def create(self):
super(WandEffectOptions, self).create()
self.toleranceFrame = qt.QFrame(self.frame)
self.toleranceFrame.setLayout(qt.QHBoxLayout())
self.frame.layout().addWidget(self.toleranceFrame)
self.widgets.append(self.toleranceFrame)
self.toleranceLabel = qt.QLabel("Tolerance:", self.toleranceFrame)
self.toleranceLabel.setToolTip("Set the tolerance of the wand in terms of background pixel values")
self.toleranceFrame.layout().addWidget(self.toleranceLabel)
self.widgets.append(self.toleranceLabel)
self.toleranceSpinBox = ctk.ctkDoubleSpinBox(self.toleranceFrame)
self.toleranceSpinBox.setToolTip("Set the tolerance of the wand in terms of background pixel values")
self.toleranceSpinBox.minimum = 0
self.toleranceSpinBox.maximum = 1000
self.toleranceSpinBox.suffix = ""
self.toleranceFrame.layout().addWidget(self.toleranceSpinBox)
self.widgets.append(self.toleranceSpinBox)
self.maxPixelsFrame = qt.QFrame(self.frame)
self.maxPixelsFrame.setLayout(qt.QHBoxLayout())
self.frame.layout().addWidget(self.maxPixelsFrame)
self.widgets.append(self.maxPixelsFrame)
self.maxPixelsLabel = qt.QLabel("Max Pixels per click:", self.maxPixelsFrame)
self.maxPixelsLabel.setToolTip("Set the maxPixels for each click")
self.maxPixelsFrame.layout().addWidget(self.maxPixelsLabel)
self.widgets.append(self.maxPixelsLabel)
self.maxPixelsSpinBox = ctk.ctkDoubleSpinBox(self.maxPixelsFrame)
self.maxPixelsSpinBox.setToolTip("Set the maxPixels for each click")
self.maxPixelsSpinBox.minimum = 1
self.maxPixelsSpinBox.maximum = 100000
self.maxPixelsSpinBox.suffix = ""
self.maxPixelsFrame.layout().addWidget(self.maxPixelsSpinBox)
self.widgets.append(self.maxPixelsSpinBox)
self.fillModeFrame = qt.QFrame(self.frame)
self.fillModeFrame.setLayout(qt.QHBoxLayout())
self.frame.layout().addWidget(self.fillModeFrame)
self.widgets.append(self.fillModeFrame)
self.fillModeCheckBox = qt.QCheckBox(self.fillModeFrame)
self.fillModeCheckBox.text = "Fill Volume"
self.fillModeCheckBox.setToolTip("Fill in 3D when checked, else fill plane")
self.fillModeFrame.layout().addWidget(self.fillModeCheckBox)
self.widgets.append(self.fillModeCheckBox)
HelpButton(self.frame, "Use this tool to label all voxels that are within a tolerance of where you click")
# don't connect the signals and slots directly - instead, add these
# to the list of connections so that gui callbacks can be cleanly
# disabled while the gui is being updated. This allows several gui
# elements to be interlinked with signal/slots but still get updated
# as a unit to the new value of the mrml node.
self.connections.append((self.toleranceSpinBox, "valueChanged(double)", self.onToleranceSpinBoxChanged))
self.connections.append((self.maxPixelsSpinBox, "valueChanged(double)", self.onMaxPixelsSpinBoxChanged))
self.connections.append((self.fillModeCheckBox, "clicked()", self.onFillModeClicked))
# Add vertical spacer
self.frame.layout().addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# Select landmark file to import
#
self.inputFileSelector = ctk.ctkPathLineEdit()
self.inputFileSelector.setToolTip( "Select landmark file for import" )
parametersFormLayout.addRow("Select file containing landmark names and coordinates to load:", self.inputFileSelector)
#
# Get header length
#
self.headerLengthWidget = ctk.ctkDoubleSpinBox()
self.headerLengthWidget.value = 2
self.headerLengthWidget.minimum = 0
self.headerLengthWidget.singleStep = 1
self.headerLengthWidget.setToolTip("Input the number of lines in header")
parametersFormLayout.addRow("Header length:", self.headerLengthWidget)
#
# check box to trigger taking screen shots for later use in tutorials
#
self.enableScreenshotsFlagCheckBox = qt.QCheckBox()
self.enableScreenshotsFlagCheckBox.checked = 0
self.enableScreenshotsFlagCheckBox.setToolTip("If checked, take screen shots for tutorials. Use Save Data to write them to disk.")
parametersFormLayout.addRow("Enable Screenshots", self.enableScreenshotsFlagCheckBox)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = False
parametersFormLayout.addRow(self.applyButton)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.inputFileSelector.connect('validInputChanged(bool)', self.onSelect)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onSelect()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
self.maximumRunningProcessesSpinBox = ctk.ctkDoubleSpinBox()
self.maximumRunningProcessesSpinBox.minimum = 1
self.maximumRunningProcessesSpinBox.decimals = 0
self.maximumRunningProcessesSpinBox.value = self.logic.maximumRunningProcesses
parametersFormLayout.addRow("Maximum running processes",
self.maximumRunningProcessesSpinBox)
processesCollapsibleButton = ctk.ctkCollapsibleButton()
processesCollapsibleButton.text = "Processes"
self.layout.addWidget(processesCollapsibleButton)
processesFormLayout = qt.QFormLayout(processesCollapsibleButton)
self.statusLabel = qt.QLabel("No processes running")
processesFormLayout.addRow(self.statusLabel)
self.processBoxes = {}
self.processLabels = {}
for processState in self.logic.processStates:
processBox = qt.QGroupBox()
processBoxLayout = qt.QVBoxLayout(processBox)
processBox.setTitle(processState)
processesFormLayout.addRow(processBox)
processLabel = qt.QLabel(processBox)
processLabel.text = "None"
processBoxLayout.addWidget(processLabel)
self.processBoxes[processState] = processBox
self.processLabels[processState] = processLabel
self.maximumRunningProcessesSpinBox.connect("valueChanged(double)",
self.onMaximumChanged)
node = self.logic.getParameterNode()
self.nodeObserverTag = node.AddObserver(vtk.vtkCommand.ModifiedEvent,
self.onNodeModified)
# Add vertical spacer
self.layout.addStretch(1)
def default_origin_component(self):
"""
Create and initialize origin widget.
Returns:
ctk.ctkDoubleSpinBox(): Initialized origin widget.
"""
origin_widget = ctk.ctkDoubleSpinBox()
origin_widget.singleStep = 0.1
origin_widget.minimum = 50
origin_widget.maximum = 150
origin_widget.value = 100
origin_widget.setToolTip(
"Set threshold value for computing the output image. "
"Voxels that have intensities lower than this value will set to zero."
)
return origin_widget
def gui(self, action, layout):
super(CameraRotationAction,self).gui(action, layout)
self.referenceSelector = slicer.qMRMLNodeComboBox()
self.referenceSelector.nodeTypes = ["vtkMRMLCameraNode"]
self.referenceSelector.addEnabled = True
self.referenceSelector.renameEnabled = True
self.referenceSelector.removeEnabled = False
self.referenceSelector.noneEnabled = False
self.referenceSelector.selectNodeUponCreation = True
self.referenceSelector.showHidden = True
self.referenceSelector.showChildNodeTypes = True
self.referenceSelector.setMRMLScene( slicer.mrmlScene )
self.referenceSelector.setToolTip( "Pick the reference camera" )
self.referenceSelector.currentNodeID = action['referenceCameraID']
layout.addRow("Reference camera", self.referenceSelector)
self.animatedSelector = slicer.qMRMLNodeComboBox()
self.animatedSelector.nodeTypes = ["vtkMRMLCameraNode"]
self.animatedSelector.addEnabled = True
self.animatedSelector.renameEnabled = True
self.animatedSelector.removeEnabled = False
self.animatedSelector.noneEnabled = False
self.animatedSelector.selectNodeUponCreation = True
self.animatedSelector.showHidden = True
self.animatedSelector.showChildNodeTypes = True
self.animatedSelector.setMRMLScene( slicer.mrmlScene )
self.animatedSelector.setToolTip( "Pick the animated camera" )
self.animatedSelector.currentNodeID = action['animatedCameraID']
layout.addRow("Animated camera", self.animatedSelector)
self.rate = ctk.ctkDoubleSpinBox()
self.rate.suffix = " degreesPerSecond"
self.rate.decimals = 2
self.rate.minimum = 0
self.rate.maximum = 1000
self.rate.value = action['degreesPerSecond']
layout.addRow("Rotation rate", self.rate)
self.method = qt.QComboBox()
for method in self.animationMethods:
self.method.addItem(method)
self.method.currentText = action['animationMethod']
layout.addRow("Animation method", self.method)
def addAdvancedMenu(self, currentWidgetLayout):
#
# Advanced menu for single run
#
advancedCollapsibleButton = ctk.ctkCollapsibleButton()
advancedCollapsibleButton.text = "Advanced parameter settings"
advancedCollapsibleButton.collapsed = True
currentWidgetLayout.addRow(advancedCollapsibleButton)
advancedFormLayout = qt.QFormLayout(advancedCollapsibleButton)
# Point density label
pointDensityCollapsibleButton = ctk.ctkCollapsibleButton()
pointDensityCollapsibleButton.text = "Point density"
advancedFormLayout.addRow(pointDensityCollapsibleButton)
pointDensityFormLayout = qt.QFormLayout(pointDensityCollapsibleButton)
# Rigid registration label
rigidRegistrationCollapsibleButton = ctk.ctkCollapsibleButton()
rigidRegistrationCollapsibleButton.text = "Rigid registration"
advancedFormLayout.addRow(rigidRegistrationCollapsibleButton)
rigidRegistrationFormLayout = qt.QFormLayout(
rigidRegistrationCollapsibleButton)
# Point Density slider
pointDensity = ctk.ctkSliderWidget()
pointDensity.singleStep = 0.1
pointDensity.minimum = 0.1
pointDensity.maximum = 3
pointDensity.value = 1
pointDensity.setToolTip(
"Adjust the density of the pointclouds. Larger values increase the number of points, and vice versa."
)
pointDensityFormLayout.addRow("Point Density Adjustment: ",
pointDensity)
# Normal search radius slider
normalSearchRadius = ctk.ctkSliderWidget()
normalSearchRadius.singleStep = 1
normalSearchRadius.minimum = 2
normalSearchRadius.maximum = 12
normalSearchRadius.value = 2
normalSearchRadius.setToolTip(
"Set size of the neighborhood used when computing normals")
rigidRegistrationFormLayout.addRow("Normal search radius: ",
normalSearchRadius)
#FPFH Search Radius slider
FPFHSearchRadius = ctk.ctkSliderWidget()
FPFHSearchRadius.singleStep = 1
FPFHSearchRadius.minimum = 3
FPFHSearchRadius.maximum = 20
FPFHSearchRadius.value = 5
FPFHSearchRadius.setToolTip(
"Set size of the neighborhood used when computing FPFH features")
rigidRegistrationFormLayout.addRow("FPFH Search radius: ",
FPFHSearchRadius)
# Maximum distance threshold slider
distanceThreshold = ctk.ctkSliderWidget()
distanceThreshold.singleStep = .25
distanceThreshold.minimum = 0.5
distanceThreshold.maximum = 4
distanceThreshold.value = 1.5
distanceThreshold.setToolTip(
"Maximum correspondence points-pair distance threshold")
rigidRegistrationFormLayout.addRow(
"Maximum corresponding point distance: ", distanceThreshold)
# Maximum RANSAC iterations slider
maxRANSAC = ctk.ctkDoubleSpinBox()
maxRANSAC.singleStep = 1
maxRANSAC.setDecimals(0)
maxRANSAC.minimum = 1
maxRANSAC.maximum = 500000000
maxRANSAC.value = 4000000
maxRANSAC.setToolTip(
"Maximum number of iterations of the RANSAC algorithm")
rigidRegistrationFormLayout.addRow("Maximum RANSAC iterations: ",
maxRANSAC)
# Maximum RANSAC validation steps
maxRANSACValidation = ctk.ctkDoubleSpinBox()
maxRANSACValidation.singleStep = 1
maxRANSACValidation.setDecimals(0)
maxRANSACValidation.minimum = 1
maxRANSACValidation.maximum = 500000000
maxRANSACValidation.value = 500
maxRANSACValidation.setToolTip(
"Maximum number of RANSAC validation steps")
rigidRegistrationFormLayout.addRow("Maximum RANSAC validation steps: ",
maxRANSACValidation)
# ICP distance threshold slider
ICPDistanceThreshold = ctk.ctkSliderWidget()
ICPDistanceThreshold.singleStep = .1
ICPDistanceThreshold.minimum = 0.1
ICPDistanceThreshold.maximum = 2
ICPDistanceThreshold.value = 0.4
ICPDistanceThreshold.setToolTip(
"Maximum ICP points-pair distance threshold")
rigidRegistrationFormLayout.addRow("Maximum ICP distance: ",
ICPDistanceThreshold)
return pointDensity, normalSearchRadius, FPFHSearchRadius, distanceThreshold, maxRANSAC, maxRANSACValidation, ICPDistanceThreshold
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
self.meshDirectory = ctk.ctkPathLineEdit()
self.meshDirectory.filters = ctk.ctkPathLineEdit.Dirs
self.meshDirectory.setToolTip("Select directory containing landmarks")
parametersFormLayout.addRow("Mesh directory: ", self.meshDirectory)
self.landmarkDirectory = ctk.ctkPathLineEdit()
self.landmarkDirectory.filters = ctk.ctkPathLineEdit.Dirs
self.landmarkDirectory.setToolTip("Select directory containing meshes")
parametersFormLayout.addRow("Landmark directory: ",
self.landmarkDirectory)
self.gridFile = ctk.ctkPathLineEdit()
self.gridFile.filters = ctk.ctkPathLineEdit().Files
self.gridFile.setToolTip(
"Select file specifying semi-landmark connectivity")
parametersFormLayout.addRow("Grid connectivity file: ", self.gridFile)
# Select output directory
self.outputDirectory = ctk.ctkPathLineEdit()
self.outputDirectory.filters = ctk.ctkPathLineEdit.Dirs
self.outputDirectory.setToolTip("Select directory for output models: ")
parametersFormLayout.addRow("Output directory: ", self.outputDirectory)
#
# set sample rate value
#
self.sampleRate = ctk.ctkDoubleSpinBox()
self.sampleRate.singleStep = 1
self.sampleRate.minimum = 1
self.sampleRate.maximum = 100
self.sampleRate.setDecimals(0)
self.sampleRate.value = 10
self.sampleRate.setToolTip(
"Select sample rate for semi-landmark interpolation")
parametersFormLayout.addRow("Sample rate for interpolation:",
self.sampleRate)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Generate PlaceSemiLMPatchess."
self.applyButton.enabled = False
parametersFormLayout.addRow(self.applyButton)
# connections
self.meshDirectory.connect('validInputChanged(bool)', self.onSelect)
self.landmarkDirectory.connect('validInputChanged(bool)',
self.onSelect)
self.gridFile.connect('validInputChanged(bool)', self.onSelect)
self.outputDirectory.connect('validInputChanged(bool)', self.onSelect)
self.applyButton.connect('clicked(bool)', self.onApplyButton)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# tracks the modified event observer on the currently
# selected sequence browser node
self.sequenceBrowserObserverRecord = None
self.animatorActionsGUI = None
self.logic = AnimatorLogic()
# Instantiate and connect widgets ...
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Animation Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
self.durationBox = ctk.ctkDoubleSpinBox()
self.durationBox.suffix = " seconds"
self.durationBox.decimals = 1
self.durationBox.minimum = 1
self.durationBox.value = 5
self.durationBox.toolTip = "Duration cannot be changed after animation created"
parametersFormLayout.addRow("New animation duration", self.durationBox)
#
# animation selector
#
self.animationSelector = slicer.qMRMLNodeComboBox()
self.animationSelector.nodeTypes = ["vtkMRMLScriptedModuleNode"]
self.animationSelector.setNodeTypeLabel("Animation", "vtkMRMLScriptedModuleNode")
self.animationSelector.selectNodeUponCreation = True
self.animationSelector.addEnabled = True
self.animationSelector.addAttribute("vtkMRMLScriptedModuleNode", "ModuleName", "Animation")
self.animationSelector.baseName = "Animation"
self.animationSelector.removeEnabled = True
self.animationSelector.noneEnabled = True
self.animationSelector.showHidden = True
self.animationSelector.showChildNodeTypes = False
self.animationSelector.setMRMLScene( slicer.mrmlScene )
self.animationSelector.setToolTip( "Pick the animation description." )
parametersFormLayout.addRow("Animation Node: ", self.animationSelector)
self.sequencePlay = slicer.qMRMLSequenceBrowserPlayWidget()
self.sequencePlay.setMRMLScene(slicer.mrmlScene)
self.sequenceSeek = slicer.qMRMLSequenceBrowserSeekWidget()
self.sequenceSeek.setMRMLScene(slicer.mrmlScene)
parametersFormLayout.addRow(self.sequencePlay)
parametersFormLayout.addRow(self.sequenceSeek)
self.actionsMenuButton = qt.QPushButton("Add Action")
self.actionsMenuButton.enabled = False
self.actionsMenu = qt.QMenu()
self.actionsMenuButton.setMenu(self.actionsMenu)
for actionName in slicer.modules.animatorActionPlugins.keys():
qAction = qt.QAction(actionName, self.actionsMenu)
qAction.connect('triggered()', lambda actionName=actionName: self.onAddAction(actionName))
self.actionsMenu.addAction(qAction)
parametersFormLayout.addWidget(self.actionsMenuButton)
#
# Actions Area
#
self.actionsCollapsibleButton = ctk.ctkCollapsibleButton()
self.actionsCollapsibleButton.text = "Actions"
self.layout.addWidget(self.actionsCollapsibleButton)
# Layout within the dummy collapsible button
self.actionsFormLayout = qt.QFormLayout(self.actionsCollapsibleButton)
#
# Export Area
#
self.exportCollapsibleButton = ctk.ctkCollapsibleButton()
self.exportCollapsibleButton.text = "Export"
self.layout.addWidget(self.exportCollapsibleButton)
self.exportCollapsibleButton.enabled = False
self.exportFormLayout = qt.QFormLayout(self.exportCollapsibleButton)
self.sizeSelector = qt.QComboBox()
for size in self.sizes.keys():
self.sizeSelector.addItem(size)
self.sizeSelector.currentText = self.defaultSize
self.exportFormLayout.addRow("Animation size", self.sizeSelector)
self.fileFormatSelector = qt.QComboBox()
for format in self.fileFormats.keys():
self.fileFormatSelector.addItem(format)
self.fileFormatSelector.currentText = self.defaultFileFormat
self.exportFormLayout.addRow("Animation format", self.fileFormatSelector)
self.outputFileButton = qt.QPushButton("Select a file...")
self.exportFormLayout.addRow("Output file", self.outputFileButton)
self.exportButton = qt.QPushButton("Export")
self.exportButton.enabled = False
self.exportFormLayout.addRow("", self.exportButton)
# connections
self.animationSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.outputFileButton.connect("clicked()", self.selectExportFile)
self.exportButton.connect("clicked()", self.onExport)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# Select landmark file to import
#
self.inputFileSelector = ctk.ctkPathLineEdit()
self.inputFileSelector.filters = ctk.ctkPathLineEdit().Files
self.inputFileSelector.setToolTip("Select landmark file for import")
parametersFormLayout.addRow(
"Select file containing landmark names and coordinates to load:",
self.inputFileSelector)
#
# output directory selector
#
self.outputDirectory = ctk.ctkDirectoryButton()
self.outputDirectory.directory = slicer.mrmlScene.GetCacheManager(
).GetRemoteCacheDirectory()
parametersFormLayout.addRow("Output Directory:", self.outputDirectory)
#
# Get header length
#
self.headerLengthWidget = ctk.ctkDoubleSpinBox()
self.headerLengthWidget.value = 2
self.headerLengthWidget.minimum = 0
self.headerLengthWidget.singleStep = 1
self.headerLengthWidget.setToolTip(
"Input the number of lines in header")
parametersFormLayout.addRow("Header length:", self.headerLengthWidget)
#
# check box to trigger taking screen shots for later use in tutorials
#
self.loadLandmarkNode = qt.QCheckBox()
self.loadLandmarkNode.checked = 0
self.loadLandmarkNode.setToolTip(
"After conversion, load landmarks into the scene.")
parametersFormLayout.addRow("Load landmarks into scene",
self.loadLandmarkNode)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = False
parametersFormLayout.addRow(self.applyButton)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.inputFileSelector.connect('validInputChanged(bool)',
self.onSelect)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onSelect()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# Select landmark file to import
#
self.inputDirectory = ctk.ctkPathLineEdit()
self.inputDirectory.filters = ctk.ctkPathLineEdit.Dirs
self.inputDirectory.setToolTip(
"Select directory containing curves to resample")
parametersFormLayout.addRow("Input Directory:", self.inputDirectory)
#
# output directory selector
#
self.outputDirectory = ctk.ctkPathLineEdit()
self.outputDirectory.filters = ctk.ctkPathLineEdit.Dirs
self.outputDirectory.currentPath = slicer.app.temporaryPath
parametersFormLayout.addRow("Output Directory:", self.outputDirectory)
#
# Get Resample number
#
self.ResampleRateWidget = ctk.ctkDoubleSpinBox()
self.ResampleRateWidget.value = 50
self.ResampleRateWidget.minimum = 3
self.ResampleRateWidget.maximum = 5000
self.ResampleRateWidget.singleStep = 1
self.ResampleRateWidget.setDecimals(0)
self.ResampleRateWidget.setToolTip(
"Select the number of points for resampling: ")
parametersFormLayout.addRow("Output sample number: ",
self.ResampleRateWidget)
#
# Get open or closed curve option
#
curveTypeSelector = qt.QHBoxLayout()
self.curveTypeOpen = qt.QRadioButton("open")
self.curveTypeOpen.setToolTip(
"Select option for no interpolation between first and last points")
self.curveTypeOpen.setChecked(True)
self.curveTypeClosed = qt.QRadioButton("closed")
self.curveTypeClosed.setToolTip(
"Select option to interpolate between first and last points")
curveTypeSelector.addWidget(self.curveTypeOpen)
curveTypeSelector.addWidget(self.curveTypeClosed)
curveTypeSelector.addStretch()
parametersFormLayout.addRow("Curve Type: ", curveTypeSelector)
#
# check box to trigger taking screen shots for later use in tutorials
#
self.enableScreenshotsFlagCheckBox = qt.QCheckBox()
self.enableScreenshotsFlagCheckBox.checked = 0
self.enableScreenshotsFlagCheckBox.setToolTip(
"If checked, take screen shots for tutorials. Use Save Data to write them to disk."
)
parametersFormLayout.addRow("Enable Screenshots",
self.enableScreenshotsFlagCheckBox)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Run the conversion."
self.applyButton.enabled = False
parametersFormLayout.addRow(self.applyButton)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.inputDirectory.connect('validInputChanged(bool)',
self.onSelectInput)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onSelectInput()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
medicalimageButton = ctk.ctkCollapsibleButton()
medicalimageButton.text = "Input CT image"
self.layout.addWidget(medicalimageButton)
medicalimageFormLayout = qt.QFormLayout(medicalimageButton)
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Transducer Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# input volume selector
#
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.inputSelector.selectNodeUponCreation = True
self.inputSelector.addEnabled = False
self.inputSelector.removeEnabled = False
self.inputSelector.noneEnabled = False
self.inputSelector.showHidden = False
self.inputSelector.showChildNodeTypes = False
self.inputSelector.setMRMLScene(slicer.mrmlScene)
self.inputSelector.setToolTip("Pick the input to the algorithm.")
medicalimageFormLayout.addRow("Input CT Volume: ", self.inputSelector)
#
# output volume selector
#
self.outputSelector = slicer.qMRMLNodeComboBox()
self.outputSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.outputSelector.selectNodeUponCreation = True
self.outputSelector.addEnabled = True
self.outputSelector.removeEnabled = True
self.outputSelector.noneEnabled = True
self.outputSelector.showHidden = False
self.outputSelector.showChildNodeTypes = False
self.outputSelector.setMRMLScene(slicer.mrmlScene)
self.outputSelector.setToolTip("Pick the output to the algorithm.")
#parametersFormLayout.addRow("Output Volume: ", self.outputSelector)
#
# threshold value
#
self.ROC = ctk.ctkSliderWidget()
self.ROC.singleStep = 0.1
self.ROC.minimum = 0
self.ROC.maximum = 100
self.ROC.value = 71
parametersFormLayout.addRow("ROC", self.ROC)
self.width = ctk.ctkSliderWidget()
self.width.singleStep = 0.1
self.width.minimum = 0
self.width.maximum = 100
self.width.value = 71
parametersFormLayout.addRow("Width", self.width)
self.freq = ctk.ctkSliderWidget()
self.freq.singleStep = 1
self.freq.minimum = 20
self.freq.maximum = 10000
self.freq.value = 200
parametersFormLayout.addRow("kHz", self.freq)
self.test = ctk.ctkDoubleSpinBox()
self.test.value = 1.0
self.test2 = ctk.ctkDoubleSpinBox()
self.test2.value = 2.0
self.test3 = ctk.ctkDoubleSpinBox()
self.test3.value = 3.0
self.label1 = qt.QLabel("Test1")
self.label1.setFixedWidth(50)
rowLayout = qt.QHBoxLayout()
rowLayout.addWidget(self.label1)
rowLayout.addWidget(self.test)
rowLayout.addWidget(self.test2)
parametersFormLayout.addRow(rowLayout)
#parametersFormLayout.insertRow(2, self.test)
#
# check box to trigger taking screen shots for later use in tutorials
#
#
# Apply Button
#
self.applyButton = qt.QPushButton("Run simulation")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = True
parametersFormLayout.addRow(self.applyButton)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
self.outputSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# File area
#
filesCollapsibleButton = ctk.ctkCollapsibleButton()
filesCollapsibleButton.text = "Files"
filesCollapsibleButton.collapsed = False
self.layout.addWidget(filesCollapsibleButton)
# Layout within the files collapsible button
filesFormLayout = qt.QFormLayout(filesCollapsibleButton)
self.fileModel = qt.QStandardItemModel()
self.fileTable = qt.QTableView()
self.fileTable.horizontalHeader().stretchLastSection = True
self.fileTable.horizontalHeader().visible = False
self.fileTable.setModel(self.fileModel)
filesFormLayout.addRow(self.fileTable)
buttonLayout = qt.QHBoxLayout()
self.addByBrowsingButton = qt.QPushButton("Browse for files")
self.clearFilesButton = qt.QPushButton("Clear files")
buttonLayout.addWidget(self.addByBrowsingButton)
buttonLayout.addWidget(self.clearFilesButton)
filesFormLayout.addRow(buttonLayout)
self.propertiesLabel = qt.QLabel()
filesFormLayout.addRow(self.propertiesLabel)
#
# output area
#
outputCollapsibleButton = ctk.ctkCollapsibleButton()
outputCollapsibleButton.text = "Output"
outputCollapsibleButton.collapsed = False
self.layout.addWidget(outputCollapsibleButton)
outputFormLayout = qt.QFormLayout(outputCollapsibleButton)
#
# output volume selector
#
self.outputSelector = slicer.qMRMLNodeComboBox()
self.outputSelector.nodeTypes = [
"vtkMRMLScalarVolumeNode",
]
self.outputSelector.showChildNodeTypes = False
self.outputSelector.showHidden = False
self.outputSelector.showChildNodeTypes = False
self.outputSelector.selectNodeUponCreation = True
self.outputSelector.noneEnabled = True
self.outputSelector.removeEnabled = True
self.outputSelector.renameEnabled = True
self.outputSelector.addEnabled = True
self.outputSelector.setMRMLScene(slicer.mrmlScene)
self.outputSelector.setToolTip(
"Pick the output volume to populate or None to autogenerate.")
outputFormLayout.addRow("Output Volume: ", self.outputSelector)
self.spacing = ctk.ctkCoordinatesWidget()
self.spacing.decimals = 8
self.spacing.coordinates = "1,1,1"
self.spacing.toolTip = "Set the colunm, row, slice spacing in mm; original spacing not including downsample"
outputFormLayout.addRow("Spacing: ", self.spacing)
self.downsample = qt.QCheckBox()
self.downsample.toolTip = "Reduces data size by half in each dimension by skipping every other pixel and slice (uses about 1/8 memory)"
outputFormLayout.addRow("Downsample: ", self.downsample)
self.reverse = qt.QCheckBox()
self.reverse.toolTip = "Read the images in reverse order"
outputFormLayout.addRow("Reverse: ", self.reverse)
self.sliceSkip = ctk.ctkDoubleSpinBox()
self.sliceSkip.decimals = 0
self.sliceSkip.minimum = 0
self.sliceSkip.toolTip = "Skips the selected number of slices (use, for example, on long thin samples with more slices than in-plane resolution)"
outputFormLayout.addRow("Slice skip: ", self.sliceSkip)
self.loadButton = qt.QPushButton("Load files")
outputFormLayout.addRow(self.loadButton)
#
# Add by name area
#
addByNameCollapsibleButton = ctk.ctkCollapsibleButton()
addByNameCollapsibleButton.text = "Add files by name"
addByNameCollapsibleButton.collapsed = True
addByNameFormLayout = qt.QFormLayout(addByNameCollapsibleButton)
# Don't enable Add by name for now - let's see if it's actually needed
# self.layout.addWidget(addByNameCollapsibleButton)
forExample = """
directoryPath = '/Volumes/SSD2T/data/SlicerMorph/Sample_for_steve/1326_Rec'
pathFormat = '%s/1326__rec%04d.png'
start, end = (50, 621)
"""
self.archetypePathEdit = ctk.ctkPathLineEdit()
addByNameFormLayout.addRow("Archetype file", self.archetypePathEdit)
self.archetypeFormat = qt.QLineEdit()
addByNameFormLayout.addRow("Name format", self.archetypeFormat)
self.indexRange = ctk.ctkRangeWidget()
self.indexRange.decimals = 0
self.indexRange.maximum = 0
addByNameFormLayout.addRow("Index range", self.indexRange)
self.generateNamesButton = qt.QPushButton("Apply")
self.generateNamesButton.toolTip = "Run the algorithm."
self.generateNamesButton.enabled = False
addByNameFormLayout.addRow(self.generateNamesButton)
# connections
self.addByBrowsingButton.connect('clicked()', self.addByBrowsing)
self.clearFilesButton.connect('clicked()', self.onClearFiles)
self.archetypePathEdit.connect('currentPathChanged(QString)',
self.validateInput)
self.archetypePathEdit.connect('currentPathChanged(QString)',
self.updateGUIFromArchetype)
self.archetypeFormat.connect('textChanged(QString)',
self.validateInput)
self.generateNamesButton.connect('clicked()', self.onGenerateNames)
# self.outputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.validateInput) # TODO - this is missing
self.loadButton.connect('clicked()', self.onLoadButton)
# refill last selection
self.archetypePathEdit.currentPath = slicer.util.settingsValue(
"ImageStacks/lastArchetypePath", "")
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.validateInput()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
self.inputDirectory = ctk.ctkPathLineEdit()
self.inputDirectory.filters = ctk.ctkPathLineEdit.Dirs
self.inputDirectory.setToolTip("Select directory containing volumes")
parametersFormLayout.addRow("Input directory: ", self.inputDirectory)
# Select output directory
self.outputDirectory = ctk.ctkPathLineEdit()
self.outputDirectory.filters = ctk.ctkPathLineEdit.Dirs
self.outputDirectory.setToolTip("Select directory for output models: ")
parametersFormLayout.addRow("Output directory: ", self.outputDirectory)
#
# Select the extension type
#
self.extensionOptionGZ = qt.QRadioButton(".nii.gz")
self.extensionOptionGZ.setChecked(True)
parametersFormLayout.addRow("Select extension type: ",
self.extensionOptionGZ)
#
# set threshold value
#
self.threshold = ctk.ctkDoubleSpinBox()
self.threshold.singleStep = 1
self.threshold.minimum = 0
self.threshold.maximum = 100000
self.threshold.setDecimals(0)
self.threshold.value = 500
self.threshold.setToolTip(
"Select threshold for segmentation of volume")
parametersFormLayout.addRow("Threshold for segmentation:",
self.threshold)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Generate VolumeToMeshs."
self.applyButton.enabled = False
parametersFormLayout.addRow(self.applyButton)
#
# check box to trigger taking screen shots for later use in tutorials
#
self.enableScreenshotsFlagCheckBox = qt.QCheckBox()
self.enableScreenshotsFlagCheckBox.checked = 0
self.enableScreenshotsFlagCheckBox.setToolTip(
"If checked, take screen shots for tutorials. Use Save Data to write them to disk."
)
parametersFormLayout.addRow("Enable Screenshots",
self.enableScreenshotsFlagCheckBox)
# connections
self.inputDirectory.connect('validInputChanged(bool)',
self.onSelectInput)
self.outputDirectory.connect('validInputChanged(bool)',
self.onSelectOutput)
self.applyButton.connect('clicked(bool)', self.onApplyButton)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# input landmark directory selector
#
self.inputLandmarkDirectory = ctk.ctkDirectoryButton()
self.inputLandmarkDirectory.directory = qt.QDir.homePath()
parametersFormLayout.addRow("Landmark Directory:",
self.inputLandmarkDirectory)
self.inputLandmarkDirectory.setToolTip(
"Select directory containing landmark files")
#
# input landmark numbers for grid
#
gridPointsLayout = qt.QGridLayout()
self.landmarkGridPoint1 = ctk.ctkDoubleSpinBox()
self.landmarkGridPoint1.minimum = 0
self.landmarkGridPoint1.singleStep = 1
self.landmarkGridPoint1.setDecimals(0)
self.landmarkGridPoint1.setToolTip(
"Input the landmark numbers to create grid")
self.landmarkGridPoint2 = ctk.ctkDoubleSpinBox()
self.landmarkGridPoint2.minimum = 0
self.landmarkGridPoint2.singleStep = 1
self.landmarkGridPoint2.setDecimals(0)
self.landmarkGridPoint2.setToolTip(
"Input the landmark numbers to create grid")
self.landmarkGridPoint3 = ctk.ctkDoubleSpinBox()
self.landmarkGridPoint3.minimum = 0
self.landmarkGridPoint3.singleStep = 1
self.landmarkGridPoint3.setDecimals(0)
self.landmarkGridPoint3.setToolTip(
"Input the landmark numbers to create grid")
self.landmarkGridPoint4 = ctk.ctkDoubleSpinBox()
self.landmarkGridPoint4.minimum = 0
self.landmarkGridPoint4.singleStep = 1
self.landmarkGridPoint4.setDecimals(0)
self.landmarkGridPoint4.setToolTip(
"Input the landmark numbers to create grid")
gridPointsLayout.addWidget(self.landmarkGridPoint1, 1, 2)
gridPointsLayout.addWidget(self.landmarkGridPoint2, 1, 3)
gridPointsLayout.addWidget(self.landmarkGridPoint3, 1, 4)
gridPointsLayout.addWidget(self.landmarkGridPoint4, 1, 5)
parametersFormLayout.addRow("Semi-landmark grid points:",
gridPointsLayout)
#
# input mesh directory selector
#
self.inputMeshDirectory = ctk.ctkDirectoryButton()
self.inputMeshDirectory.directory = qt.QDir.homePath()
parametersFormLayout.addRow("Mesh Directory:", self.inputMeshDirectory)
self.inputMeshDirectory.setToolTip(
"Select directory containing mesh files")
#
# output directory selector
#
self.outputDirectory = ctk.ctkDirectoryButton()
self.outputDirectory.directory = qt.QDir.homePath()
parametersFormLayout.addRow("Output Directory:", self.outputDirectory)
self.inputMeshDirectory.setToolTip(
"Select directory for output semi-landmark files")
#
# check box to trigger taking screen shots for later use in tutorials
#
self.enableScreenshotsFlagCheckBox = qt.QCheckBox()
self.enableScreenshotsFlagCheckBox.checked = 0
self.enableScreenshotsFlagCheckBox.setToolTip(
"If checked, take screen shots for tutorials. Use Save Data to write them to disk."
)
parametersFormLayout.addRow("Enable Screenshots",
self.enableScreenshotsFlagCheckBox)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Run the conversion."
self.applyButton.enabled = True
parametersFormLayout.addRow(self.applyButton)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
###################################
# Import node graph json file Area
###################################
self.fileCollapsibleButton = ctk.ctkCollapsibleButton()
self.fileCollapsibleButton.text = "Import Node Graph Json File"
self.layout.addWidget(self.fileCollapsibleButton)
self.fileImportFormLayout = qt.QFormLayout(self.fileCollapsibleButton)
self.fileImport = ctk.ctkPathLineEdit()
self.fileImport.filters = ctk.ctkPathLineEdit.Files
self.fileImport.settingKey = 'JsonInputFile'
self.fileImport.currentPath = os.path.normpath(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
'./Resources/nodeGraph_3D.json'))
self.fileImportFormLayout.addRow("Input Json File:", self.fileImport)
self.fileImportButton = qt.QPushButton('Load File')
self.fileImportFormLayout.addRow(self.fileImportButton)
###################################
# Node Table Area
###################################
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Node Table"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# Checkbox to see whether or not the input table has a header
#
self.headerCheckBox = qt.QCheckBox()
self.headerCheckBox.checked = 0
self.headerCheckBox.setToolTip(
"If checked, it means that the input node table contains a header."
)
parametersFormLayout.addRow("Header in Node Table",
self.headerCheckBox)
#
# input table selector
#
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = ["vtkMRMLTableNode"]
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(
"The input file loaded trough the import Data module should be a one line table (with or without header)."
)
parametersFormLayout.addRow("Input Table: ", self.inputSelector)
#
# Table start column spinBox
#
self.min_column = 1
self.tableStartSpinBox = qt.QDoubleSpinBox()
self.tableStartSpinBox.singleStep = 1
self.tableStartSpinBox.setValue(self.min_column)
self.tableStartSpinBox.setDecimals(0)
self.tableStartSpinBox.setToolTip(
"Set start column, if the first column contains a string of characters(ex: subject name) then this column should be skipped and the start column is thus 1. This should be an integer (int)"
)
parametersFormLayout.addRow("Start Column:", self.tableStartSpinBox)
###################################
# Region Selector Area
###################################
self.nodeselectCollapsibleButton = ctk.ctkCollapsibleButton()
self.nodeselectCollapsibleButton.text = "Selection of Node Region"
self.layout.addWidget(self.nodeselectCollapsibleButton)
# Layout within the collapsible button
self.nodeselectFormLayout = qt.QFormLayout(
self.nodeselectCollapsibleButton)
# Search Box to filter regions to display
self.searchLayout = qt.QHBoxLayout()
self.nodeselectFormLayout.addRow('Search:', self.searchLayout)
self.regionSearchBox = ctk.ctkSearchBox()
self.regionSearchBox.placeholderText = "search region"
self.regionSearchBox.searchIcon
self.searchLayout.addWidget(self.regionSearchBox)
self.logic = visuThreeDLogic()
self.regionsLayout = qt.QHBoxLayout()
self.nodeselectFormLayout.addRow('Regions:', self.regionsLayout)
self.regionButtons = ctk.ctkCheckableComboBox()
self.regionsLayout.addWidget(self.regionButtons)
# Add buttons to select all or no region
self.buttonsLayout = qt.QHBoxLayout()
self.nodeselectFormLayout.addRow('Select:', self.buttonsLayout)
self.calculateAllregionsButton = qt.QPushButton('Select All')
self.calculateAllregionsButton.toolTip = 'Select all regions.'
self.calculateAllregionsButton.enabled = True
self.buttonsLayout.addWidget(self.calculateAllregionsButton)
self.calculateAllFilteredregionsButton = qt.QPushButton(
'Select Filtered')
self.calculateAllFilteredregionsButton.toolTip = 'Select all filtered regions.'
self.calculateAllFilteredregionsButton.enabled = True
self.buttonsLayout.addWidget(self.calculateAllFilteredregionsButton)
self.deselectButtonsLayout = qt.QHBoxLayout()
self.nodeselectFormLayout.addRow('Deselect:',
self.deselectButtonsLayout)
self.calculateNoregionsButton = qt.QPushButton('Deselect All')
self.calculateNoregionsButton.toolTip = 'Deselect all regions.'
self.calculateNoregionsButton.enabled = True
self.deselectButtonsLayout.addWidget(self.calculateNoregionsButton)
self.calculateNoFilteredregionsButton = qt.QPushButton(
'Deselect Filtered')
self.calculateNoFilteredregionsButton.toolTip = 'Deselect all filtered regions.'
self.calculateNoFilteredregionsButton.enabled = True
self.deselectButtonsLayout.addWidget(
self.calculateNoFilteredregionsButton)
###################################
# Node Size and colorbar thresholding Area
###################################
self.colorbarCollapsibleButton = ctk.ctkCollapsibleButton()
self.colorbarCollapsibleButton.text = "Node Size and Color Thresholding"
self.layout.addWidget(self.colorbarCollapsibleButton)
# Layout within the collapsible button
self.regioncheckFormLayout = qt.QFormLayout(
self.colorbarCollapsibleButton)
self.ColorTable = slicer.qMRMLColorTableComboBox()
self.ColorTable.nodeTypes = ["vtkMRMLColorTableNode"]
self.ColorTable.addEnabled = True
self.ColorTable.removeEnabled = True
self.ColorTable.noneEnabled = True
self.ColorTable.showHidden = True
self.ColorTable.setMRMLScene(slicer.mrmlScene)
self.regioncheckFormLayout.addRow("Input Color Map: ", self.ColorTable)
#
# Threshold node value
#
# default values
self.minVal = 0.0
self.maxVal = 1.0
self.nodeThresholdSliderWidget = ctk.ctkRangeWidget()
self.nodeThresholdSliderWidget.singleStep = 0.01
self.nodeThresholdSliderWidget.setValues(self.minVal, self.maxVal)
self.nodeThresholdSliderWidget.setMaximumValue(self.maxVal)
self.nodeThresholdSliderWidget.setMinimumValue(self.minVal)
self.nodeThresholdSliderWidget.setRange(self.minVal, self.maxVal)
self.nodeThresholdSliderWidget.setMouseTracking(True)
self.nodeThresholdSliderWidget.setEnabled(True)
self.nodeThresholdSliderWidget.setToolTip(
"Set threshold node value for computing the node value.")
self.regioncheckFormLayout.addRow("Plot Property Range:",
self.nodeThresholdSliderWidget)
#
# Node size min spinBox
#
# default value for min size (l: lowest , h: highest)
self.minSize_l = 0.0
self.minSize_h = 100.0
self.nodeMinSizeSpinBox = qt.QDoubleSpinBox()
self.nodeMinSizeSpinBox.singleStep = 0.01
self.nodeMinSizeSpinBox.setRange(self.minSize_l, self.minSize_h)
self.nodeMinSizeSpinBox.setToolTip("Set minimum node size.")
self.regioncheckFormLayout.addRow("Min Size:", self.nodeMinSizeSpinBox)
#
# Node size max spinBox
#
# default value for max size (l: lowest , h: highest)
self.maxSize_l = 0.0
self.maxSize_h = 100.0
self.nodeMaxSizeSpinBox = qt.QDoubleSpinBox()
self.nodeMaxSizeSpinBox.singleStep = 0.01
self.nodeMaxSizeSpinBox.setRange(self.maxSize_l, self.maxSize_h)
self.nodeMaxSizeSpinBox.setToolTip("Set maximum node size.")
self.regioncheckFormLayout.addRow("Max Size:", self.nodeMaxSizeSpinBox)
###################################
# Connections line/tube Area
###################################
self.lineCollapsibleButton = ctk.ctkCollapsibleButton()
self.lineCollapsibleButton.text = "Connection Size and Color Thresholding"
self.layout.addWidget(self.lineCollapsibleButton)
# Layout within the collapsible button
self.lineconnectFormLayout = qt.QFormLayout(self.lineCollapsibleButton)
#
# input connection matrix selector
#
self.matrixConnectSelector = slicer.qMRMLNodeComboBox()
self.matrixConnectSelector.nodeTypes = ["vtkMRMLTableNode"]
self.matrixConnectSelector.selectNodeUponCreation = True
self.matrixConnectSelector.addEnabled = False
self.matrixConnectSelector.removeEnabled = False
self.matrixConnectSelector.noneEnabled = False
self.matrixConnectSelector.showHidden = False
self.matrixConnectSelector.showChildNodeTypes = False
self.matrixConnectSelector.setMRMLScene(slicer.mrmlScene)
self.matrixConnectSelector.setToolTip(
"Pick the connection matrix input to the algorithm.")
self.lineconnectFormLayout.addRow("Input Connection Table: ",
self.matrixConnectSelector)
#
# Checkbox to choose whether or not the connection distribution follows a log scale or else a linear distribution
#
self.connectionDistCheckBox = qt.QCheckBox()
self.connectionDistCheckBox.checked = 0
self.connectionDistCheckBox.setToolTip(
"If checked, it means that the connection distribution follows a log scale."
)
self.lineconnectFormLayout.addRow("Log Distribution",
self.connectionDistCheckBox)
self.connectionColorTable = slicer.qMRMLColorTableComboBox()
self.connectionColorTable.nodeTypes = ["vtkMRMLColorTableNode"]
self.connectionColorTable.addEnabled = True
self.connectionColorTable.removeEnabled = True
self.connectionColorTable.noneEnabled = True
self.connectionColorTable.showHidden = True
self.connectionColorTable.setMRMLScene(slicer.mrmlScene)
self.lineconnectFormLayout.addRow("Input Color Map: ",
self.connectionColorTable)
#
# Threshold node connection strength
#
# default values
self.logic = visuThreeDLogic()
self.min_strength = 0.0
self.max_strength = 1.0
self.connectionThresholdSliderWidget = ctk.ctkRangeWidget()
self.connectionThresholdSliderWidget.singleStep = 0.01
self.connectionThresholdSliderWidget.setValues(self.min_strength,
self.max_strength)
self.connectionThresholdSliderWidget.setMaximumValue(self.max_strength)
self.connectionThresholdSliderWidget.setMinimumValue(self.min_strength)
self.connectionThresholdSliderWidget.setRange(self.minVal,
self.max_strength)
self.connectionThresholdSliderWidget.setMouseTracking(True)
self.connectionThresholdSliderWidget.setEnabled(True)
self.connectionThresholdSliderWidget.setToolTip(
"Set threshold node value for computing the node value.")
self.lineconnectFormLayout.addRow("Plot Strength Range:",
self.connectionThresholdSliderWidget)
#
# Connection min strength spinBox
#
# default value for min strength (l: lowest , h: highest)
self.minStrength_l = 0.0
self.minStrength_h = 50.0
self.minConnectionSpinBox = qt.QDoubleSpinBox()
self.minConnectionSpinBox.singleStep = 0.01
self.minConnectionSpinBox.setRange(self.minStrength_l,
self.minStrength_h)
self.minConnectionSpinBox.setToolTip(
"Set minimum connection strength.")
self.lineconnectFormLayout.addRow("Min Strength:",
self.minConnectionSpinBox)
#
# Node size max spinBox
#
# default value for max size (l: lowest , h: highest)
self.maxStrength_l = 0.0
self.maxStrength_h = 100.0
self.maxConnectionSpinBox = qt.QDoubleSpinBox()
self.maxConnectionSpinBox.singleStep = 0.01
self.maxConnectionSpinBox.setRange(self.maxStrength_l,
self.maxStrength_h)
self.maxConnectionSpinBox.setToolTip(
"Set maximum connection strength.")
self.lineconnectFormLayout.addRow("Max Strenght:",
self.maxConnectionSpinBox)
###################################
# Advanced Connections scale factors Area
###################################
self.scaleCollapsibleButton = ctk.ctkCollapsibleButton()
self.scaleCollapsibleButton.text = "Advanced Connection Scale Factors"
self.layout.addWidget(self.scaleCollapsibleButton)
# Layout within the collapsible button
self.scaleconnectFormLayout = qt.QFormLayout(
self.scaleCollapsibleButton)
#Double SpinBox for default scale factor "f" :
#computation of value in matrix by the number of connexions * f factor
self.fscaleDoubleSpinBox = ctk.ctkDoubleSpinBox()
self.fscaleDoubleSpinBox.setValue(0.000033)
self.fscaleDoubleSpinBox.setDecimals(6)
self.fscaleDoubleSpinBox.enabled = True
self.scaleconnectFormLayout.addWidget(self.fscaleDoubleSpinBox)
self.scaleconnectFormLayout.addRow("f Scale:",
self.fscaleDoubleSpinBox)
#Double SpinBox for log scale factor "C" :
self.logScaleDoubleSpinBox = ctk.ctkDoubleSpinBox()
self.logScaleDoubleSpinBox.setValue(10)
self.logScaleDoubleSpinBox.setDecimals(0.)
self.logScaleDoubleSpinBox.enabled = False
self.scaleconnectFormLayout.addWidget(self.logScaleDoubleSpinBox)
self.scaleconnectFormLayout.addRow("C Log Scale:",
self.logScaleDoubleSpinBox)
###################################
# Connections
###################################
self.coord = []
self.index = []
self.position = []
self.visu = []
self.fileImportButton.connect('clicked(bool)',
self.on_node_graph_json_load)
self.inputSelector.connect("nodeActivated(vtkMRMLNode*)",
self.on_select)
self.regionButtons.connect('checkedIndexesChanged()',
self.on_regions_checked)
self.calculateAllFilteredregionsButton.connect(
'clicked(bool)', self.on_select_all_filtered_regionButtons)
self.calculateAllregionsButton.connect(
'clicked(bool)', self.on_select_all_regionButtons)
self.calculateNoregionsButton.connect(
'clicked(bool)', self.on_deselect_all_regionButtons)
self.calculateNoFilteredregionsButton.connect(
'clicked(bool)', self.on_deselect_all_filtered_regionButtons)
self.regionSearchBox.connect("textChanged(QString)", self.on_search)
self.ColorTable.connect("currentNodeChanged(vtkMRMLNode*)",
self.on_node_color_clicked)
self.nodeThresholdSliderWidget.connect("valuesChanged(double, double)",
self.sliderbar_changed)
self.nodeMinSizeSpinBox.connect("valueChanged(double)",
self.min_nodesize_changed)
self.nodeMaxSizeSpinBox.connect("valueChanged(double)",
self.max_nodesize_changed)
self.tableStartSpinBox.connect("valueChanged(double)",
self.table_start_changed)
self.matrixConnectSelector.connect("nodeActivated(vtkMRMLNode*)",
self.on_select_matrix)
self.connectionThresholdSliderWidget.connect(
"valuesChanged(double, double)", self.sliderbar2_changed)
self.maxConnectionSpinBox.connect("valueChanged(double)",
self.max_connection_changed)
self.connectionColorTable.connect("currentNodeChanged(vtkMRMLNode*)",
self.on_connect_color_clicked)
self.fscaleDoubleSpinBox.connect("valueChanged(double)",
self.on_fscale_changed)
self.logScaleDoubleSpinBox.connect("valueChanged(double)",
self.on_logscale_changed)
# Add vertical spacer
self.layout.addStretch(1)
self.header = None
self.connection_d = None
self.value = 'None'
self.on_node_graph_json_load()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
# 3D view set up tab
self.meshSelect = slicer.qMRMLNodeComboBox()
self.meshSelect.nodeTypes = (("vtkMRMLModelNode"), "")
self.meshSelect.selectNodeUponCreation = False
self.meshSelect.addEnabled = False
self.meshSelect.removeEnabled = False
self.meshSelect.noneEnabled = True
self.meshSelect.showHidden = False
self.meshSelect.setMRMLScene(slicer.mrmlScene)
self.meshSelect.connect("currentNodeChanged(vtkMRMLNode*)",
self.onMeshSelect)
parametersFormLayout.addRow("Model: ", self.meshSelect)
self.meshSelect.setToolTip("Select model node for semilandmarking")
self.LMSelect = slicer.qMRMLNodeComboBox()
self.LMSelect.nodeTypes = (('vtkMRMLMarkupsFiducialNode'), "")
self.LMSelect.selectNodeUponCreation = False
self.LMSelect.addEnabled = False
self.LMSelect.removeEnabled = False
self.LMSelect.noneEnabled = True
self.LMSelect.showHidden = False
self.LMSelect.showChildNodeTypes = False
self.LMSelect.setMRMLScene(slicer.mrmlScene)
self.LMSelect.connect("currentNodeChanged(vtkMRMLNode*)",
self.onLMSelect)
parametersFormLayout.addRow("Landmark set: ", self.LMSelect)
self.LMSelect.setToolTip(
"Select the landmark set that corresponds to the model")
#
# input landmark numbers for grid
#
gridPointsLayout = qt.QGridLayout()
self.landmarkGridPoint1 = ctk.ctkDoubleSpinBox()
self.landmarkGridPoint1.minimum = 0
self.landmarkGridPoint1.singleStep = 1
self.landmarkGridPoint1.setDecimals(0)
self.landmarkGridPoint1.setToolTip(
"Input the landmark numbers to create grid")
self.landmarkGridPoint2 = ctk.ctkDoubleSpinBox()
self.landmarkGridPoint2.minimum = 0
self.landmarkGridPoint2.singleStep = 1
self.landmarkGridPoint2.setDecimals(0)
self.landmarkGridPoint2.setToolTip(
"Input the landmark numbers to create grid")
self.landmarkGridPoint3 = ctk.ctkDoubleSpinBox()
self.landmarkGridPoint3.minimum = 0
self.landmarkGridPoint3.singleStep = 1
self.landmarkGridPoint3.setDecimals(0)
self.landmarkGridPoint3.setToolTip(
"Input the landmark numbers to create grid")
gridPointsLayout.addWidget(self.landmarkGridPoint1, 1, 2)
gridPointsLayout.addWidget(self.landmarkGridPoint2, 1, 3)
gridPointsLayout.addWidget(self.landmarkGridPoint3, 1, 4)
parametersFormLayout.addRow("Semi-landmark grid points:",
gridPointsLayout)
#
# set number of sample points in each triangle
#
self.gridSamplingRate = ctk.ctkDoubleSpinBox()
self.gridSamplingRate.minimum = 3
self.gridSamplingRate.maximum = 50
self.gridSamplingRate.singleStep = 1
self.gridSamplingRate.setDecimals(0)
self.gridSamplingRate.value = 10
self.gridSamplingRate.setToolTip(
"Input the landmark numbers to create grid")
parametersFormLayout.addRow(
"Select number of rows/columns in resampled grid:",
self.gridSamplingRate)
#
# check box to trigger taking screen shots for later use in tutorials
#
self.enableScreenshotsFlagCheckBox = qt.QCheckBox()
self.enableScreenshotsFlagCheckBox.checked = 0
self.enableScreenshotsFlagCheckBox.setToolTip(
"If checked, take screen shots for tutorials. Use Save Data to write them to disk."
)
parametersFormLayout.addRow("Enable Screenshots",
self.enableScreenshotsFlagCheckBox)
#
# Advanced menu
#
advancedCollapsibleButton = ctk.ctkCollapsibleButton()
advancedCollapsibleButton.text = "Advanced"
advancedCollapsibleButton.collapsed = True
parametersFormLayout.addRow(advancedCollapsibleButton)
# Layout within the dummy collapsible button
advancedFormLayout = qt.QFormLayout(advancedCollapsibleButton)
#
# Maximum projection slider
#
self.projectionDistanceSlider = ctk.ctkSliderWidget()
self.projectionDistanceSlider.singleStep = 1
self.projectionDistanceSlider.minimum = 0
self.projectionDistanceSlider.maximum = 100
self.projectionDistanceSlider.value = 25
self.projectionDistanceSlider.setToolTip(
"Set maximum projection distance as a percentage of image size")
advancedFormLayout.addRow("Set maximum projection distance: ",
self.projectionDistanceSlider)
#
# Normal smoothing slider
#
self.smoothingSlider = ctk.ctkSliderWidget()
self.smoothingSlider.singleStep = 1
self.smoothingSlider.minimum = 0
self.smoothingSlider.maximum = 100
self.smoothingSlider.value = 0
self.smoothingSlider.setToolTip(
"Set smothing of normal vectors for projection")
advancedFormLayout.addRow("Set smoothing of projection vectors: ",
self.smoothingSlider)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Generate semilandmarks."
self.applyButton.enabled = False
parametersFormLayout.addRow(self.applyButton)
#
# Fiducials view
#
self.fiducialView = slicer.qMRMLSubjectHierarchyTreeView()
self.fiducialView.setMRMLScene(slicer.mrmlScene)
self.fiducialView.setMultiSelection(True)
self.fiducialView.setAlternatingRowColors(True)
self.fiducialView.setDragDropMode(True)
self.fiducialView.setColumnHidden(
self.fiducialView.model().transformColumn, True)
self.fiducialView.sortFilterProxyModel().setNodeTypes(
["vtkMRMLMarkupsFiducialNode"])
parametersFormLayout.addRow(self.fiducialView)
#
# Apply Button
#
self.mergeButton = qt.QPushButton("Merge highlighted nodes")
self.mergeButton.toolTip = "Generate a single merged landmark file from the selected nodes"
self.mergeButton.enabled = False
parametersFormLayout.addRow(self.mergeButton)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.mergeButton.connect('clicked(bool)', self.onMergeButton)
self.fiducialView.connect('currentItemChanged(vtkIdType)',
self.updateMergeButton)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
# Instantiate and connect widgets ...
# Collapsible button
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the parameters collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
# fiber
self.fiberSelector = slicer.qMRMLNodeComboBox(
parametersCollapsibleButton)
self.fiberSelector.nodeTypes = ["vtkMRMLFiberBundleNode"]
self.fiberSelector.selectNodeUponCreation = False
self.fiberSelector.addEnabled = False
self.fiberSelector.removeEnabled = False
self.fiberSelector.noneEnabled = True
self.fiberSelector.showHidden = False
self.fiberSelector.showChildNodeTypes = False
self.fiberSelector.setMRMLScene(slicer.mrmlScene)
self.fiberSelector.setToolTip("Pick the fiber bundle to be converted.")
parametersFormLayout.addRow("Fiber Bundle", self.fiberSelector)
# label map
self.labelSelector = slicer.qMRMLNodeComboBox(
parametersCollapsibleButton)
self.labelSelector.nodeTypes = ["vtkMRMLLabelMapVolumeNode"]
self.labelSelector.selectNodeUponCreation = False
self.labelSelector.addEnabled = False
self.labelSelector.removeEnabled = False
self.labelSelector.noneEnabled = True
self.labelSelector.showHidden = False
self.labelSelector.showChildNodeTypes = False
self.labelSelector.setMRMLScene(slicer.mrmlScene)
self.labelSelector.setToolTip(
"Pick the target label volume. Must already exists in order to define sampling grid. If needed, create one in the Editor module based on template volume."
)
parametersFormLayout.addRow("Target LabelMap", self.labelSelector)
# label value
self.labelValue = qt.QSpinBox(parametersCollapsibleButton)
self.labelValue.setToolTip(
"The numerical value for the rasterized fiber label.")
self.labelValue.setValue(1)
parametersFormLayout.addRow("Label Value", self.labelValue)
# apply
self.applyButton = qt.QPushButton(parametersCollapsibleButton)
self.applyButton.text = "Apply"
parametersFormLayout.addWidget(self.applyButton)
self.applyButton.connect('clicked()', self.onApply)
# 'Advanced' collapsible button
advancedCollapsibleButton = ctk.ctkCollapsibleButton()
advancedCollapsibleButton.text = "Advanced"
advancedCollapsibleButton.collapsed = True
self.layout.addWidget(advancedCollapsibleButton)
advancedFormLayout = qt.QFormLayout(advancedCollapsibleButton)
self.samplingDistance = ctk.ctkDoubleSpinBox()
self.samplingDistance.minimum = 0.01
self.samplingDistance.maximum = 5.0
self.samplingDistance.decimals = 2
self.samplingDistance.singleStep = 0.1
self.samplingDistance.value = 0.1
self.samplingDistance.decimalsOption = (
ctk.ctkDoubleSpinBox.ReplaceDecimals
| ctk.ctkDoubleSpinBox.DecimalsByKey)
advancedFormLayout.addRow("Sampling distance (mm)",
self.samplingDistance)
# Add vertical spacer
self.layout.addStretch(1)
def setupOptionsFrame(self):
self.operationRadioButtons = []
self.updatingGUIFromMRML = False
self.visibleIcon = qt.QIcon(":/Icons/Small/SlicerVisible.png")
self.invisibleIcon = qt.QIcon(":/Icons/Small/SlicerInvisible.png")
# Fill operation buttons
self.fillInsideButton = qt.QRadioButton("Fill inside")
self.operationRadioButtons.append(self.fillInsideButton)
self.buttonToOperationNameMap[self.fillInsideButton] = 'FILL_INSIDE'
self.fillOutsideButton = qt.QRadioButton("Fill outside")
self.operationRadioButtons.append(self.fillOutsideButton)
self.buttonToOperationNameMap[self.fillOutsideButton] = 'FILL_OUTSIDE'
self.binaryMaskFillButton = qt.QRadioButton("Fill inside and outside")
self.binaryMaskFillButton.setToolTip("Create a labelmap volume with specified inside and outside fill values.")
self.operationRadioButtons.append(self.binaryMaskFillButton)
self.buttonToOperationNameMap[self.binaryMaskFillButton] = 'FILL_INSIDE_AND_OUTSIDE'
# Operation buttons layout
operationLayout = qt.QGridLayout()
operationLayout.addWidget(self.fillInsideButton, 0, 0)
operationLayout.addWidget(self.fillOutsideButton, 1, 0)
operationLayout.addWidget(self.binaryMaskFillButton, 0, 1)
self.scriptedEffect.addLabeledOptionsWidget("Operation:", operationLayout)
# fill value
self.fillValueEdit = ctk.ctkDoubleSpinBox()
self.fillValueEdit.setToolTip("Choose the voxel intensity that will be used to fill the masked region.")
self.fillValueLabel = qt.QLabel("Fill value: ")
# Binary mask fill outside value
self.binaryMaskFillOutsideEdit = ctk.ctkDoubleSpinBox()
self.binaryMaskFillOutsideEdit.setToolTip("Choose the voxel intensity that will be used to fill outside the mask.")
self.fillOutsideLabel = qt.QLabel("Outside fill value: ")
# Binary mask fill outside value
self.binaryMaskFillInsideEdit = ctk.ctkDoubleSpinBox()
self.binaryMaskFillInsideEdit.setToolTip("Choose the voxel intensity that will be used to fill inside the mask.")
self.fillInsideLabel = qt.QLabel(" Inside fill value: ")
for fillValueEdit in [self.fillValueEdit, self.binaryMaskFillOutsideEdit, self.binaryMaskFillInsideEdit]:
fillValueEdit.decimalsOption = ctk.ctkDoubleSpinBox.DecimalsByValue + ctk.ctkDoubleSpinBox.DecimalsByKey + ctk.ctkDoubleSpinBox.InsertDecimals
fillValueEdit.minimum = vtk.vtkDoubleArray().GetDataTypeMin(vtk.VTK_DOUBLE)
fillValueEdit.maximum = vtk.vtkDoubleArray().GetDataTypeMax(vtk.VTK_DOUBLE)
fillValueEdit.connect("valueChanged(double)", self.fillValueChanged)
# Fill value layouts
fillValueLayout = qt.QFormLayout()
fillValueLayout.addRow(self.fillValueLabel, self.fillValueEdit)
fillOutsideLayout = qt.QFormLayout()
fillOutsideLayout.addRow(self.fillOutsideLabel, self.binaryMaskFillOutsideEdit)
fillInsideLayout = qt.QFormLayout()
fillInsideLayout.addRow(self.fillInsideLabel, self.binaryMaskFillInsideEdit)
binaryMaskFillLayout = qt.QHBoxLayout()
binaryMaskFillLayout.addLayout(fillOutsideLayout)
binaryMaskFillLayout.addLayout(fillInsideLayout)
fillValuesSpinBoxLayout = qt.QFormLayout()
fillValuesSpinBoxLayout.addRow(binaryMaskFillLayout)
fillValuesSpinBoxLayout.addRow(fillValueLayout)
self.scriptedEffect.addOptionsWidget(fillValuesSpinBoxLayout)
# input volume selector
self.inputVolumeSelector = slicer.qMRMLNodeComboBox()
self.inputVolumeSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.inputVolumeSelector.selectNodeUponCreation = True
self.inputVolumeSelector.addEnabled = True
self.inputVolumeSelector.removeEnabled = True
self.inputVolumeSelector.noneEnabled = True
self.inputVolumeSelector.noneDisplay = "(Source volume)"
self.inputVolumeSelector.showHidden = False
self.inputVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.inputVolumeSelector.setToolTip("Volume to mask. Default is current source volume node.")
self.inputVolumeSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onInputVolumeChanged)
self.inputVisibilityButton = qt.QToolButton()
self.inputVisibilityButton.setIcon(self.invisibleIcon)
self.inputVisibilityButton.connect('clicked()', self.onInputVisibilityButtonClicked)
inputLayout = qt.QHBoxLayout()
inputLayout.addWidget(self.inputVisibilityButton)
inputLayout.addWidget(self.inputVolumeSelector)
self.scriptedEffect.addLabeledOptionsWidget("Input Volume: ", inputLayout)
# output volume selector
self.outputVolumeSelector = slicer.qMRMLNodeComboBox()
self.outputVolumeSelector.nodeTypes = ["vtkMRMLScalarVolumeNode", "vtkMRMLLabelMapVolumeNode"]
self.outputVolumeSelector.selectNodeUponCreation = True
self.outputVolumeSelector.addEnabled = True
self.outputVolumeSelector.removeEnabled = True
self.outputVolumeSelector.renameEnabled = True
self.outputVolumeSelector.noneEnabled = True
self.outputVolumeSelector.noneDisplay = "(Create new Volume)"
self.outputVolumeSelector.showHidden = False
self.outputVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.outputVolumeSelector.setToolTip("Masked output volume. It may be the same as the input volume for cumulative masking.")
self.outputVolumeSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onOutputVolumeChanged)
self.outputVisibilityButton = qt.QToolButton()
self.outputVisibilityButton.setIcon(self.invisibleIcon)
self.outputVisibilityButton.connect('clicked()', self.onOutputVisibilityButtonClicked)
outputLayout = qt.QHBoxLayout()
outputLayout.addWidget(self.outputVisibilityButton)
outputLayout.addWidget(self.outputVolumeSelector)
self.scriptedEffect.addLabeledOptionsWidget("Output Volume: ", outputLayout)
# Apply button
self.applyButton = qt.QPushButton("Apply")
self.applyButton.objectName = self.__class__.__name__ + 'Apply'
self.applyButton.setToolTip("Apply segment as volume mask. No undo operation available once applied.")
self.scriptedEffect.addOptionsWidget(self.applyButton)
self.applyButton.connect('clicked()', self.onApply)
for button in self.operationRadioButtons:
button.connect('toggled(bool)',
lambda toggle, widget=self.buttonToOperationNameMap[button]: self.onOperationSelectionChanged(widget, toggle))
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
###################################################################
## ##
## Collapsible part for input/output parameters for Groups CLI ##
## ##
###################################################################
self.ioCollapsibleButton = ctk.ctkCollapsibleButton()
self.ioCollapsibleButton.text = "IO"
self.layout.addWidget(self.ioCollapsibleButton)
self.ioQVBox = qt.QVBoxLayout(self.ioCollapsibleButton)
# --------------------------------- #
# ----- Group Box DIRECTORIES ----- #
# --------------------------------- #
self.directoryGroupBox = qt.QGroupBox("Groups Dircetories")
self.ioQVBox.addWidget(self.directoryGroupBox)
self.ioQFormLayout = qt.QFormLayout(self.directoryGroupBox)
# Selection of the directory containing the input models (option: --surfaceDir) and option procalign shape
self.inputMeshTypeHBox = qt.QVBoxLayout(self.directoryGroupBox)
self.inputModelsDirectorySelector = ctk.ctkDirectoryButton()
self.inputMeshTypeHBox.addWidget(self.inputModelsDirectorySelector)
self.ioQFormLayout.addRow(qt.QLabel("Input Models Directory:"), self.inputMeshTypeHBox)
# Selection of the directory which contains each spherical model (option: --sphereDir)
self.sphericalModelsDirectorySelector = ctk.ctkDirectoryButton()
self.ioQFormLayout.addRow("Spherical Models Directory:", self.sphericalModelsDirectorySelector)
# Selection of the output directory for Groups (option: --outputDir)
self.outputDirectorySelector = ctk.ctkDirectoryButton()
self.ioQFormLayout.addRow(qt.QLabel("Output Directory:"), self.outputDirectorySelector)
# CheckBox. If checked, Group Box 'Parameters' will be enabled
self.enableRigidAlignmentCB = ctk.ctkCheckBox()
self.enableRigidAlignmentCB.setText("Perform Rigid Alignment")
self.ioQFormLayout.addRow(self.enableRigidAlignmentCB)
# CheckBox. If checked, Group Box 'Parameters' will be enabled
self.enableParamCB = ctk.ctkCheckBox()
self.enableParamCB.setText("Personalize Groups parameters")
self.ioQFormLayout.addRow(self.enableParamCB)
# Connections
self.inputModelsDirectorySelector.connect("directoryChanged(const QString &)", self.onSelect)
self.sphericalModelsDirectorySelector.connect("directoryChanged(const QString &)", self.onSelect)
self.outputDirectorySelector.connect("directoryChanged(const QString &)", self.onSelect)
self.enableRigidAlignmentCB.connect("stateChanged(int)", self.onCheckBoxRigidAlignment)
self.enableParamCB.connect("stateChanged(int)", self.onCheckBoxParam)
# Name simplification (string)
self.modelsDirectory = str(self.inputModelsDirectorySelector.directory)
self.sphericalmodelsDirectory = str(self.sphericalModelsDirectorySelector.directory)
self.outputDirectory = str(self.outputDirectorySelector.directory)
# ------------------------------------------ #
# ----- RigidAlignment Box DIRECTORIES ----- #
# ------------------------------------------ #
self.rigidalignmentdirectoryGroupBox = qt.QGroupBox("Rigid Alignment Directories")
self.ioQVBox.addWidget(self.rigidalignmentdirectoryGroupBox)
self.ioQFormLayout = qt.QFormLayout(self.rigidalignmentdirectoryGroupBox)
self.rigidalignmentdirectoryGroupBox.setEnabled(False)
# Selection of the directory which contains each landmark fcsv file (option: --landmark)
self.inputlandmarksfiducialfilesDirectorySelector = ctk.ctkDirectoryButton()
self.ioQFormLayout.addRow("Input Landmarks Fiducial Files Directory:", self.inputlandmarksfiducialfilesDirectorySelector)
# Selection of the directory which contains common unit sphere file (option: --sphere)
self.inputunitspherefileDirectorySelector = ctk.ctkDirectoryButton()
self.ioQFormLayout.addRow("Input Unit Sphere File Directory:", self.inputunitspherefileDirectorySelector)
# Connections
self.inputlandmarksfiducialfilesDirectorySelector.connect("directoryChanged(const QString &)", self.onSelect)
self.inputunitspherefileDirectorySelector.connect("directoryChanged(const QString &)", self.onSelect)
# Name simplification (string)
self.landmarksDirectory = str(self.inputlandmarksfiducialfilesDirectorySelector.directory)
self.sphereDirectory = str(self.inputunitspherefileDirectorySelector.directory)
# -------------------------------- #
# ----- Group Box PARAMETERS ----- #
# -------------------------------- #
self.parametersGroupBox = qt.QGroupBox("Groups Parameters")
self.ioQVBox.addWidget(self.parametersGroupBox)
self.paramQFormLayout = qt.QFormLayout(self.parametersGroupBox)
self.parametersGroupBox.setEnabled(False)
# Selection of the property we want to use
self.specifyPropertySelector = ctk.ctkCheckableComboBox()
self.specifyPropertySelector.addItems(("Curvedness","Shape_Index"))
self.paramQFormLayout.addRow(qt.QLabel("Properties name to use:"), self.specifyPropertySelector)
# Weights of each property - Choices on 1 lines
self.weightLayout = qt.QVBoxLayout(self.parametersGroupBox)
self.weightline1 = qt.QHBoxLayout(self.parametersGroupBox) # Line 1
self.weightLayout.addLayout(self.weightline1)
# Fill out first line
self.labelCurvedness = qt.QLabel("Curvedness")
self.weightline1.addWidget(self.labelCurvedness)
self.weightCurvedness = ctk.ctkDoubleSpinBox()
self.weightCurvedness.enabled = False
self.weightCurvedness.value = 1
self.weightline1.addWidget(self.weightCurvedness)
self.labelShape_Index = qt.QLabel(" Shape_Index")
self.weightline1.addWidget(self.labelShape_Index)
self.weightShape_Index = ctk.ctkDoubleSpinBox()
self.weightShape_Index.enabled = False
self.weightShape_Index.value = 1
self.weightline1.addWidget(self.weightShape_Index)
self.paramQFormLayout.addRow("Weight of each property:", self.weightLayout)
# CheckBox. If checked, Landmarks enabled
self.enableLandmarks = ctk.ctkCheckBox()
self.enableLandmarks.setText("Enable Landmarks")
self.paramQFormLayout.addRow(self.enableLandmarks)
# Specification of the SPHARM decomposition degree (option: -d)
self.degreeSpharm = ctk.ctkSliderWidget()
self.degreeSpharm.minimum = 0
self.degreeSpharm.maximum = 50
self.degreeSpharm.value = 5 # initial value
self.degreeSpharm.setDecimals(0)
self.paramQFormLayout.addRow(qt.QLabel("Degree of SPHARM decomposition:"), self.degreeSpharm)
# Maximum iteration (option: --maxIter)
self.maxIter = qt.QSpinBox()
self.maxIter.minimum = 0 # Check the range authorized
self.maxIter.maximum = 100000
self.maxIter.value = 5000
self.paramQFormLayout.addRow("Maximum number of iteration:", self.maxIter)
# Name simplification
self.property = ""
self.propertyValue = ""
# Connections
self.specifyPropertySelector.connect("checkedIndexesChanged()", self.onSpecifyPropertyChanged)
# ------------------------------------------ #
# ----- Apply button to launch the CLI ----- #
# ------------------------------------------ #
self.applyButton = qt.QPushButton("Apply")
self.applyButton.enabled = False
self.ioQVBox.addWidget(self.applyButton)
self.errorLabel = qt.QLabel("Error: Invalide inputs")
self.errorLabel.hide()
self.errorLabel.setStyleSheet("color: rgb(255, 0, 0);")
self.ioQVBox.addWidget(self.errorLabel)
# Connections
self.applyButton.connect('clicked(bool)', self.onApplyButtonClicked)
# ----- Add vertical spacer ----- #
self.layout.addStretch(1)
def setup(self):
# Instantiate and connect widgets ...
# Collapsible button
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the parameters collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
# fiber
self.fiberSelector = slicer.qMRMLNodeComboBox(parametersCollapsibleButton)
self.fiberSelector.nodeTypes = ["vtkMRMLFiberBundleNode"]
self.fiberSelector.selectNodeUponCreation = False
self.fiberSelector.addEnabled = False
self.fiberSelector.removeEnabled = False
self.fiberSelector.noneEnabled = True
self.fiberSelector.showHidden = False
self.fiberSelector.showChildNodeTypes = False
self.fiberSelector.setMRMLScene( slicer.mrmlScene )
self.fiberSelector.setToolTip( "Pick the fiber bundle to be converted." )
parametersFormLayout.addRow("Fiber Bundle", self.fiberSelector)
# label map
self.labelSelector = slicer.qMRMLNodeComboBox(parametersCollapsibleButton)
self.labelSelector.nodeTypes = ["vtkMRMLLabelMapVolumeNode"]
self.labelSelector.selectNodeUponCreation = False
self.labelSelector.addEnabled = False
self.labelSelector.removeEnabled = False
self.labelSelector.noneEnabled = True
self.labelSelector.showHidden = False
self.labelSelector.showChildNodeTypes = False
self.labelSelector.setMRMLScene( slicer.mrmlScene )
self.labelSelector.setToolTip( "Pick the target label volume. Must already exists in order to define sampling grid. If needed, create one in the Editor module based on template volume." )
parametersFormLayout.addRow("Target LabelMap", self.labelSelector)
# label value
self.labelValue = qt.QSpinBox(parametersCollapsibleButton)
self.labelValue.setToolTip( "The numerical value for the rasterized fiber label." )
self.labelValue.setValue(1)
parametersFormLayout.addRow("Label Value", self.labelValue)
# apply
self.applyButton = qt.QPushButton(parametersCollapsibleButton)
self.applyButton.text = "Apply"
parametersFormLayout.addWidget(self.applyButton)
self.applyButton.connect('clicked()', self.onApply)
# 'Advanced' collapsible button
advancedCollapsibleButton = ctk.ctkCollapsibleButton()
advancedCollapsibleButton.text = "Advanced"
advancedCollapsibleButton.collapsed = True
self.layout.addWidget(advancedCollapsibleButton)
advancedFormLayout = qt.QFormLayout(advancedCollapsibleButton)
self.samplingDistance = ctk.ctkDoubleSpinBox()
self.samplingDistance.minimum = 0.01
self.samplingDistance.maximum = 5.0
self.samplingDistance.decimals = 2
self.samplingDistance.singleStep = 0.1
self.samplingDistance.value = 0.1
self.samplingDistance.decimalsOption = (ctk.ctkDoubleSpinBox.ReplaceDecimals |
ctk.ctkDoubleSpinBox.DecimalsByKey)
advancedFormLayout.addRow("Sampling distance (mm)", self.samplingDistance)
# Add vertical spacer
self.layout.addStretch(1)
def create(self):
super().create()
self.toleranceFrame = qt.QFrame(self.frame)
self.toleranceFrame.setLayout(qt.QHBoxLayout())
self.frame.layout().addWidget(self.toleranceFrame)
self.widgets.append(self.toleranceFrame)
self.toleranceLabel = qt.QLabel("Tolerance:", self.toleranceFrame)
self.toleranceLabel.setToolTip(
"Set the tolerance of the wand in terms of background pixel values"
)
self.toleranceFrame.layout().addWidget(self.toleranceLabel)
self.widgets.append(self.toleranceLabel)
self.toleranceSpinBox = ctk.ctkDoubleSpinBox(self.toleranceFrame)
self.toleranceSpinBox.setToolTip(
"Set the tolerance of the wand in terms of background pixel values"
)
self.toleranceSpinBox.minimum = 0
self.toleranceSpinBox.maximum = 1000
self.toleranceSpinBox.suffix = ""
self.toleranceFrame.layout().addWidget(self.toleranceSpinBox)
self.widgets.append(self.toleranceSpinBox)
self.maxPixelsFrame = qt.QFrame(self.frame)
self.maxPixelsFrame.setLayout(qt.QHBoxLayout())
self.frame.layout().addWidget(self.maxPixelsFrame)
self.widgets.append(self.maxPixelsFrame)
self.maxPixelsLabel = qt.QLabel("Max Pixels per click:",
self.maxPixelsFrame)
self.maxPixelsLabel.setToolTip("Set the maxPixels for each click")
self.maxPixelsFrame.layout().addWidget(self.maxPixelsLabel)
self.widgets.append(self.maxPixelsLabel)
self.maxPixelsSpinBox = ctk.ctkDoubleSpinBox(self.maxPixelsFrame)
self.maxPixelsSpinBox.setToolTip("Set the maxPixels for each click")
self.maxPixelsSpinBox.minimum = 1
self.maxPixelsSpinBox.maximum = 100000
self.maxPixelsSpinBox.suffix = ""
self.maxPixelsFrame.layout().addWidget(self.maxPixelsSpinBox)
self.widgets.append(self.maxPixelsSpinBox)
self.fillModeFrame = qt.QFrame(self.frame)
self.fillModeFrame.setLayout(qt.QHBoxLayout())
self.frame.layout().addWidget(self.fillModeFrame)
self.widgets.append(self.fillModeFrame)
self.fillModeCheckBox = qt.QCheckBox(self.fillModeFrame)
self.fillModeCheckBox.text = "Fill Volume"
self.fillModeCheckBox.setToolTip(
"Fill in 3D when checked, else fill plane")
self.fillModeFrame.layout().addWidget(self.fillModeCheckBox)
self.widgets.append(self.fillModeCheckBox)
HelpButton(
self.frame,
"Use this tool to label all voxels that are within a tolerance of where you click"
)
# don't connect the signals and slots directly - instead, add these
# to the list of connections so that gui callbacks can be cleanly
# disabled while the gui is being updated. This allows several gui
# elements to be interlinked with signal/slots but still get updated
# as a unit to the new value of the mrml node.
self.connections.append((self.toleranceSpinBox, 'valueChanged(double)',
self.onToleranceSpinBoxChanged))
self.connections.append((self.maxPixelsSpinBox, 'valueChanged(double)',
self.onMaxPixelsSpinBoxChanged))
self.connections.append(
(self.fillModeCheckBox, 'clicked()', self.onFillModeClicked))
# Add vertical spacer
self.frame.layout().addStretch(1)