, "vtkDelaunay3D")
self.alphaSlider = ctk.ctkSliderWidget()
self.alphaSlider.setDecimals(1)
self.alphaSlider.singleStep = 0.1
self.alphaSlider.minimum = 0.0
self.alphaSlider.maximum = 100.0
self.alphaSlider.value = 0.0
self.alphaSlider.setToolTip('')
vtkDelaunay3DFormLayout.addRow('Alpha: ', self.alphaSlider)
self.toleranceSlider = ctk.ctkSliderWidget()
self.toleranceSlider.setDecimals(2)
self.toleranceSlider.singleStep = 0.01
self.toleranceSlider.minimum = 0.0
self.toleranceSlider.maximum = 1.0
self.toleranceSlider.value = 0.0
self.toleranceSlider.setToolTip('')
vtkDelaunay3DFormLayout.addRow('Tolerance: ', self.toleranceSlider)
self.offsetSlider = ctk.ctkSliderWidget()
self.offsetSlider.setDecimals(1)
self.offsetSlider.singleStep = 0.1
self.offsetSlider.minimum = 0.0
self.offsetSlider.maximum = 10.0
self.offsetSlider.value = 2.5
self.offsetSlider.setToolTip('')
vtkDelaunay3DFormLayout.addRow('Offset: ', self.offsetSlider)
self.boundingComboBox = qt.QComboBox()
self.boundingComboBox.addItem('False')
self.boundingComboBox.addItem('True')
self.boundingComboBox.setCurrentIndex(0)
self.boundingComboBox.setToolTip('')
vtkDelaunay3DFormLayout.addRow('Bounding Triangulations: ',
self.boundingComboBox)
self.vtkDelaunay3DButton = qt.QPushButton("Apply")
self.vtkDelaunay3DButton.enabled = False
self.vtkDelaunay3DButton.checkable = True
vtkDelaunay3DFormLayout.addRow(self.vtkDelaunay3DButton)
self.surfaceVisibleCheckBox = qt.QCheckBox('Surface Visibility: ')
self.surfaceVisibleCheckBox.checked = True
self.surfaceVisibleCheckBox.enabled = True
self.surfaceVisibleCheckBox.setLayoutDirection(1)
surfaceFormLayout.addRow(self.surfaceVisibleCheckBox)
# connections
self.vtkCleanPolyDataButton.connect('clicked(bool)',
self.vtkCleanPolyDataClicked)
self.vtkPointSetOutlierRemovalButton.connect(
'clicked(bool)', self.vtkPointSetOutlierRemovalClicked)
self.vtkPointSetNormalEstimationButton.connect(
'clicked(bool)', self.vtkPointSetNormalEstimationClicked)
self.vtkPolyDataNormalsButton.connect('clicked(bool)',
self.vtkPolyDataNormalsClicked)
self.vtkPoissionReconstructionButton.connect(
'clicked(bool)', self.vtkPoissionReconstructionClicked)
self.vtkDelaunay3DButton.connect('clicked(bool)',
self.vtkDelaunay3DClicked)
self.inputSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onSelect)
self.graphTypeComboBox.connect('currentIndexChanged(const QString &)',
self.onGraphTypeChanged)
self.modeTypeComboBox.connect('currentIndexChanged(const QString &)',
self.onModeChanged)
self.surfaceVisibleCheckBox.connect('stateChanged(int)',
self.onSurfaceVisible)
self.normalsVisibleCheckBox.connect('stateChanged(int)',
self.onNormalsVisible)
self.inputPointSizeSlider.connect('valueChanged (double)',
self.onInputPointSliderModified)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh
self.onSelect()
lm = slicer.app.layoutManager()
lm.setLayout(4) # One 3D-view
def setup(self):
# reload button
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "HeterogeneityCAD Reload"
self.layout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
# Tumor Segmentation Collapsible Button
self.TumorSegmentationCollapsibleButton = ctk.ctkCollapsibleButton()
self.TumorSegmentationCollapsibleButton.text = "SegmentCAD Segmentation"
self.layout.addWidget(self.TumorSegmentationCollapsibleButton)
self.TumorSegmentationLayout = qt.QFormLayout(self.TumorSegmentationCollapsibleButton)
# Select Volumes Collapsible Button
self.selectionsCollapsibleButton = ctk.ctkCollapsibleButton()
self.selectionsCollapsibleButton.text = "Select DCE-MRI Volumes for Segmentation"
self.TumorSegmentationLayout.addWidget(self.selectionsCollapsibleButton)
# Layout within the collapsible button
self.volumesLayout = qt.QFormLayout(self.selectionsCollapsibleButton)
# Use Multivolume Node as input
self.enableMultiVolume = qt.QCheckBox(self.selectionsCollapsibleButton)
self.enableMultiVolume.setText('Input Multi-Volume Node')
self.enableMultiVolume.checked = True
self.enableMultiVolume.setToolTip('Use Multi-Volume Node, with volumes imported in the correct order')
self.inputSelectorMultiVolume = slicer.qMRMLNodeComboBox(self.selectionsCollapsibleButton)
self.inputSelectorMultiVolume.nodeTypes = ( ("vtkMRMLMultiVolumeNode"), "" )
self.inputSelectorMultiVolume.selectNodeUponCreation = False
self.inputSelectorMultiVolume.renameEnabled = True
self.inputSelectorMultiVolume.removeEnabled = False
self.inputSelectorMultiVolume.noneEnabled = True
self.inputSelectorMultiVolume.addEnabled = False
self.inputSelectorMultiVolume.setMRMLScene(slicer.mrmlScene)
self.inputSelectorMultiVolume.setToolTip('Use Multi-Volume Node, with volumes imported in the correct order')
self.volumesLayout.addRow (self.enableMultiVolume, self.inputSelectorMultiVolume)
self.nodeInputFrame = ctk.ctkCollapsibleGroupBox(self.selectionsCollapsibleButton)
self.nodeInputFrame.title = "Input Scalar Volume Nodes"
self.nodeInputFrame.collapsed = True
self.nodeInputFrame.enabled = False
self.nodeInputFrame.setLayout(qt.QFormLayout())
self.volumesLayout.addRow(self.nodeInputFrame)
# Select Pre Node
self.inputPre = qt.QLabel("Pre-contrast Volume", self.nodeInputFrame)
self.inputPre.setToolTip('Select the initial pre-contrast volume node.')
self.inputSelectorPre = slicer.qMRMLNodeComboBox(self.nodeInputFrame)
self.inputSelectorPre.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.inputSelectorPre.addAttribute(("vtkMRMLScalarVolumeNode"), "LabelMap", "0")
self.inputSelectorPre.selectNodeUponCreation = False
self.inputSelectorPre.addEnabled = False
self.inputSelectorPre.removeEnabled = False
self.inputSelectorPre.noneEnabled = True
self.inputSelectorPre.noneDisplay = 'Please Select Volume'
self.inputSelectorPre.setMRMLScene(slicer.mrmlScene)
self.inputSelectorPre.setToolTip('Select the initial pre-contrast volume node.')
#self.volumesLayout.addRow(self.inputPre, self.inputSelectorPre)
self.nodeInputFrame.layout().addRow(self.inputPre, self.inputSelectorPre)
# Select First Node
self.inputFirst = qt.QLabel("First Post-contrast Volume", self.nodeInputFrame)
self.inputFirst.setToolTip('Select the first post-contrast volume node to calculate intitial enhancement and curve type.')
self.inputSelectorFirst = slicer.qMRMLNodeComboBox(self.nodeInputFrame)
self.inputSelectorFirst.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.inputSelectorFirst.addAttribute(("vtkMRMLScalarVolumeNode"), "LabelMap", "0")
self.inputSelectorFirst.selectNodeUponCreation = False
self.inputSelectorFirst.addEnabled = False
self.inputSelectorFirst.removeEnabled = False
self.inputSelectorFirst.noneEnabled = True
self.inputSelectorFirst.noneDisplay = 'Please Select Volume'
self.inputSelectorFirst.setMRMLScene(slicer.mrmlScene)
self.inputSelectorFirst.setToolTip('Select the first post-contrast volume node to calculate intitial enhancement and curve type.')
#self.volumesLayout.addRow(self.inputFirst, self.inputSelectorFirst)
self.nodeInputFrame.layout().addRow(self.inputFirst, self.inputSelectorFirst)
# Select Second Node
self.inputSecond = qt.QLabel("Second Post-contrast Volume", self.nodeInputFrame)
self.inputSecond.setToolTip('Select a second post-contrast volume node (not required).')
self.inputSelectorSecond = slicer.qMRMLNodeComboBox(self.nodeInputFrame)
self.inputSelectorSecond.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.inputSelectorSecond.addAttribute(("vtkMRMLScalarVolumeNode"), "LabelMap", "0")
self.inputSelectorSecond.selectNodeUponCreation = False
self.inputSelectorSecond.addEnabled = False
self.inputSelectorSecond.removeEnabled = False
self.inputSelectorSecond.noneEnabled = True
self.inputSelectorSecond.noneDisplay = 'Please Select Volume'
self.inputSelectorSecond.setMRMLScene(slicer.mrmlScene)
self.inputSelectorSecond.setToolTip('Select a second post-contrast volume node (not required).')
#self.volumesLayout.addRow(self.inputSecond, self.inputSelectorSecond)
self.nodeInputFrame.layout().addRow(self.inputSecond, self.inputSelectorSecond)
# Select Third Node
self.inputThird = qt.QLabel("Third Post-contrast Volume", self.nodeInputFrame)
self.inputThird.setToolTip('Select a third post-contrast volume node (not required).')
self.inputSelectorThird = slicer.qMRMLNodeComboBox(self.nodeInputFrame)
self.inputSelectorThird.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
self.inputSelectorThird.addAttribute( ("vtkMRMLScalarVolumeNode"), "LabelMap", "0")
self.inputSelectorThird.selectNodeUponCreation = False
self.inputSelectorThird.addEnabled = False
self.inputSelectorThird.removeEnabled = False
self.inputSelectorThird.noneEnabled = True
self.inputSelectorThird.noneDisplay = 'Please Select Volume'
self.inputSelectorThird.setMRMLScene(slicer.mrmlScene)
self.inputSelectorThird.setToolTip('Select a third post-contrast volume node (not required).')
#self.volumesLayout.addRow(self.inputThird, self.inputSelectorThird)
self.nodeInputFrame.layout().addRow(self.inputThird, self.inputSelectorThird)
# Select Fourth Node
self.inputFourth = qt.QLabel("Fourth Post-contrast Volume", self.nodeInputFrame)
self.inputFourth.setToolTip('Select the fourth or final post-contrast volume node to calculate curve type based on the delayed curve slope.')
self.inputSelectorFourth = slicer.qMRMLNodeComboBox(self.nodeInputFrame)
self.inputSelectorFourth.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
self.inputSelectorFourth.addAttribute( ("vtkMRMLScalarVolumeNode"), "LabelMap", "0")
self.inputSelectorFourth.selectNodeUponCreation = False
self.inputSelectorFourth.addEnabled = False
self.inputSelectorFourth.removeEnabled = False
self.inputSelectorFourth.noneEnabled = True
self.inputSelectorFourth.noneDisplay = 'Please Select Volume'
self.inputSelectorFourth.setMRMLScene(slicer.mrmlScene)
self.inputSelectorFourth.setToolTip('Select the fourth or final post-contrast volume node to calculate curve type based on the delayed curve slope.')
#self.volumesLayout.addRow(self.inputFourth, self.inputSelectorFourth)
self.nodeInputFrame.layout().addRow(self.inputFourth, self.inputSelectorFourth)
# Enable and Select Input Label Map as ROI
self.enableLabel = qt.QCheckBox(self.selectionsCollapsibleButton)
self.enableLabel.setText('Use Label Map as ROI')
self.enableLabel.checked = True
self.enableLabel.setToolTip('Select and identify a custom label map node to define an ROI over the input volumes for faster segmentation.')
self.inputSelectorLabel = slicer.qMRMLNodeComboBox(self.selectionsCollapsibleButton)
self.inputSelectorLabel.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
self.inputSelectorLabel.addAttribute( ("vtkMRMLScalarVolumeNode"), "LabelMap", "1")
self.inputSelectorLabel.selectNodeUponCreation = False
self.inputSelectorLabel.renameEnabled = True
self.inputSelectorLabel.removeEnabled = False
self.inputSelectorLabel.noneEnabled = True
self.inputSelectorLabel.addEnabled = False
self.inputSelectorLabel.setMRMLScene(slicer.mrmlScene)
self.inputSelectorLabel.setToolTip('Select and identify a custom label map node to define an ROI over the input volumes for faster segmentation.')
self.volumesLayout.addRow (self.enableLabel, self.inputSelectorLabel)
# Select output SegmentCAD Label collapsible button
self.outlabelCollapsibleButton = ctk.ctkCollapsibleButton()
self.outlabelCollapsibleButton.text = "Select or Create Output SegmentCAD Label Map"
self.TumorSegmentationLayout.addWidget(self.outlabelCollapsibleButton)
# Layout within the collapsible button
self.outlabelLayout = qt.QFormLayout(self.outlabelCollapsibleButton)
# Select or create output SegmentCAD Label Map
self.outputLabel = qt.QLabel("Output SegmentCAD Label Map", self.outlabelCollapsibleButton)
self.outputLabel.setToolTip('Select or create a label map volume node as the SegmentCAD segmentation output.')
self.outputSelectorLabel = slicer.qMRMLNodeComboBox(self.outlabelCollapsibleButton)
self.outputSelectorLabel.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
self.outputSelectorLabel.addAttribute( ("vtkMRMLScalarVolumeNode"), "LabelMap", "1")
self.outputSelectorLabel.baseName = "SegmentCAD Label Map"
self.outputSelectorLabel.selectNodeUponCreation = True
self.outputSelectorLabel.renameEnabled = True
self.outputSelectorLabel.removeEnabled = True
self.outputSelectorLabel.noneEnabled = False
self.outputSelectorLabel.addEnabled = True
self.outputSelectorLabel.setMRMLScene(slicer.mrmlScene)
self.outputSelectorLabel.setToolTip('Select or create a label map volume node as the SegmentCAD segmentation output.')
self.outlabelLayout.addRow(self.outputLabel, self.outputSelectorLabel)
# SegmentCAD Label Map Legend
self.outputLegend = qt.QLabel("| Type I Persistent: Blue | Type II Plateau: Yellow | Type III Washout: Red |", self.outlabelCollapsibleButton)
self.outputLegend.setToolTip('SegmentCAD Label Map Legend | Blue: Type I Persistent curve | Yellow: Type II Plateau curve | Red: Type III Washout curve |')
self.outlabelLayout.addRow(self.outputLegend)
# Enable Volume Rendering of the SegmentCAD label map
self.enableVolumeRendering = qt.QCheckBox(self.selectionsCollapsibleButton)
self.enableVolumeRendering.setText('Display Volume Rendering')
self.enableVolumeRendering.checked = True
self.enableVolumeRendering.setToolTip('Display volume rendering of the SegmentCAD Label Map in the 3D View')
self.outlabelLayout.addRow (self.enableVolumeRendering)
# Enable Label Statistics Table and Data
self.enableStats = qt.QCheckBox(self.selectionsCollapsibleButton)
self.enableStats.setText('Calculate SegmentCAD Label statistics')
self.enableStats.checked = False
self.enableStats.setToolTip('Use logic from Label Statistics Module to calculate statistics for first post-contrast voxels within the SegmentCAD Label Map.')
self.outlabelLayout.addRow (self.enableStats)
# Set Advanced Parameters Collapsible Button
self.parametersCollapsibleButton = ctk.ctkCollapsibleButton()
self.parametersCollapsibleButton.text = "Set Advanced Segmentation Parameters"
self.TumorSegmentationLayout.addWidget(self.parametersCollapsibleButton)
self.parametersCollapsibleButton.collapsed = True
# Layout within the collapsible button
self.parametersLayout = qt.QFormLayout(self.parametersCollapsibleButton)
# Set Minimum Threshold of Percentage Increase to First Post-Contrast Image
self.inputMinimumThreshold = qt.QLabel("Minimum Threshold of Increase", self.parametersCollapsibleButton)
self.inputMinimumThreshold.setToolTip('Minimum Threshold of Percentage Increase (Pre- to First Post-contrast (Range: 10% to 150%)')
self.inputSelectorMinimumThreshold = qt.QDoubleSpinBox(self.parametersCollapsibleButton)
self.inputSelectorMinimumThreshold.setSuffix("%")
self.inputSelectorMinimumThreshold.singleStep = (1)
self.inputSelectorMinimumThreshold.minimum = (10)
self.inputSelectorMinimumThreshold.maximum = (150)
self.inputSelectorMinimumThreshold.value = (75)
self.inputSelectorMinimumThreshold.setToolTip('Minimum Threshold of Percentage Increase (Pre- to First Post-contrast (Range: 10% to 150%)')
self.parametersLayout.addRow(self.inputMinimumThreshold, self.inputSelectorMinimumThreshold)
# Curve 1 Type Parameters (Slopes from First to Fourth Post-Contrast Images)
self.inputCurve1 = qt.QLabel("Type 1 (Persistent) Curve Minimum Slope", self.parametersCollapsibleButton)
self.inputCurve1.setToolTip('Minimum Slope of Delayed Curve to classify as Persistent (Range: 0.02 to 0.3)')
self.inputSelectorCurve1 = qt.QDoubleSpinBox(self.parametersCollapsibleButton)
self.inputSelectorCurve1.singleStep = (0.02)
self.inputSelectorCurve1.minimum = (0.02)
self.inputSelectorCurve1.maximum = (0.3)
self.inputSelectorCurve1.value = (0.20)
self.inputSelectorCurve1.setToolTip('Minimum Slope of Delayed Curve to classify as Persistent (Range: 0.02 to 0.3)')
self.parametersLayout.addRow(self.inputCurve1, self.inputSelectorCurve1)
# Curve 3 Type Parameters (Slopes from First to Fourth Post-Contrast Images)
self.inputCurve3 = qt.QLabel("Type 3 (Washout) Curve Maximum Slope", self.parametersCollapsibleButton)
self.inputCurve3.setToolTip('Maximum Slope of Delayed Curve to classify as Washout (Range: -0.02 to -0.3)')
self.inputSelectorCurve3 = qt.QDoubleSpinBox(self.parametersCollapsibleButton)
self.inputSelectorCurve3.singleStep = (0.02)
self.inputSelectorCurve3.setPrefix("-")
self.inputSelectorCurve3.minimum = (0.02)
self.inputSelectorCurve3.maximum = (0.30)
self.inputSelectorCurve3.value = (0.20)
self.inputSelectorCurve3.setToolTip('Maximum Slope of Delayed Curve to classify as Washout (Range: -0.02 to -0.3)')
self.parametersLayout.addRow(self.inputCurve3, self.inputSelectorCurve3)
# Apply Tumor Adaptive Segmentation button
self.SegmentCADButton = qt.QPushButton("Apply SegmentCAD")
self.SegmentCADButton.toolTip = "Apply SegmentCAD segmentation to selected volumes."
self.TumorSegmentationLayout.addWidget(self.SegmentCADButton)
# LabelStatistics Table Collapsible Button
self.labelstatisticsCollapsibleButton = ctk.ctkCollapsibleButton()
self.labelstatisticsCollapsibleButton.text = "SegmentCAD Label Statistics"
self.layout.addWidget(self.labelstatisticsCollapsibleButton)
self.labelstatisticsCollapsibleButton.collapsed = True
# Layout within the collapsible button
self.labelstatisticsLayout = qt.QFormLayout(self.labelstatisticsCollapsibleButton)
# Table View to display Label statistics
self.labelStatisticsTableView = qt.QTableView()
self.labelStatisticsTableView.sortingEnabled = True
self.labelstatisticsLayout.addWidget(self.labelStatisticsTableView)
self.labelStatisticsTableView.minimumHeight = 200
# Charting Statistics Button
self.chartOptions = ("Volume", "Curve Type", "Voxel Count", "Volume mm^3", "Volume cc", "Minimum Intensity", "Maximum Intensity", "Mean Intensity", "Standard Deviation")
self.chartFrame = qt.QFrame()
self.chartFrame.setLayout(qt.QHBoxLayout())
self.labelstatisticsLayout.addWidget(self.chartFrame)
self.chartButton = qt.QPushButton("Chart Statistics", self.labelstatisticsCollapsibleButton)
self.chartButton.toolTip = "Make a chart from the current statistics."
self.chartFrame.layout().addWidget(self.chartButton)
self.chartOption = qt.QComboBox(self.labelstatisticsCollapsibleButton)
self.chartOption.addItems(self.chartOptions)
self.chartFrame.layout().addWidget(self.chartOption)
self.chartIgnoreZero = qt.QCheckBox(self.labelstatisticsCollapsibleButton)
self.chartIgnoreZero.setText('Ignore Zero Label')
self.chartIgnoreZero.checked = False
self.chartIgnoreZero.setToolTip('Do not include the zero index in the chart to avoid dwarfing other bars')
self.chartFrame.layout().addWidget(self.chartIgnoreZero)
self.chartButton.enabled = False
# Interactive Charting Settings Collapsible Button
self.iChartingCollapsibleButton = ctk.ctkCollapsibleButton()
self.iChartingCollapsibleButton.text = "Interactive Charting Settings"
self.iChartingCollapsibleButton.collapsed = True
self.layout.addWidget(self.iChartingCollapsibleButton)
# Layout within the collapsible button
self.iChartingLayout = qt.QFormLayout(self.iChartingCollapsibleButton)
# iCharting toggle button
self.iCharting = qt.QPushButton("Enable Interactive Charting")
self.iCharting.checkable = True
self.iCharting.setChecked(False)
self.iCharting.enabled = False
self.iCharting.toolTip = "Toggle the real-time charting of the %increase from baseline of the selected voxel from each input volume."
self.iChartingLayout.addRow(self.iCharting)
# Initialize slice observers (from DataProbe.py)
# Keep list of pairs: [observee,tag] so they can be removed easily
self.styleObserverTags = []
# Keep a map of interactor styles to sliceWidgets so we can easily get sliceLogic
self.sliceWidgetsPerStyle = {}
self.refreshObservers()
# Connections
self.SegmentCADButton.connect('clicked()', self.onSegmentCADButtonClicked)
self.enableLabel.connect('stateChanged(int)', self.onEnableLabel)
self.enableMultiVolume.connect('stateChanged(int)', self.onEnableMultiVolume)
self.chartButton.connect('clicked()', self.onChart)
self.iCharting.connect('toggled(bool)', self.onInteractiveChartingChanged)
def setup(self):
# Instantiate and connect widgets ...
#
# Reload and Test area
#
reloadCollapsibleButton = ctk.ctkCollapsibleButton()
reloadCollapsibleButton.text = "Reload && Test"
self.layout.addWidget(reloadCollapsibleButton)
reloadFormLayout = qt.QFormLayout(reloadCollapsibleButton)
# reload button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadButton = qt.QPushButton("Reload")
self.reloadButton.toolTip = "Reload this module."
self.reloadButton.name = "DICOMAnnotations Reload"
reloadFormLayout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
# reload and test button
# (use this during development, but remove it when delivering
# your module to users)
self.reloadAndTestButton = qt.QPushButton("Reload and Test")
self.reloadAndTestButton.toolTip = "Reload this module and then run the self tests."
reloadFormLayout.addWidget(self.reloadAndTestButton)
self.reloadAndTestButton.connect('clicked()', self.onReloadAndTest)
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# DICOM Annotations Checkbox
#
self.dicomAnnotationsCheckBox = qt.QCheckBox('DICOM Slice Annotations')
parametersFormLayout.addRow(self.dicomAnnotationsCheckBox)
#
# Corner Annotations Activation Checkboxes
#
self.cornerActivationsGroupBox = ctk.ctkCollapsibleGroupBox()
self.cornerActivationsGroupBox.setTitle('Active Corners')
self.cornerActivationsGroupBox.enabled = False
parametersFormLayout.addRow(self.cornerActivationsGroupBox)
cornerActionHBoxLayout = qt.QHBoxLayout(self.cornerActivationsGroupBox)
self.cornerActivationCheckbox = []
for i in xrange(4):
self.cornerActivationCheckbox.append(qt.QCheckBox())
self.cornerActivationCheckbox[i].checked = True
cornerActionHBoxLayout.addWidget(self.cornerActivationCheckbox[i])
self.cornerActivationCheckbox[i].connect('clicked()', self.updateSliceViewFromGUI)
self.cornerActivationCheckbox[0].setText('Top Left')
self.cornerActivationCheckbox[1].setText('Top Right')
self.cornerActivationCheckbox[2].setText('Bottom Left')
self.cornerActivationCheckbox[3].setText('Bottom Right')
#
# Corner Annotations Font Properties
#
self.fontPropertiesGroupBox = ctk.ctkCollapsibleGroupBox()
self.fontPropertiesGroupBox.setTitle('Font Properties')
self.fontPropertiesGroupBox.enabled = False
parametersFormLayout.addRow(self.fontPropertiesGroupBox)
fontPropertiesHBoxLayout = qt.QHBoxLayout(self.fontPropertiesGroupBox)
fontFamilyLabel = qt.QLabel('Font Family: ')
fontPropertiesHBoxLayout.addWidget(fontFamilyLabel)
self.timesFontRadioButton = qt.QRadioButton('Times')
fontPropertiesHBoxLayout.addWidget(self.timesFontRadioButton)
self.timesFontRadioButton.connect('clicked()', self.updateSliceViewFromGUI)
self.timesFontRadioButton.checked = True
self.arialFontRadioButton = qt.QRadioButton('Arial')
self.arialFontRadioButton.connect('clicked()', self.updateSliceViewFromGUI)
fontPropertiesHBoxLayout.addWidget(self.arialFontRadioButton)
fontSizeLabel = qt.QLabel('Font Size: ')
fontPropertiesHBoxLayout.addWidget(fontSizeLabel)
self.fontSizeSpinBox = qt.QSpinBox()
self.fontSizeSpinBox.setMinimum(10)
self.fontSizeSpinBox.setMaximum(20)
self.fontSizeSpinBox.value = 14
fontPropertiesHBoxLayout.addWidget(self.fontSizeSpinBox)
self.fontSizeSpinBox.connect('valueChanged(int)', self.updateSliceViewFromGUI)
# connections
# Add vertical spacer
self.layout.addStretch(1)
self.dicomAnnotationsCheckBox.connect('clicked()', self.updateSliceViewFromGUI)
