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 volume selector
#
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = ["vtkMRMLMarkupsFiducialNode"]
self.inputSelector.selectNodeUponCreation = True
self.inputSelector.addEnabled = True
self.inputSelector.removeEnabled = False
self.inputSelector.noneEnabled = False
self.inputSelector.showHidden = False
self.inputSelector.showChildNodeTypes = False
self.inputSelector.setMRMLScene(slicer.mrmlScene)
self.inputSelector.setToolTip("Pick the input to the algorithm.")
parametersFormLayout.addRow("Input Volume: ", self.inputSelector)
#
# output volume selector
#
self.outputSelector = slicer.qMRMLNodeComboBox()
self.outputSelector.nodeTypes = ["vtkMRMLModelNode"]
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 model to the algorithm.")
parametersFormLayout.addRow("Output Model: ", self.outputSelector)
#
# threshold value
#
self.imageThresholdSliderWidget = ctk.ctkSliderWidget()
self.imageThresholdSliderWidget.singleStep = 0.1
self.imageThresholdSliderWidget.minimum = -100
self.imageThresholdSliderWidget.maximum = 100
self.imageThresholdSliderWidget.value = 0.5
self.imageThresholdSliderWidget.setToolTip(
"Set threshold value for computing the output image. Voxels that have intensities lower than this value will set to zero."
)
parametersFormLayout.addRow("Image threshold",
self.imageThresholdSliderWidget)
#
# check box to trigger taking screen shots for later use in tutorials
#
self.enableScreenshotsFlagCheckBox = qt.QCheckBox()
self.enableScreenshotsFlagCheckBox.checked = 0
self.enableScreenshotsFlagCheckBox.setToolTip("Enable auto-update")
parametersFormLayout.addRow("Auto-update",
self.enableScreenshotsFlagCheckBox)
self.observedMarkupNode = None
self.markupsObserverTag = None
self.enableScreenshotsFlagCheckBox.connect("toggled(bool)",
self.onEnableAutoUpdate)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = False
parametersFormLayout.addRow(self.applyButton)
self.centreOfMassValueLabel = qt.QLabel()
parametersFormLayout.addRow("Center of mass",
self.centreOfMassValueLabel)
# 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)
# Refresh Apply button state
self.onSelect()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# This module is often used in developer mode, therefore
# collapse reload & test section by default.
if hasattr(self, "reloadCollapsibleButton"):
self.reloadCollapsibleButton.collapsed = True
self.dragAndDropEventFilter = DICOMLoadingByDragAndDropEventFilter()
globals()['d'] = self
self.testingServer = None
self.browserWidget = None
self.directoryButton = None
# Load widget from .ui file (created by Qt Designer)
uiWidget = slicer.util.loadUI(self.resourcePath('UI/DICOM.ui'))
self.layout.addWidget(uiWidget)
self.ui = slicer.util.childWidgetVariables(uiWidget)
self.browserWidget = DICOMLib.SlicerDICOMBrowser()
self.browserWidget.objectName = 'SlicerDICOMBrowser'
slicer.modules.DICOMInstance.setBrowserWidgetInDICOMLayout(
self.browserWidget)
layoutManager = slicer.app.layoutManager()
if layoutManager is not None:
layoutManager.layoutChanged.connect(self.onLayoutChanged)
viewArrangement = slicer.app.layoutManager().layoutLogic(
).GetLayoutNode().GetViewArrangement()
self.ui.showBrowserButton.checked = (
viewArrangement ==
slicer.vtkMRMLLayoutNode.SlicerLayoutDicomBrowserView)
# connect to the 'Show DICOM Browser' button
self.ui.showBrowserButton.connect('clicked()',
self.toggleBrowserWidget)
self.ui.importButton.connect('clicked()', self.importFolder)
self.ui.subjectHierarchyTree.setMRMLScene(slicer.mrmlScene)
self.ui.subjectHierarchyTree.currentItemChanged.connect(
self.onCurrentItemChanged)
self.ui.subjectHierarchyTree.currentItemModified.connect(
self.onCurrentItemModified)
self.subjectHierarchyCurrentVisibility = False
self.ui.subjectHierarchyTree.setColumnHidden(
self.ui.subjectHierarchyTree.model().idColumn, True)
#
# DICOM networking
#
self.ui.networkingFrame.collapsed = True
self.ui.queryServerButton.connect('clicked()',
self.browserWidget.dicomBrowser,
"openQueryDialog()")
self.ui.toggleListener.connect('toggled(bool)', self.onToggleListener)
settings = qt.QSettings()
self.ui.runListenerAtStart.checked = settingsValue(
'DICOM/RunListenerAtStart', False, converter=toBool)
self.ui.runListenerAtStart.connect('toggled(bool)',
self.onRunListenerAtStart)
# Testing server - not exposed (used for development)
self.toggleServer = qt.QPushButton("Start Testing Server")
self.ui.networkingFrame.layout().addWidget(self.toggleServer)
self.toggleServer.connect('clicked()', self.onToggleServer)
self.verboseServer = qt.QCheckBox("Verbose")
self.ui.networkingFrame.layout().addWidget(self.verboseServer)
# advanced options - not exposed to end users
# developers can uncomment these lines to access testing server
self.toggleServer.hide()
self.verboseServer.hide()
#
# Browser settings
#
self.ui.browserSettingsFrame.collapsed = True
self.updateDatabaseDirectoryFromBrowser(
self.browserWidget.dicomBrowser.databaseDirectory)
# Synchronize database selection between browser and this widget
self.ui.directoryButton.directoryChanged.connect(
self.updateDatabaseDirectoryFromWidget)
self.browserWidget.dicomBrowser.databaseDirectoryChanged.connect(
self.updateDatabaseDirectoryFromBrowser)
self.ui.browserAutoHideCheckBox.checked = not settingsValue(
'DICOM/BrowserPersistent', False, converter=toBool)
self.ui.browserAutoHideCheckBox.stateChanged.connect(
self.onBrowserAutoHideStateChanged)
self.ui.repairDatabaseButton.connect('clicked()',
self.browserWidget.dicomBrowser,
"onRepairAction()")
self.ui.clearDatabaseButton.connect('clicked()', self.onClearDatabase)
# connect to the main window's dicom button
mw = slicer.util.mainWindow()
if mw:
try:
action = slicer.util.findChildren(mw,
name='LoadDICOMAction')[0]
action.connect('triggered()', self.onOpenBrowserWidget)
except IndexError:
logging.error(
'Could not connect to the main window DICOM button')
self.databaseRefreshRequestTimer = qt.QTimer()
self.databaseRefreshRequestTimer.setSingleShot(True)
# If not receiving new file for 2 seconds then a database update is triggered.
self.databaseRefreshRequestTimer.setInterval(2000)
self.databaseRefreshRequestTimer.connect('timeout()',
self.requestDatabaseRefresh)
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 VolumeToModels."
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)
# Generate Scene Button
self.generateSceneButton = qt.QPushButton('Generate Scene')
self.generateSceneButton.connect('clicked(bool)',
self.onGenerateSceneButtonClicked)
#self.generateSceneButton.setDisabled(True)
parametersFormLayout.addRow(self.generateSceneButton)
# Toggle DRR Button
self.toggleDRRButton = qt.QCheckBox()
self.toggleDRRButton.connect('toggled(bool)',
self.onToggleDRRButtonClicked)
parametersFormLayout.addRow("Toggle DRR", self.toggleDRRButton)
# Toggle VR Button - TO DO
self.toggleVRButton = qt.QCheckBox()
self.toggleVRButton.connect('toggled(bool)',
self.onToggleVRButtonClicked)
parametersFormLayout.addRow("Toggle VR", self.toggleVRButton)
# Transfer Function Presets
self.fluoroButton = qt.QRadioButton()
# parametersFormLayout.addRow("Fluoro", self.fluoroButton)
# Field of View Slider
self.fieldOfViewSlider = ctk.ctkSliderWidget()
self.fieldOfViewSlider.singleStep = 0.1
self.fieldOfViewSlider.minimum = 0
self.fieldOfViewSlider.maximum = 60
self.fieldOfViewSlider.setToolTip("Increase/Decrease Field of View.")
self.fieldOfViewSlider.connect('valueChanged(double)',
self.onFieldOfViewValueChanged)
parametersFormLayout.addRow("Field Of View", self.fieldOfViewSlider)
# Zoom Slider
self.zoomSlider = ctk.ctkSliderWidget()
self.zoomSlider.singleStep = 0.1
self.zoomSlider.minimum = 0
self.zoomSlider.maximum = 50
self.zoomSlider.value = 0
self.zoomSlider.setToolTip("Zoom Factor")
self.zoomSlider.connect('valueChanged(double)',
self.onZoomValueChanged)
parametersFormLayout.addRow("Zoom", self.zoomSlider)
# C Rotation
self.xRotationSliderWidget = ctk.ctkSliderWidget()
self.xRotationSliderWidget.singleStep = 0.01
self.xRotationSliderWidget.minimum = -15
self.xRotationSliderWidget.maximum = 115
self.xRotationSliderWidget.value = 0.0
self.xRotationSliderWidget.setToolTip("C Rotation about the Z axis.")
self.xRotationSliderWidget.connect('valueChanged(double)',
self.onCRotationValuesChanged)
parametersFormLayout.addRow("C Rotation", self.xRotationSliderWidget)
# Gantry Rotation
self.zRotationSliderWidget = ctk.ctkSliderWidget()
self.zRotationSliderWidget.singleStep = 0.01
self.zRotationSliderWidget.minimum = -55
self.zRotationSliderWidget.maximum = 55
self.zRotationSliderWidget.value = 0.0
self.zRotationSliderWidget.setToolTip(
"Gantry Rotation about the X axis.")
self.zRotationSliderWidget.connect('valueChanged(double)',
self.onGantryRotationValuesChanged)
parametersFormLayout.addRow("Gantry Rotation",
self.zRotationSliderWidget)
# Wag Rotation
self.wagRotationSliderWidget = ctk.ctkSliderWidget()
self.wagRotationSliderWidget.singleStep = 0.005
self.wagRotationSliderWidget.minimum = -40
self.wagRotationSliderWidget.maximum = 40
self.wagRotationSliderWidget.value = 0.0
self.wagRotationSliderWidget.setToolTip(
"Wag Rotation about the Y axis.")
self.wagRotationSliderWidget.connect('valueChanged(double)',
self.onWagRotationValuesChanged)
parametersFormLayout.addRow("Wag Rotation",
self.wagRotationSliderWidget)
self.tableSliderWidget = ctk.ctkSliderWidget()
self.tableSliderWidget.singleStep = 0.05
self.tableSliderWidget.minimum = -155
self.tableSliderWidget.maximum = 155
self.tableSliderWidget.value = 0.0
self.tableSliderWidget.setToolTip("Table Translation.")
self.tableSliderWidget.connect('valueChanged(double)',
self.onTableValuesChanged)
parametersFormLayout.addRow("Table Translation",
self.tableSliderWidget)
# Start Module Button
self.startModuleButton = qt.QPushButton('Start Module')
self.startModuleButton.connect('clicked(bool)',
self.onStartModuleButtonClicked)
parametersFormLayout.addRow(self.startModuleButton)
# Collect Image Button
self.collectImageButton = qt.QPushButton('Collect Image')
self.collectImageButton.connect('clicked(bool)',
self.onCollectImageButtonClicked)
parametersFormLayout.addRow(self.collectImageButton)
# Shoot Fluoro Button
self.shootFluoroButton = qt.QPushButton('ShootFluoro')
self.shootFluoroButton.connect('clicked(bool)',
self.onShootFluoroButtonClicked)
parametersFormLayout.addRow(self.shootFluoroButton)
# Create Logic Instance
self.logic = CarmSimulatorLogic()
# Disable All Buttons until generate scene is clicked
self.toggleDRRButton.setDisabled(True)
self.fieldOfViewSlider.setDisabled(True)
self.toggleVRButton.setDisabled(True)
self.zoomSlider.setDisabled(True)
self.xRotationSliderWidget.setDisabled(True)
self.zRotationSliderWidget.setDisabled(True)
self.wagRotationSliderWidget.setDisabled(True)
self.tableSliderWidget.setDisabled(True)
self.startModuleButton.setDisabled(True)
self.collectImageButton.setDisabled(True)
#self.interactorObserver = slicer.modules.virtualReality
self.vrInteractorObserver = 0
self.gestureObserverNum = 0
self.vrInteractor = None
# Grab gesturerecognition logic instance so we can observe for events
#self.gestureObserver = slicer.modules.gesturerecognition.logic()
#self.useGestureRecognition = True
#self.gestureObserverNum = 0
#if not self.gestureObserver:
# self.useGestureRecognition = False
#self.useGestureRecognition = False
self.timer = qt.QTimer()
self.elapsed = qt.QElapsedTimer()
self.timerIteration = 0
self.movement = 1
self.direction = 0
self.timer.connect('timeout()', self.processOneThing)
#self.timer.setInterval(30)
self.timer.start()
# Add vertical Spacer
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
#
# Parameter Combobox
#
self.parameterSelector = slicer.qMRMLNodeComboBox()
self.parameterLabel = qt.QLabel(" Parameter set: ")
self.parameterSelector.nodeTypes = ["vtkMRMLScriptedModuleNode"]
self.parameterSelector.removeEnabled = False
self.parameterSelector.showHidden = True
self.parameterSelector.setMRMLScene( slicer.mrmlScene )
self.parameterLayout = qt.QHBoxLayout()
self.parameterLayout.addWidget(self.parameterLabel)
self.parameterLayout.addWidget(self.parameterSelector)
self.layout.addLayout(self.parameterLayout)
#
# Input Area
#
inputCollapsibleButton = ctk.ctkCollapsibleButton()
inputCollapsibleButton.text = "Input"
self.layout.addWidget(inputCollapsibleButton)
# Layout within the dummy collapsible button
inputFormLayout = qt.QFormLayout(inputCollapsibleButton)
#
# Input first DVH selector
#
self.dvh1Selector = slicer.qMRMLNodeComboBox()
self.dvh1Selector.nodeTypes = ["vtkMRMLTableNode"]
self.dvh1Selector.addAttribute("vtkMRMLTableNode", "DoseVolumeHistogram.DVH")
self.dvh1Selector.removeEnabled = False
self.dvh1Selector.setMRMLScene( slicer.mrmlScene )
inputFormLayout.addRow("DVH 1: ", self.dvh1Selector)
#
# Input second DVH selector
#
self.dvh2Selector = slicer.qMRMLNodeComboBox()
self.dvh2Selector.nodeTypes = ["vtkMRMLTableNode"]
self.dvh1Selector.addAttribute("vtkMRMLTableNode", "DoseVolumeHistogram.DVH")
self.dvh2Selector.removeEnabled = False
self.dvh2Selector.setMRMLScene( slicer.mrmlScene )
inputFormLayout.addRow("DVH 2: ", self.dvh2Selector)
#
# Input the dose volume
#
self.doseVolumeSelector = slicer.qMRMLNodeComboBox()
self.doseVolumeSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.doseVolumeSelector.addAttribute("vtkMRMLScalarVolumeNode", "DicomRtImport.DoseVolume")
self.doseVolumeSelector.removeEnabled = False
self.doseVolumeSelector.setMRMLScene( slicer.mrmlScene )
inputFormLayout.addRow("Dose Volume: ", self.doseVolumeSelector)
#
# Dose volume only check box
#
self.showDoseVolumeOnlyCheckbox = qt.QCheckBox("Show dose volume only")
self.showDoseVolumeOnlyCheckbox.setChecked(2)
inputFormLayout.addWidget(self.showDoseVolumeOnlyCheckbox)
#
# Volume difference criterion spin box
#
self.volumeDifferenceSpinbox = qt.QDoubleSpinBox()
self.volumeDifferenceSpinbox.setValue(1.0)
self.volumeDifferenceSpinbox.setDecimals(1)
self.volumeDifferenceSpinbox.setSingleStep(0.1)
inputFormLayout.addRow("Volume difference criterion: ", self.volumeDifferenceSpinbox)
#
# Dose to agreement criterion spin box
#
self.doseToAgreementSpinbox = qt.QDoubleSpinBox()
self.doseToAgreementSpinbox.setValue(1.0)
self.doseToAgreementSpinbox.setDecimals(1)
self.doseToAgreementSpinbox.setSingleStep(0.1)
inputFormLayout.addRow("Dose to agreement criterion: ", self.doseToAgreementSpinbox)
#
# Compute button
#
self.computeButton = qt.QPushButton("Compute")
self.computeButtonLayout = qt.QVBoxLayout()
self.computeButtonLayout.addStrut(100)
self.computeButtonLayout.setAlignment(2)
self.computeButtonLayout.addWidget(self.computeButton)
self.computeButtonFont = qt.QFont()
self.computeButtonFont.setBold(True)
self.computeButton.setFont(self.computeButtonFont)
inputFormLayout.addRow(self.computeButtonLayout)
#
# Output Area
#
outputCollapsibleButton = ctk.ctkCollapsibleButton()
outputCollapsibleButton.text = "Output"
self.layout.addWidget(outputCollapsibleButton)
# Layout within the dummy collapsible button
outputFormLayout = qt.QFormLayout(outputCollapsibleButton)
self.agreementAcceptanceOutput = qt.QLineEdit()
self.agreementAcceptanceOutput.setReadOnly(True)
outputFormLayout.addRow("Agreement acceptance %: ", self.agreementAcceptanceOutput)
#
# Visualize Area
#
visualizeCollapsibleButton = ctk.ctkCollapsibleButton()
visualizeCollapsibleButton.text = "Visualize"
sizePolicy = qt.QSizePolicy()
sizePolicy.setHorizontalPolicy(qt.QSizePolicy.Preferred)
sizePolicy.setVerticalPolicy(qt.QSizePolicy.Expanding)
visualizeCollapsibleButton.setSizePolicy(sizePolicy)
self.layout.addWidget(visualizeCollapsibleButton)
# Layout within the dummy collapsible button
visualizeLayout = qt.QVBoxLayout(visualizeCollapsibleButton)
#
# DVH Table
#
self.dvhTable = slicer.qMRMLTableView()
self.dvhTable.setMRMLScene(slicer.mrmlScene)
self.dvhTable.setSelectionMode(qt.QAbstractItemView.NoSelection)
self.dvhTable.setSizePolicy(sizePolicy)
visualizeLayout.addWidget(self.dvhTable)
# Connections
self.parameterSelector.connect('nodeAddedByUser(vtkMRMLNode*)', self.parameterNodeCreated)
self.parameterSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.updateWidgetFromMRML)
self.showDoseVolumeOnlyCheckbox.connect('stateChanged(int)', self.showDoseVolumesOnlyCheckboxChanged)
self.dvh1Selector.connect("currentNodeChanged(vtkMRMLNode*)", self.dvh1SelectorChanged)
self.dvh2Selector.connect("currentNodeChanged(vtkMRMLNode*)", self.dvh2SelectorChanged)
self.doseVolumeSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.doseVolumeSelectorChanged)
self.volumeDifferenceSpinbox.connect("valueChanged(double)", self.volumeDifferenceSpinboxChanged)
self.doseToAgreementSpinbox.connect("valueChanged(double)", self.doseToAgreementSpinboxChanged)
self.computeButton.connect('clicked(bool)', self.onComputeButton)
self.updateWidgetFromMRML()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.reloadCollapsibleButton.collapsed = 1
# Instantiate and connect widgets ...
#
# Data selection area
#
self.DataCollapsibleButton = ctk.ctkCollapsibleButton()
self.DataCollapsibleButton.text = "Data Selection"
self.layout.addWidget(self.DataCollapsibleButton)
self.DataInterfaceLayout = qt.QGridLayout(self.DataCollapsibleButton)
self.DataInterfaceLayout.setHorizontalSpacing(12)
# Checkbox to indicate whether to operate on all MarkupsNodes, or to select one
self.ModifyAllNodesCheckBox = qt.QCheckBox()
self.ModifyAllNodesCheckBox.checked = 0
self.ModifyAllNodesCheckBox.toolTip = "Check if you want to operate on all MarkupsNodes in the scene, uncheck if you want to select one"
self.DataInterfaceLayout.addWidget(qt.QLabel("All Nodes?"), 0, 0, 1, 1)
self.DataInterfaceLayout.addWidget(self.ModifyAllNodesCheckBox, 0, 1,
1, 1)
# Single node ComboBox selector
self.SingleNodeSelector = slicer.qMRMLNodeComboBox()
self.SingleNodeSelector.nodeTypes = [
"vtkMRMLMarkupsFiducialNode",
]
self.SingleNodeSelector.enabled = True
self.SingleNodeSelector.selectNodeUponCreation = True
self.SingleNodeSelector.addEnabled = False
self.SingleNodeSelector.removeEnabled = False
self.SingleNodeSelector.noneEnabled = True
self.SingleNodeSelector.showHidden = False
self.SingleNodeSelector.showChildNodeTypes = False
self.SingleNodeSelector.setMRMLScene(slicer.mrmlScene)
self.SingleNodeSelector.setToolTip("Pick the input to the algorithm.")
self.DataInterfaceLayout.addWidget(qt.QLabel("Node selector"), 0, 2, 1,
1)
self.DataInterfaceLayout.addWidget(self.SingleNodeSelector, 0, 3, 1, 1)
#
# Operations Interface
#
self.OperationsCollapsibleButton = ctk.ctkCollapsibleButton()
self.OperationsCollapsibleButton.text = "Operations"
self.layout.addWidget(self.OperationsCollapsibleButton)
self.DataInterfaceLayout = qt.QGridLayout(
self.OperationsCollapsibleButton)
self.DataInterfaceLayout.setHorizontalSpacing(12)
# Extrapolate button
self.ExtrapolateLandmarksButton = qt.QPushButton(
"Extrapolate Landmarks")
self.ExtrapolateLandmarksButton.toolTip = "Extend incomplete (but gap-free) landmark set to include T1-L5"
self.ExtrapolateLandmarksButton.enabled = True
self.ExtrapolateLandmarksButton.checkable = True
self.DataInterfaceLayout.addWidget(self.ExtrapolateLandmarksButton, 1,
1, 1, 2)
# Center button
self.CenterLandmarksButton = qt.QPushButton("Center Landmarks")
self.CenterLandmarksButton.toolTip = "Center the landmarks about the origin (subtract average locations)"
self.CenterLandmarksButton.enabled = True
self.CenterLandmarksButton.checkable = True
self.DataInterfaceLayout.addWidget(self.CenterLandmarksButton, 2, 1, 1,
2)
# Normalize button
self.NormalizeLandmarksButton = qt.QPushButton("Normalize Landmarks")
self.NormalizeLandmarksButton.toolTip = "Normalize landmarks coordinate over range [0,1] (divide by largest coordinate in each node)"
self.NormalizeLandmarksButton.enabled = True
self.NormalizeLandmarksButton.checkable = True
self.DataInterfaceLayout.addWidget(self.NormalizeLandmarksButton, 3, 1,
1, 2)
# Apply Button
self.PerformOperationsButton = qt.QPushButton("Perform Operations")
self.PerformOperationsButton.toolTip = "Run the algorithm."
self.PerformOperationsButton.enabled = False
self.DataInterfaceLayout.addWidget(self.PerformOperationsButton, 4, 1,
1, 2)
#
# Connections
#
self.ModifyAllNodesCheckBox.connect('stateChanged(int)',
self.OnAllNodesChecked)
self.SingleNodeSelector.connect('currentNodeChanged(bool)',
self.OnSelectedNodeChanged)
self.PerformOperationsButton.connect('clicked(bool)',
self.OnPerformOperationsButton)
#
# Seperate reload button
#
self.ReloadButton = qt.QPushButton("Reload Module")
self.ReloadButton.toolTip = "Reload this module, reflecting any changes in its code"
self.ReloadButton.enabled = True
self.layout.addWidget(self.ReloadButton)
self.ReloadButton.connect('clicked(bool)', self.OnReloadButtonClicked)
def _createSmall(self):
"""Make the internals of the widget to display in the
Data Probe frame (lower left of slicer main window by default)"""
# this method makes SliceView Annotation
self.sliceAnnotations = DataProbeLib.SliceAnnotations()
# goto module button
self.goToModule = qt.QPushButton('->', self.frame)
self.goToModule.setToolTip(
'Go to the DataProbe module for more information and options')
self.frame.layout().addWidget(self.goToModule)
self.goToModule.connect("clicked()", self.onGoToModule)
# hide this for now - there's not much to see in the module itself
self.goToModule.hide()
# image view: To ensure the height of the checkbox matches the height of the
# viewerFrame, it is added to a frame setting the layout and hard-coding the
# content margins.
# TODO: Revisit the approach and avoid hard-coding content margins
self.showImageFrame = qt.QFrame(self.frame)
self.frame.layout().addWidget(self.showImageFrame)
self.showImageFrame.setLayout(qt.QHBoxLayout())
self.showImageFrame.layout().setContentsMargins(0, 3, 0, 3)
self.showImageBox = qt.QCheckBox('Show Zoomed Slice',
self.showImageFrame)
self.showImageFrame.layout().addWidget(self.showImageBox)
self.showImageBox.connect("toggled(bool)", self.onShowImage)
self.showImageBox.setChecked(False)
self.imageLabel = qt.QLabel()
# qt.QSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
# fails on some systems, therefore set the policies using separate method calls
qSize = qt.QSizePolicy()
qSize.setHorizontalPolicy(qt.QSizePolicy.Expanding)
qSize.setVerticalPolicy(qt.QSizePolicy.Expanding)
self.imageLabel.setSizePolicy(qSize)
#self.imageLabel.setScaledContents(True)
self.frame.layout().addWidget(self.imageLabel)
self.onShowImage(False)
# top row - things about the viewer itself
self.viewerFrame = qt.QFrame(self.frame)
self.viewerFrame.setLayout(qt.QHBoxLayout())
self.frame.layout().addWidget(self.viewerFrame)
self.viewerColor = qt.QLabel(self.viewerFrame)
self.viewerFrame.layout().addWidget(self.viewerColor)
self.viewInfo = qt.QLabel()
self.viewerFrame.layout().addWidget(self.viewInfo)
self.viewerFrame.layout().addStretch(1)
def _setFixedFontFamily(widget, family='Monospace'):
font = widget.font
font.setFamily(family)
widget.font = font
_setFixedFontFamily(self.viewInfo)
# the grid - things about the layers
# this method makes labels
self.layerGrid = qt.QFrame(self.frame)
layout = qt.QGridLayout()
self.layerGrid.setLayout(layout)
self.frame.layout().addWidget(self.layerGrid)
layers = ('L', 'F', 'B')
self.layerNames = {}
self.layerIJKs = {}
self.layerValues = {}
for (row, layer) in enumerate(layers):
col = 0
layout.addWidget(qt.QLabel(layer), row, col)
col += 1
self.layerNames[layer] = qt.QLabel()
layout.addWidget(self.layerNames[layer], row, col)
col += 1
self.layerIJKs[layer] = qt.QLabel()
layout.addWidget(self.layerIJKs[layer], row, col)
col += 1
self.layerValues[layer] = qt.QLabel()
layout.addWidget(self.layerValues[layer], row, col)
layout.setColumnStretch(col, 100)
_setFixedFontFamily(self.layerNames[layer])
_setFixedFontFamily(self.layerIJKs[layer])
_setFixedFontFamily(self.layerValues[layer])
# information collected about the current crosshair position
# from displayable managers registered to the current view
self.displayableManagerInfo = qt.QLabel()
self.displayableManagerInfo.indent = 6
self.displayableManagerInfo.wordWrap = True
self.frame.layout().addWidget(self.displayableManagerInfo)
# only show if not empty
self.displayableManagerInfo.hide()
# goto module button
self.goToModule = qt.QPushButton('->', self.frame)
self.goToModule.setToolTip(
'Go to the DataProbe module for more information and options')
self.frame.layout().addWidget(self.goToModule)
self.goToModule.connect("clicked()", self.onGoToModule)
# hide this for now - there's not much to see in the module itself
self.goToModule.hide()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.logic = ElastixLogic()
self.logic.logCallback = self.addLog
self.registrationInProgress = False
# Instantiate and connect widgets ...
# Parameter sets
defaultinputParametersCollapsibleButton = ctk.ctkCollapsibleButton()
defaultinputParametersCollapsibleButton.text = "Parameter set"
defaultinputParametersCollapsibleButton.collapsed = True
self.layout.addWidget(defaultinputParametersCollapsibleButton)
defaultParametersLayout = qt.QFormLayout(
defaultinputParametersCollapsibleButton)
self.parameterNodeSelector = slicer.qMRMLNodeComboBox()
self.parameterNodeSelector.nodeTypes = ["vtkMRMLScriptedModuleNode"]
self.parameterNodeSelector.addAttribute("vtkMRMLScriptedModuleNode",
"ModuleName", "Elastix")
self.parameterNodeSelector.selectNodeUponCreation = True
self.parameterNodeSelector.addEnabled = True
self.parameterNodeSelector.renameEnabled = True
self.parameterNodeSelector.removeEnabled = True
self.parameterNodeSelector.noneEnabled = False
self.parameterNodeSelector.showHidden = True
self.parameterNodeSelector.showChildNodeTypes = False
self.parameterNodeSelector.baseName = "General Registration (Elastix)"
self.parameterNodeSelector.setMRMLScene(slicer.mrmlScene)
self.parameterNodeSelector.setToolTip("Pick parameter set")
defaultParametersLayout.addRow("Parameter set: ",
self.parameterNodeSelector)
#
# Inputs
#
inputParametersCollapsibleButton = ctk.ctkCollapsibleButton()
inputParametersCollapsibleButton.text = "Inputs"
self.layout.addWidget(inputParametersCollapsibleButton)
# Layout within the dummy collapsible button
inputParametersFormLayout = qt.QFormLayout(
inputParametersCollapsibleButton)
#
# fixed volume selector
#
self.fixedVolumeSelector = slicer.qMRMLNodeComboBox()
self.fixedVolumeSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.fixedVolumeSelector.selectNodeUponCreation = True
self.fixedVolumeSelector.addEnabled = False
self.fixedVolumeSelector.removeEnabled = False
self.fixedVolumeSelector.noneEnabled = False
self.fixedVolumeSelector.showHidden = False
self.fixedVolumeSelector.showChildNodeTypes = False
self.fixedVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.fixedVolumeSelector.setToolTip(
"The moving volume will be transformed into this image space.")
inputParametersFormLayout.addRow("Fixed volume: ",
self.fixedVolumeSelector)
#
# moving volume selector
#
self.movingVolumeSelector = slicer.qMRMLNodeComboBox()
self.movingVolumeSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.movingVolumeSelector.selectNodeUponCreation = True
self.movingVolumeSelector.addEnabled = False
self.movingVolumeSelector.removeEnabled = False
self.movingVolumeSelector.noneEnabled = False
self.movingVolumeSelector.showHidden = False
self.movingVolumeSelector.showChildNodeTypes = False
self.movingVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.movingVolumeSelector.setToolTip(
"This volume will be transformed into the fixed image space")
inputParametersFormLayout.addRow("Moving volume: ",
self.movingVolumeSelector)
self.registrationPresetSelector = qt.QComboBox()
for preset in self.logic.getRegistrationPresets():
self.registrationPresetSelector.addItem("{0} ({1})".format(
preset[RegistrationPresets_Modality],
preset[RegistrationPresets_Content]))
inputParametersFormLayout.addRow("Preset: ",
self.registrationPresetSelector)
#
# Outputs
#
maskingParametersCollapsibleButton = ctk.ctkCollapsibleButton()
maskingParametersCollapsibleButton.text = "Masking"
maskingParametersCollapsibleButton.collapsed = True
self.layout.addWidget(maskingParametersCollapsibleButton)
# Layout within the dummy collapsible button
maskingParametersFormLayout = qt.QFormLayout(
maskingParametersCollapsibleButton)
#
# fixed volume mask selector
#
self.fixedVolumeMaskSelector = slicer.qMRMLNodeComboBox()
self.fixedVolumeMaskSelector.nodeTypes = ["vtkMRMLLabelMapVolumeNode"]
self.fixedVolumeMaskSelector.addEnabled = False
self.fixedVolumeMaskSelector.removeEnabled = False
self.fixedVolumeMaskSelector.noneEnabled = True
self.fixedVolumeMaskSelector.showHidden = False
self.fixedVolumeMaskSelector.showChildNodeTypes = False
self.fixedVolumeMaskSelector.setMRMLScene(slicer.mrmlScene)
self.fixedVolumeMaskSelector.setToolTip(
"Areas of the fixed volume where mask label is 0 will be ignored in the registration."
)
maskingParametersFormLayout.addRow("Fixed volume mask: ",
self.fixedVolumeMaskSelector)
#
# moving volume mask selector
#
self.movingVolumeMaskSelector = slicer.qMRMLNodeComboBox()
self.movingVolumeMaskSelector.nodeTypes = ["vtkMRMLLabelMapVolumeNode"]
self.movingVolumeMaskSelector.selectNodeUponCreation = True
self.movingVolumeMaskSelector.addEnabled = False
self.movingVolumeMaskSelector.removeEnabled = False
self.movingVolumeMaskSelector.noneEnabled = True
self.movingVolumeMaskSelector.showHidden = False
self.movingVolumeMaskSelector.showChildNodeTypes = False
self.movingVolumeMaskSelector.setMRMLScene(slicer.mrmlScene)
self.movingVolumeMaskSelector.setToolTip(
"Areas of the moving volume where mask label is 0 will be ignored in the registration"
)
maskingParametersFormLayout.addRow("Moving volume mask: ",
self.movingVolumeMaskSelector)
#
# Outputs
#
outputParametersCollapsibleButton = ctk.ctkCollapsibleButton()
outputParametersCollapsibleButton.text = "Outputs"
self.layout.addWidget(outputParametersCollapsibleButton)
# Layout within the dummy collapsible button
outputParametersFormLayout = qt.QFormLayout(
outputParametersCollapsibleButton)
#
# output volume selector
#
self.outputVolumeSelector = slicer.qMRMLNodeComboBox()
self.outputVolumeSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.outputVolumeSelector.selectNodeUponCreation = True
self.outputVolumeSelector.addEnabled = True
self.outputVolumeSelector.renameEnabled = True
self.outputVolumeSelector.removeEnabled = True
self.outputVolumeSelector.noneEnabled = True
self.outputVolumeSelector.showHidden = False
self.outputVolumeSelector.showChildNodeTypes = False
self.outputVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.outputVolumeSelector.setToolTip(
"(optional) The moving image warped to the fixed image space. NOTE: You must set at least one output object (transform and/or output volume)"
)
outputParametersFormLayout.addRow("Output volume: ",
self.outputVolumeSelector)
#
# output transform selector
#
self.outputTransformSelector = slicer.qMRMLNodeComboBox()
self.outputTransformSelector.nodeTypes = ["vtkMRMLTransformNode"]
self.outputTransformSelector.selectNodeUponCreation = True
self.outputTransformSelector.addEnabled = True
self.outputTransformSelector.renameEnabled = True
self.outputTransformSelector.removeEnabled = True
self.outputTransformSelector.noneEnabled = True
self.outputTransformSelector.showHidden = False
self.outputTransformSelector.showChildNodeTypes = False
self.outputTransformSelector.setMRMLScene(slicer.mrmlScene)
self.outputTransformSelector.setToolTip(
"(optional) Computed displacement field that transform nodes from moving volume space to fixed volume space. NOTE: You must set at least one output object (transform and/or output volume)."
)
outputParametersFormLayout.addRow("Output transform: ",
self.outputTransformSelector)
#
# Advanced area
#
self.advancedCollapsibleButton = ctk.ctkCollapsibleButton()
self.advancedCollapsibleButton.text = "Advanced"
self.advancedCollapsibleButton.collapsed = True
self.layout.addWidget(self.advancedCollapsibleButton)
advancedFormLayout = qt.QFormLayout(self.advancedCollapsibleButton)
self.showDetailedLogDuringExecutionCheckBox = qt.QCheckBox(" ")
self.showDetailedLogDuringExecutionCheckBox.checked = False
self.showDetailedLogDuringExecutionCheckBox.setToolTip(
"Show detailed log during registration.")
advancedFormLayout.addRow("Show detailed log during registration:",
self.showDetailedLogDuringExecutionCheckBox)
self.keepTemporaryFilesCheckBox = qt.QCheckBox(" ")
self.keepTemporaryFilesCheckBox.checked = False
self.keepTemporaryFilesCheckBox.setToolTip(
"Keep temporary files (inputs, computed outputs, logs) after the registration is completed."
)
self.showTemporaryFilesFolderButton = qt.QPushButton(
"Show temp folder")
self.showTemporaryFilesFolderButton.toolTip = "Open the folder where temporary files are stored."
self.showTemporaryFilesFolderButton.setSizePolicy(
qt.QSizePolicy.MinimumExpanding, qt.QSizePolicy.Preferred)
hbox = qt.QHBoxLayout()
hbox.addWidget(self.keepTemporaryFilesCheckBox)
hbox.addWidget(self.showTemporaryFilesFolderButton)
advancedFormLayout.addRow("Keep temporary files:", hbox)
self.showRegistrationParametersDatabaseFolderButton = qt.QPushButton(
"Show database folder")
self.showRegistrationParametersDatabaseFolderButton.toolTip = "Open the folder where temporary files are stored."
self.showRegistrationParametersDatabaseFolderButton.setSizePolicy(
qt.QSizePolicy.MinimumExpanding, qt.QSizePolicy.Preferred)
advancedFormLayout.addRow(
"Registration presets:",
self.showRegistrationParametersDatabaseFolderButton)
customElastixBinDir = self.logic.getCustomElastixBinDir()
self.customElastixBinDirSelector = ctk.ctkPathLineEdit()
self.customElastixBinDirSelector.filters = ctk.ctkPathLineEdit.Dirs
self.customElastixBinDirSelector.setCurrentPath(customElastixBinDir)
self.customElastixBinDirSelector.setSizePolicy(
qt.QSizePolicy.MinimumExpanding, qt.QSizePolicy.Preferred)
self.customElastixBinDirSelector.setToolTip(
"Set bin directory of an Elastix installation (where elastix executable is located). "
"If value is empty then default elastix (bundled with SlicerElastix extension) will be used."
)
advancedFormLayout.addRow("Custom Elastix toolbox location:",
self.customElastixBinDirSelector)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = False
self.layout.addWidget(self.applyButton)
self.statusLabel = qt.QPlainTextEdit()
self.statusLabel.setTextInteractionFlags(qt.Qt.TextSelectableByMouse)
self.statusLabel.setCenterOnScroll(True)
self.layout.addWidget(self.statusLabel)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.showTemporaryFilesFolderButton.connect(
'clicked(bool)', self.onShowTemporaryFilesFolder)
self.showRegistrationParametersDatabaseFolderButton.connect(
'clicked(bool)', self.onShowRegistrationParametersDatabaseFolder)
self.fixedVolumeSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
self.movingVolumeSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
self.outputVolumeSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
self.outputTransformSelector.connect(
"currentNodeChanged(vtkMRMLNode*)", self.onSelect)
# Immediately update deleteTemporaryFiles in the logic to make it possible to decide to
# keep the temporary file while the registration is running
self.keepTemporaryFilesCheckBox.connect(
"toggled(bool)", self.onKeepTemporaryFilesToggled)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onSelect()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# File area
#
filesCollapsibleButton = ctk.ctkCollapsibleButton()
filesCollapsibleButton.text = "Input files"
filesCollapsibleButton.collapsed = False
self.layout.addWidget(filesCollapsibleButton)
# Layout within the files collapsible button
filesFormLayout = qt.QFormLayout(filesCollapsibleButton)
# select one file
buttonLayout = qt.QHBoxLayout()
self.archetypeText = qt.QLineEdit()
buttonLayout.addWidget(self.archetypeText)
self.addFromArchetype = qt.QPushButton("Browse...")
buttonLayout.addWidget(self.addFromArchetype)
self.archetypeStartNumber = 0
filesFormLayout.addRow("Filename pattern: ", buttonLayout)
# file list group
fileListGroupBox = ctk.ctkCollapsibleGroupBox()
fileListGroupBox.title = "File list"
fileListLayout = qt.QVBoxLayout()
fileListGroupBox.setLayout(fileListLayout)
filesFormLayout.addRow("", fileListGroupBox)
self.addByBrowsingButton = qt.QPushButton("Select files...")
fileListLayout.addWidget(self.addByBrowsingButton)
self.fileTable = qt.QTextBrowser()
fileListLayout.addWidget(self.fileTable)
fileListGroupBox.collapsed = True
# original volume size
self.originalVolumeSizeLabel = qt.QLabel()
filesFormLayout.addRow("Size: ", self.originalVolumeSizeLabel)
# reverse slice order
self.reverseCheckBox = qt.QCheckBox()
self.reverseCheckBox.toolTip = "Read the images in reverse order (flips loaded volume along IS axis)"
filesFormLayout.addRow("Reverse: ", self.reverseCheckBox)
# original spacing
self.spacingWidget = slicer.qMRMLCoordinatesWidget()
self.spacingWidget.setMRMLScene(slicer.mrmlScene)
self.spacingWidget.decimalsOption = ctk.ctkDoubleSpinBox.DecimalsByKey | ctk.ctkDoubleSpinBox.DecimalsByShortcuts | ctk.ctkDoubleSpinBox.DecimalsByValue
self.spacingWidget.minimum = 0.0
self.spacingWidget.maximum = 1000000000.0
self.spacingWidget.quantity = "length"
self.spacingWidget.unitAwareProperties = slicer.qMRMLCoordinatesWidget.Precision | slicer.qMRMLCoordinatesWidget.Prefix | slicer.qMRMLCoordinatesWidget.Scaling | slicer.qMRMLCoordinatesWidget.Suffix
self.spacingWidget.coordinates = "1,1,1"
self.spacingWidget.toolTip = "Set the colunm, row, slice spacing; original spacing not including downsample"
filesFormLayout.addRow("Spacing: ", self.spacingWidget)
#
# 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", "vtkMRMLVectorVolumeNode"
]
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.noneDisplay = "(Create new volume)"
self.outputSelector.setMRMLScene(slicer.mrmlScene)
self.outputSelector.setToolTip(
"Pick the output volume to populate or None to autogenerate.")
outputFormLayout.addRow("Output Volume: ", self.outputSelector)
#
# output ROI selector
#
self.outputROISelector = slicer.qMRMLNodeComboBox()
self.outputROISelector.nodeTypes = [
"vtkMRMLAnnotationROINode", "vtkMRMLMarkupsROINode"
]
self.outputROISelector.showChildNodeTypes = False
self.outputROISelector.showHidden = False
self.outputROISelector.showChildNodeTypes = False
self.outputROISelector.noneEnabled = True
self.outputROISelector.removeEnabled = True
self.outputROISelector.renameEnabled = True
self.outputROISelector.addEnabled = False
self.outputROISelector.noneDisplay = "(Full volume)"
self.outputROISelector.setMRMLScene(slicer.mrmlScene)
self.outputROISelector.setToolTip(
"Set the region of the volume that will be loaded")
outputFormLayout.addRow("Region of interest: ", self.outputROISelector)
#
# Quality selector
#
qualityLayout = qt.QVBoxLayout()
self.qualityPreviewRadioButton = qt.QRadioButton("preview")
self.qualityHalfRadioButton = qt.QRadioButton("half resolution")
self.qualityFullRadioButton = qt.QRadioButton("full resolution")
qualityLayout.addWidget(self.qualityPreviewRadioButton)
qualityLayout.addWidget(self.qualityHalfRadioButton)
qualityLayout.addWidget(self.qualityFullRadioButton)
self.qualityPreviewRadioButton.setChecked(True)
outputFormLayout.addRow("Quality: ", qualityLayout)
self.sliceSkipSpinBox = qt.QSpinBox()
self.sliceSkipSpinBox.toolTip = "Skips the selected number of slices between each pair of output volume slices (use, for example, on long thin samples with more slices than in-plane resolution)"
outputFormLayout.addRow("Slice skip: ", self.sliceSkipSpinBox)
# Force grayscale output
self.grayscaleCheckBox = qt.QCheckBox()
self.grayscaleCheckBox.toolTip = "Force reading the image in grayscale. Only makes a difference if the input has color (RGB or RGBA) voxels."
self.grayscaleCheckBox.checked = True
outputFormLayout.addRow("Grayscale: ", self.grayscaleCheckBox)
# output volume size
self.outputVolumeSizeLabel = qt.QLabel()
outputFormLayout.addRow("Output size: ", self.outputVolumeSizeLabel)
# output volume spacing
self.outputSpacingWidget = slicer.qMRMLCoordinatesWidget()
self.outputSpacingWidget.setMRMLScene(slicer.mrmlScene)
self.outputSpacingWidget.readOnly = True
self.outputSpacingWidget.frame = False
self.outputSpacingWidget.decimalsOption = ctk.ctkDoubleSpinBox.DecimalsByKey | ctk.ctkDoubleSpinBox.DecimalsByShortcuts | ctk.ctkDoubleSpinBox.DecimalsByValue
self.outputSpacingWidget.minimum = 0.0
self.outputSpacingWidget.maximum = 1000000000.0
self.outputSpacingWidget.quantity = "length"
self.outputSpacingWidget.unitAwareProperties = slicer.qMRMLCoordinatesWidget.Precision | slicer.qMRMLCoordinatesWidget.Prefix | slicer.qMRMLCoordinatesWidget.Scaling | slicer.qMRMLCoordinatesWidget.Suffix
self.outputSpacingWidget.coordinates = "1,1,1"
self.outputSpacingWidget.toolTip = "Slice spacing of the volume that will be loaded"
outputFormLayout.addRow("Output spacing: ", self.outputSpacingWidget)
self.loadButton = qt.QPushButton("Load files")
self.loadButton.toolTip = "Load files as a 3D volume"
self.loadButton.enabled = False
outputFormLayout.addRow(self.loadButton)
# connections
self.reverseCheckBox.connect('toggled(bool)',
self.updateLogicFromWidget)
self.sliceSkipSpinBox.connect("valueChanged(int)",
self.updateLogicFromWidget)
self.spacingWidget.connect("coordinatesChanged(double*)",
self.updateLogicFromWidget)
self.qualityPreviewRadioButton.connect(
"toggled(bool)",
lambda toggled, widget=self.qualityPreviewRadioButton: self.
onQualityToggled(toggled, widget))
self.qualityHalfRadioButton.connect(
"toggled(bool)",
lambda toggled, widget=self.qualityHalfRadioButton: self.
onQualityToggled(toggled, widget))
self.qualityFullRadioButton.connect(
"toggled(bool)",
lambda toggled, widget=self.qualityFullRadioButton: self.
onQualityToggled(toggled, widget))
self.grayscaleCheckBox.connect('toggled(bool)',
self.updateLogicFromWidget)
self.outputROISelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.setOutputROINode)
self.addByBrowsingButton.connect('clicked()', self.addByBrowsing)
self.addFromArchetype.connect('clicked()', self.selectArchetype)
self.archetypeText.connect('textChanged(const QString &)',
self.populateFromArchetype)
self.loadButton.connect('clicked()', self.onLoadButton)
# Add vertical spacer
self.layout.addStretch(1)
self.loadButton.enabled = False
def __init__(self, logic):
super(VisualizationWidget, self).__init__()
self.rockCount = 0
self.rocking = False
self.rockTimer = None
self.flickerTimer = None
self.logic = logic
self.revealCursor = None
self.volumes = (
"Fixed",
"Moving",
"Transformed",
)
self.layoutOptions = (
"Axial",
"Coronal",
"Sagittal",
"Axi/Sag/Cor",
)
self.layoutOption = 'Axi/Sag/Cor'
self.volumeDisplayCheckboxes = {}
# mimic the structure of the LandmarksWidget for visual
# consistency (it needs sub widget so it can delete and refresh the internals)
self.widget = qt.QWidget()
self.layout = qt.QFormLayout(self.widget)
self.boxHolder = qt.QWidget()
self.boxHolder.setLayout(qt.QVBoxLayout())
self.layout.addRow(self.boxHolder)
self.groupBox = qt.QGroupBox("Visualization")
self.groupBoxLayout = qt.QFormLayout(self.groupBox)
self.boxHolder.layout().addWidget(self.groupBox)
#
# layout selection
#
layoutHolder = qt.QWidget()
layout = qt.QHBoxLayout()
layoutHolder.setLayout(layout)
for layoutOption in self.layoutOptions:
layoutButton = qt.QPushButton(layoutOption)
layoutButton.connect('clicked()',
lambda lo=layoutOption: self.selectLayout(lo))
layout.addWidget(layoutButton)
self.groupBoxLayout.addRow("Layout", layoutHolder)
#
# Volume display selection
#
checkboxHolder = qt.QWidget()
layout = qt.QHBoxLayout()
checkboxHolder.setLayout(layout)
for volume in self.volumes:
checkBox = qt.QCheckBox()
checkBox.text = volume
checkBox.checked = True
checkBox.connect('toggled(bool)', self.updateVisualization)
layout.addWidget(checkBox)
self.volumeDisplayCheckboxes[volume] = checkBox
checkBox = qt.QCheckBox()
checkBox.text = "RevealCursor"
checkBox.checked = False
checkBox.connect('toggled(bool)', self.revealToggled)
layout.addWidget(checkBox)
self.groupBoxLayout.addRow("Display", checkboxHolder)
#
# fade slider
#
fadeHolder = qt.QWidget()
fadeLayout = qt.QHBoxLayout()
fadeHolder.setLayout(fadeLayout)
self.fadeSlider = ctk.ctkSliderWidget()
self.fadeSlider.minimum = 0
self.fadeSlider.maximum = 1.0
self.fadeSlider.value = 0.5
self.fadeSlider.singleStep = 0.05
self.fadeSlider.connect('valueChanged(double)', self.onFadeChanged)
fadeLayout.addWidget(self.fadeSlider)
#
# Rock and Flicker
#
animaHolder = qt.QWidget()
animaLayout = qt.QVBoxLayout()
animaHolder.setLayout(animaLayout)
fadeLayout.addWidget(animaHolder)
# Rock
checkBox = qt.QCheckBox()
checkBox.text = "Rock"
checkBox.checked = False
checkBox.connect('toggled(bool)', self.onRockToggled)
animaLayout.addWidget(checkBox)
# Flicker
checkBox = qt.QCheckBox()
checkBox.text = "Flicker"
checkBox.checked = False
checkBox.connect('toggled(bool)', self.onFlickerToggled)
animaLayout.addWidget(checkBox)
self.groupBoxLayout.addRow("Fade", fadeHolder)
#
# zoom control
#
zoomHolder = qt.QWidget()
layout = qt.QHBoxLayout()
zoomHolder.setLayout(layout)
zooms = {
"+": 0.7,
"-": 1.3,
"Fit": "Fit",
}
for zoomLabel, zoomFactor in zooms.items():
zoomButton = qt.QPushButton(zoomLabel)
zoomButton.connect('clicked()',
lambda zf=zoomFactor: self.onZoom(zf))
layout.addWidget(zoomButton)
self.groupBoxLayout.addRow("Zoom", zoomHolder)
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)
# Instantiate and connect widgets ...
#
# input warp selector
#
inputFrame = qt.QFrame()
inputFrame.setLayout(qt.QHBoxLayout())
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = ["vtkMRMLGridTransformNode"]
self.inputSelector.selectNodeUponCreation = False
self.inputSelector.addEnabled = True
self.inputSelector.removeEnabled = False
self.inputSelector.noneEnabled = True
self.inputSelector.showHidden = False
self.inputSelector.showChildNodeTypes = False
self.inputSelector.setMRMLScene(slicer.mrmlScene)
self.inputSelector.setToolTip("Pick the input to the algorithm.")
inputFrame.layout().addWidget(qt.QLabel('Input Transform: '))
inputFrame.layout().addWidget(self.inputSelector)
self.layout.addWidget(inputFrame)
#
# Grid reference
#
emptyTransformCollapsibleButton = ctk.ctkCollapsibleButton()
emptyTransformCollapsibleButton.text = "Grid Reference"
self.layout.addWidget(emptyTransformCollapsibleButton)
# Layout within the dummy collapsible button
emptyTransformFormLayout = qt.QFormLayout(
emptyTransformCollapsibleButton)
self.transformSizeSelect = ctk.ctkCoordinatesWidget()
self.transformSizeSelect.coordinates = '193,229,193'
self.transformSizeSelect.setDecimals(0)
emptyTransformFormLayout.addRow("Size", self.transformSizeSelect)
self.transformOriginSelect = ctk.ctkCoordinatesWidget()
self.transformOriginSelect.coordinates = '-96.0, -132.0, -78.0'
emptyTransformFormLayout.addRow("Origin", self.transformOriginSelect)
self.transformSpacingSelect = ctk.ctkCoordinatesWidget()
self.transformSpacingSelect.coordinates = '1.0, 1.0, 1.0'
emptyTransformFormLayout.addRow("Spacing", self.transformSpacingSelect)
#
# Operations
#
operationsCollapsibleButton = ctk.ctkCollapsibleButton()
operationsCollapsibleButton.text = "Operations"
self.layout.addWidget(operationsCollapsibleButton)
# Layout within the dummy collapsible button
operationsFormLayout = qt.QFormLayout(operationsCollapsibleButton)
# Empty Button
self.emptyButton = qt.QPushButton("Empty Transform")
self.emptyButton.enabled = False
operationsFormLayout.addRow(self.emptyButton)
# Flatten Button & opts
flattenFrame = qt.QFrame()
flattenFrame.setLayout(qt.QHBoxLayout())
self.includeFirstLayerCB = qt.QCheckBox('Include First Layer')
self.includeFirstLayerCB.toolTip = "If selected all the layers of the composite transform will be flattened taking the first grid as reference. If not, the layers starting from the second one will be flattened and append to the first one. In this case the reference grid is used to flatten the transform"
flattenFrame.layout().addWidget(self.includeFirstLayerCB)
self.flattenButton = qt.QPushButton("Flatten Transform")
self.flattenButton.enabled = False
flattenFrame.layout().addWidget(self.flattenButton, 2)
operationsFormLayout.addRow(flattenFrame)
# Remove last layer
self.removeLastLayerButton = qt.QPushButton("Remove Last Layer")
self.removeLastLayerButton.enabled = False
operationsFormLayout.addRow(self.removeLastLayerButton)
# connections
self.emptyButton.connect('clicked(bool)', self.onEmptyButton)
self.flattenButton.connect('clicked(bool)', self.onFlattenButton)
self.removeLastLayerButton.connect('clicked(bool)',
self.onRemoveLastLayerButton)
self.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onSelect()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Connection
connectionCollapsibleButton = ctk.ctkCollapsibleButton()
connectionCollapsibleButton.text = "OSC server connection"
self.layout.addWidget(connectionCollapsibleButton)
connectionFormLayout = qt.QFormLayout(connectionCollapsibleButton)
self.hostnameLineEdit = qt.QLineEdit("localhost")
connectionFormLayout.addRow("Host name: ", self.hostnameLineEdit)
self.portLineEdit = qt.QLineEdit("7400")
self.portLineEdit.setValidator(
qt.QIntValidator(0, 65535, self.portLineEdit))
connectionFormLayout.addRow("Port: ", self.portLineEdit)
self.addressRootLineEdit = qt.QLineEdit("SoundNav")
self.addressRootLineEdit.setToolTip(
"OSC address root. Complete address: /<address root>/<instrument name>/<parameter name>."
)
connectionFormLayout.addRow("Address root: ", self.addressRootLineEdit)
self.enableConnectionCheckBox = qt.QCheckBox()
self.enableConnectionCheckBox.checked = False
self.enableConnectionCheckBox.setToolTip(
"If checked, then transform changes will be immediately sent to specified OSC server."
)
connectionFormLayout.addRow("Transmission active: ",
self.enableConnectionCheckBox)
self.enableConnectionCheckBox.connect('stateChanged(int)',
self.setTransmissionActive)
# Parameters Area
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
parameterNode = self.logic.getParameterNode()
maxNumberOfInstruments = int(
parameterNode.GetParameter("MaxNumberOfInstruments"))
for instrumentIndex in range(maxNumberOfInstruments):
instrumentGroupBox = ctk.ctkCollapsibleGroupBox()
instrumentGroupBox.title = "Instrument " + str(instrumentIndex + 1)
parametersFormLayout.addWidget(instrumentGroupBox)
instrumentLayout = qt.QFormLayout(instrumentGroupBox)
nameLineEdit = qt.QLineEdit()
instrumentLayout.addRow("Instrument name: ", nameLineEdit)
nameLineEdit.connect('editingFinished()', self.updateMRMLFromGUI)
instrumentSourceSelector = slicer.qMRMLNodeComboBox()
instrumentNodeTypes = ["vtkMRMLLinearTransformNode"]
if hasattr(slicer.modules, 'breachwarning'):
instrumentNodeTypes.append("vtkMRMLBreachWarningNode")
instrumentSourceSelector.nodeTypes = instrumentNodeTypes
instrumentSourceSelector.addEnabled = True
instrumentSourceSelector.removeEnabled = True
instrumentSourceSelector.noneEnabled = True
instrumentSourceSelector.renameEnabled = True
instrumentSourceSelector.setMRMLScene(slicer.mrmlScene)
instrumentSourceSelector.setToolTip(
"Defines position and orientation of the instrument (transform or breach warning node)"
)
instrumentLayout.addRow("Instrument node: ",
instrumentSourceSelector)
instrumentSourceSelector.connect(
"currentNodeChanged(vtkMRMLNode*)", self.updateMRMLFromGUI)
instrumentReferenceSelector = slicer.qMRMLNodeComboBox()
instrumentReferenceSelector.nodeTypes = [
"vtkMRMLLinearTransformNode"
]
instrumentReferenceSelector.addEnabled = True
instrumentReferenceSelector.removeEnabled = True
instrumentReferenceSelector.noneEnabled = True
instrumentReferenceSelector.renameEnabled = True
instrumentReferenceSelector.setMRMLScene(slicer.mrmlScene)
instrumentReferenceSelector.setToolTip(
"Position and orientation is defined relative to this transform"
)
instrumentLayout.addRow("Reference transform: ",
instrumentReferenceSelector)
instrumentReferenceSelector.connect(
"currentNodeChanged(vtkMRMLNode*)", self.updateMRMLFromGUI)
widgets = {}
widgets['instrumentGroupBox'] = instrumentGroupBox
widgets['nameLineEdit'] = nameLineEdit
widgets['instrumentSourceSelector'] = instrumentSourceSelector
widgets[
'instrumentReferenceSelector'] = instrumentReferenceSelector
self.instrumentWidgets.append(widgets)
self.updateGUIFromMRML()
self.hostnameLineEdit.connect('editingFinished()',
self.updateMRMLFromGUI)
self.portLineEdit.connect('editingFinished()', self.updateMRMLFromGUI)
self.addressRootLineEdit.connect('editingFinished()',
self.updateMRMLFromGUI)
for instrumentIndex in range(len(self.instrumentWidgets)):
widgets = self.instrumentWidgets[instrumentIndex]
# Collapse unused instrument groupboxes
widgets['instrumentGroupBox'].collapsed = not widgets[
'nameLineEdit'].text
# Observe widget changes to update MRML node immediately (this way always up-to-date values will be saved in the scene)
widgets['nameLineEdit'].connect('editingFinished()',
self.updateMRMLFromGUI)
widgets['instrumentSourceSelector'].connect(
"currentNodeChanged(vtkMRMLNode*)", self.updateMRMLFromGUI)
widgets['instrumentReferenceSelector'].connect(
"currentNodeChanged(vtkMRMLNode*)", self.updateMRMLFromGUI)
self.parameterNodeObserverTag = parameterNode.AddObserver(
vtk.vtkCommand.ModifiedEvent, self.updateGUIFromMRML)
# Add vertical spacer
self.layout.addStretch(1)
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 = "NeurosurgicalPlanningTutorialTractographySelfTest 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)
#
# 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)
#
# scale factor for screen shots
#
self.screenshotScaleFactorSliderWidget = ctk.ctkSliderWidget()
self.screenshotScaleFactorSliderWidget.singleStep = 1.0
self.screenshotScaleFactorSliderWidget.minimum = 1.0
self.screenshotScaleFactorSliderWidget.maximum = 50.0
self.screenshotScaleFactorSliderWidget.value = 1.0
self.screenshotScaleFactorSliderWidget.setToolTip(
"Set scale factor for the screen shots.")
parametersFormLayout.addRow("Screenshot scale factor",
self.screenshotScaleFactorSliderWidget)
# Apply Button
#
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Run the algorithm."
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)
# 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):
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 selector
#
# File dialog to select a file template for series
self.inputFileSelector = ctk.ctkPathLineEdit()
self.inputFileSelector.filters = ctk.ctkPathLineEdit().Files
self.inputFileSelector.setToolTip(
"Select log file from a directory of images.")
parametersFormLayout.addRow("Select log file from image series:",
self.inputFileSelector)
#
# 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.renameEnabled = True
# self.outputSelector.setMRMLScene( slicer.mrmlScene )
# self.outputSelector.setToolTip( "Pick the output to the algorithm." )
# parametersFormLayout.addRow("Output Volume: ", self.outputSelector)
#
# 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.outputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.inputFileSelector.connect("currentPathChanged(const QString &)",
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 ...
inputModelSelectorFrame = qt.QFrame(self.parent)
inputModelSelectorFrame.setLayout(qt.QHBoxLayout())
self.parent.layout().addWidget(inputModelSelectorFrame)
inputModelSelectorLabel = qt.QLabel("Input Model: ",
inputModelSelectorFrame)
inputModelSelectorLabel.setToolTip("Select the input model")
inputModelSelectorFrame.layout().addWidget(inputModelSelectorLabel)
inputModelSelector = slicer.qMRMLNodeComboBox(inputModelSelectorFrame)
inputModelSelector.nodeTypes = ["vtkMRMLModelNode"]
inputModelSelector.selectNodeUponCreation = False
inputModelSelector.addEnabled = False
inputModelSelector.removeEnabled = False
inputModelSelector.noneEnabled = True
inputModelSelector.showHidden = False
inputModelSelector.showChildNodeTypes = False
inputModelSelector.setMRMLScene(slicer.mrmlScene)
inputModelSelectorFrame.layout().addWidget(inputModelSelector)
outputModelSelectorFrame = qt.QFrame(self.parent)
outputModelSelectorFrame.setLayout(qt.QHBoxLayout())
self.parent.layout().addWidget(outputModelSelectorFrame)
outputModelSelectorLabel = qt.QLabel("Output Model: ",
outputModelSelectorFrame)
outputModelSelectorLabel.setToolTip("Select the output model")
outputModelSelectorFrame.layout().addWidget(outputModelSelectorLabel)
outputModelSelector = slicer.qMRMLNodeComboBox(
outputModelSelectorFrame)
outputModelSelector.nodeTypes = ["vtkMRMLModelNode"]
outputModelSelector.selectNodeUponCreation = False
outputModelSelector.addEnabled = True
outputModelSelector.renameEnabled = True
outputModelSelector.removeEnabled = True
outputModelSelector.noneEnabled = True
outputModelSelector.showHidden = False
outputModelSelector.showChildNodeTypes = False
outputModelSelector.baseName = "Model"
outputModelSelector.selectNodeUponCreation = True
outputModelSelector.setMRMLScene(slicer.mrmlScene)
outputModelSelectorFrame.layout().addWidget(outputModelSelector)
decimationButton = qt.QPushButton("Decimation")
decimationButton.checkable = True
self.layout.addWidget(decimationButton)
decimationFrame = qt.QFrame(self.parent)
self.layout.addWidget(decimationFrame)
decimationFormLayout = qt.QFormLayout(decimationFrame)
reductionFrame, reductionSlider, reductionSpinBox = numericInputFrame(
self.parent, "Reduction:", "Tooltip", 0.0, 1.0, 0.05, 2)
decimationFormLayout.addWidget(reductionFrame)
boundaryDeletionCheckBox = qt.QCheckBox("Boundary deletion")
decimationFormLayout.addWidget(boundaryDeletionCheckBox)
smoothingButton = qt.QPushButton("Smoothing")
smoothingButton.checkable = True
self.layout.addWidget(smoothingButton)
smoothingFrame = qt.QFrame(self.parent)
self.layout.addWidget(smoothingFrame)
smoothingFormLayout = qt.QFormLayout(smoothingFrame)
smoothingMethodCombo = qt.QComboBox(smoothingFrame)
smoothingMethodCombo.addItem("Laplace")
smoothingMethodCombo.addItem("Taubin")
smoothingFormLayout.addWidget(smoothingMethodCombo)
laplaceMethodFrame = qt.QFrame(self.parent)
smoothingFormLayout.addWidget(laplaceMethodFrame)
laplaceMethodFormLayout = qt.QFormLayout(laplaceMethodFrame)
laplaceIterationsFrame, laplaceIterationsSlider, laplaceIterationsSpinBox = numericInputFrame(
self.parent, "Iterations:",
"Determines the maximum number of smoothing iterations. Higher value allows more smoothing."
+
" In general, small relaxation factors and large numbers of iterations are more stable than"
+ " larger relaxation factors and smaller numbers of iterations. ",
0.0, 500.0, 1.0, 0)
laplaceMethodFormLayout.addWidget(laplaceIterationsFrame)
laplaceRelaxationFrame, laplaceRelaxationSlider, laplaceRelaxationSpinBox = numericInputFrame(
self.parent, "Relaxation:",
"Specifies how much points may be displaced during each iteration. Higher value results in more smoothing.",
0.0, 1.0, 0.1, 1)
laplaceMethodFormLayout.addWidget(laplaceRelaxationFrame)
taubinMethodFrame = qt.QFrame(self.parent)
smoothingFormLayout.addWidget(taubinMethodFrame)
taubinMethodFormLayout = qt.QFormLayout(taubinMethodFrame)
taubinIterationsFrame, taubinIterationsSlider, taubinIterationsSpinBox = numericInputFrame(
self.parent, "Iterations:",
"Determines the maximum number of smoothing iterations. Higher value allows more accurate smoothing."
+ " Typically 10-20 iterations are enough.", 0.0, 100.0, 1.0, 0)
taubinMethodFormLayout.addWidget(taubinIterationsFrame)
taubinPassBandFrame, taubinPassBandSlider, taubinPassBandSpinBox = numericInputFrame(
self.parent, "Pass Band:",
"Number between 0 and 2. Lower values produce more smoothing.",
0.0, 2.0, 0.0001, 4)
taubinMethodFormLayout.addWidget(taubinPassBandFrame)
boundarySmoothingCheckBox = qt.QCheckBox("Boundary Smoothing")
smoothingFormLayout.addWidget(boundarySmoothingCheckBox)
normalsButton = qt.QPushButton("Normals")
normalsButton.checkable = True
self.layout.addWidget(normalsButton)
normalsFrame = qt.QFrame(self.parent)
self.layout.addWidget(normalsFrame)
normalsFormLayout = qt.QFormLayout(normalsFrame)
autoOrientNormalsCheckBox = qt.QCheckBox("Auto-orient Normals")
autoOrientNormalsCheckBox.setToolTip(
"Orient the normals outwards from closed surface")
normalsFormLayout.addWidget(autoOrientNormalsCheckBox)
flipNormalsCheckBox = qt.QCheckBox("Flip Normals")
flipNormalsCheckBox.setToolTip(
"Flip normal direction from its current or auto-oriented state")
normalsFormLayout.addWidget(flipNormalsCheckBox)
splittingCheckBox = qt.QCheckBox("Splitting")
normalsFormLayout.addWidget(splittingCheckBox)
featureAngleFrame, featureAngleSlider, featureAngleSpinBox = numericInputFrame(
self.parent, "Feature Angle:", "Tooltip", 0.0, 180.0, 1.0, 0)
normalsFormLayout.addWidget(featureAngleFrame)
mirrorButton = qt.QPushButton("Mirror")
mirrorButton.checkable = True
self.layout.addWidget(mirrorButton)
mirrorFrame = qt.QFrame(self.parent)
self.layout.addWidget(mirrorFrame)
mirrorFormLayout = qt.QFormLayout(mirrorFrame)
mirrorXCheckBox = qt.QCheckBox("X-axis")
mirrorXCheckBox.setToolTip("Flip model along its X axis")
mirrorFormLayout.addWidget(mirrorXCheckBox)
mirrorYCheckBox = qt.QCheckBox("Y-axis")
mirrorYCheckBox.setToolTip("Flip model along its Y axis")
mirrorFormLayout.addWidget(mirrorYCheckBox)
mirrorZCheckBox = qt.QCheckBox("Z-axis")
mirrorZCheckBox.setToolTip("Flip model along its Z axis")
mirrorFormLayout.addWidget(mirrorZCheckBox)
cleanerButton = qt.QPushButton("Cleaner")
cleanerButton.checkable = True
self.layout.addWidget(cleanerButton)
connectivityButton = qt.QPushButton("Connectivity")
connectivityButton.checkable = True
self.layout.addWidget(connectivityButton)
#connectivityFrame = qt.QFrame(self.parent)
#self.layout.addWidget(connectivityFrame)
#connectivityFormLayout = qt.QFormLayout(connectivityFrame)
# TODO: connectivity could be
# - largest connected
# - threshold connected (discard below point count)
# - pick a region interactively
# - turn a multiple connected surface into a model hierarchy
buttonFrame = qt.QFrame(self.parent)
buttonFrame.setLayout(qt.QHBoxLayout())
self.layout.addWidget(buttonFrame)
toggleModelsButton = qt.QPushButton("Toggle Models")
toggleModelsButton.toolTip = "Show original model."
buttonFrame.layout().addWidget(toggleModelsButton)
applyButton = qt.QPushButton("Apply")
applyButton.toolTip = "Filter surface."
buttonFrame.layout().addWidget(applyButton)
self.layout.addStretch(1)
class state(object):
inputModelNode = None
outputModelNode = None
decimation = False
reduction = 0.8
boundaryDeletion = False
smoothing = False
smoothingMethod = "Laplace"
laplaceIterations = 100.0
laplaceRelaxation = 0.5
taubinIterations = 30.0
taubinPassBand = 0.1
boundarySmoothing = True
normals = False
flipNormals = False
autoOrientNormals = False
mirror = False
mirrorX = False
mirrorY = False
mirrorZ = False
splitting = False
featureAngle = 30.0
cleaner = False
connectivity = False
scope_locals = locals()
def connect(obj, evt, cmd):
def callback(*args):
current_locals = scope_locals.copy()
current_locals.update({'args': args})
exec cmd in globals(), current_locals
updateGUI()
obj.connect(evt, callback)
def updateGUI():
def button_stylesheet(active):
if active:
return "background-color: green"
else:
return ""
decimationButton.checked = state.decimation
#decimationButton.setStyleSheet(button_stylesheet(state.decimation))
decimationFrame.visible = state.decimation
boundaryDeletionCheckBox.checked = state.boundaryDeletion
reductionSlider.value = state.reduction
reductionSpinBox.value = state.reduction
smoothingButton.checked = state.smoothing
smoothingFrame.visible = state.smoothing
laplaceMethodFrame.visible = state.smoothingMethod == "Laplace"
laplaceIterationsSlider.value = state.laplaceIterations
laplaceIterationsSpinBox.value = state.laplaceIterations
laplaceRelaxationSlider.value = state.laplaceRelaxation
laplaceRelaxationSpinBox.value = state.laplaceRelaxation
taubinMethodFrame.visible = state.smoothingMethod == "Taubin"
taubinIterationsSlider.value = state.taubinIterations
taubinIterationsSpinBox.value = state.taubinIterations
taubinPassBandSlider.value = state.taubinPassBand
taubinPassBandSpinBox.value = state.taubinPassBand
boundarySmoothingCheckBox.checked = state.boundarySmoothing
normalsButton.checked = state.normals
normalsFrame.visible = state.normals
autoOrientNormalsCheckBox.checked = state.autoOrientNormals
flipNormalsCheckBox.checked = state.flipNormals
splittingCheckBox.checked = state.splitting
featureAngleFrame.visible = state.splitting
featureAngleSlider.value = state.featureAngle
featureAngleSpinBox.value = state.featureAngle
mirrorButton.checked = state.mirror
mirrorFrame.visible = state.mirror
mirrorXCheckBox.checked = state.mirrorX
mirrorYCheckBox.checked = state.mirrorY
mirrorZCheckBox.checked = state.mirrorZ
cleanerButton.checked = state.cleaner
connectivityButton.checked = state.connectivity
toggleModelsButton.enabled = state.inputModelNode is not None and state.outputModelNode is not None
applyButton.enabled = state.inputModelNode is not None and state.outputModelNode is not None
connect(inputModelSelector, 'currentNodeChanged(vtkMRMLNode*)',
'state.inputModelNode = args[0]')
connect(outputModelSelector, 'currentNodeChanged(vtkMRMLNode*)',
'state.outputModelNode = args[0]')
def initializeModelNode(node):
displayNode = slicer.vtkMRMLModelDisplayNode()
storageNode = slicer.vtkMRMLModelStorageNode()
displayNode.SetScene(slicer.mrmlScene)
storageNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(displayNode)
slicer.mrmlScene.AddNode(storageNode)
node.SetAndObserveDisplayNodeID(displayNode.GetID())
node.SetAndObserveStorageNodeID(storageNode.GetID())
outputModelSelector.connect('nodeAddedByUser(vtkMRMLNode*)',
initializeModelNode)
connect(decimationButton, 'clicked(bool)',
'state.decimation = args[0]')
connect(reductionSlider, 'valueChanged(double)',
'state.reduction = args[0]')
connect(reductionSpinBox, 'valueChanged(double)',
'state.reduction = args[0]')
connect(boundaryDeletionCheckBox, 'stateChanged(int)',
'state.boundaryDeletion = bool(args[0])')
connect(smoothingButton, 'clicked(bool)', 'state.smoothing = args[0]')
connect(smoothingMethodCombo, 'currentIndexChanged(QString)',
'state.smoothingMethod = args[0]')
connect(laplaceIterationsSlider, 'valueChanged(double)',
'state.laplaceIterations = int(args[0])')
connect(laplaceIterationsSpinBox, 'valueChanged(double)',
'state.laplaceIterations = int(args[0])')
connect(laplaceRelaxationSlider, 'valueChanged(double)',
'state.laplaceRelaxation = args[0]')
connect(laplaceRelaxationSpinBox, 'valueChanged(double)',
'state.laplaceRelaxation = args[0]')
connect(taubinIterationsSlider, 'valueChanged(double)',
'state.taubinIterations = int(args[0])')
connect(taubinIterationsSpinBox, 'valueChanged(double)',
'state.taubinIterations = int(args[0])')
connect(taubinPassBandSlider, 'valueChanged(double)',
'state.taubinPassBand = args[0]')
connect(taubinPassBandSpinBox, 'valueChanged(double)',
'state.taubinPassBand = args[0]')
connect(boundarySmoothingCheckBox, 'stateChanged(int)',
'state.boundarySmoothing = bool(args[0])')
connect(normalsButton, 'clicked(bool)', 'state.normals = args[0]')
connect(autoOrientNormalsCheckBox, 'toggled(bool)',
'state.autoOrientNormals = bool(args[0])')
connect(flipNormalsCheckBox, 'toggled(bool)',
'state.flipNormals = bool(args[0])')
connect(splittingCheckBox, 'stateChanged(int)',
'state.splitting = bool(args[0])')
connect(featureAngleSlider, 'valueChanged(double)',
'state.featureAngle = args[0]')
connect(featureAngleSpinBox, 'valueChanged(double)',
'state.featureAngle = args[0]')
connect(mirrorButton, 'clicked(bool)', 'state.mirror = args[0]')
connect(mirrorXCheckBox, 'toggled(bool)',
'state.mirrorX = bool(args[0])')
connect(mirrorYCheckBox, 'toggled(bool)',
'state.mirrorY = bool(args[0])')
connect(mirrorZCheckBox, 'toggled(bool)',
'state.mirrorZ = bool(args[0])')
connect(cleanerButton, 'clicked(bool)', 'state.cleaner = args[0]')
connect(connectivityButton, 'clicked(bool)',
'state.connectivity = args[0]')
def onApply():
updateGUI()
applyButton.text = "Working..."
applyButton.repaint()
slicer.app.processEvents()
logic = SurfaceToolboxLogic()
result = logic.applyFilters(state)
if result:
state.inputModelNode.GetModelDisplayNode().VisibilityOff()
state.outputModelNode.GetModelDisplayNode().VisibilityOn()
else:
state.inputModelNode.GetModelDisplayNode().VisibilityOn()
state.outputModelNode.GetModelDisplayNode().VisibilityOff()
applyButton.text = "Apply"
applyButton.connect('clicked()', onApply)
def onToggleModels():
updateGUI()
if state.inputModelNode.GetModelDisplayNode().GetVisibility():
state.inputModelNode.GetModelDisplayNode().VisibilityOff()
state.outputModelNode.GetModelDisplayNode().VisibilityOn()
toggleModelsButton.text = "Toggle Models (Output)"
else:
state.inputModelNode.GetModelDisplayNode().VisibilityOn()
state.outputModelNode.GetModelDisplayNode().VisibilityOff()
toggleModelsButton.text = "Toggle Models (Input)"
toggleModelsButton.connect('clicked()', onToggleModels)
updateGUI()
self.updateGUI = updateGUI
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.logic = SegmentMesherLogic()
self.logic.logCallback = self.addLog
self.modelGenerationInProgress = False
# Instantiate and connect widgets ...
# Parameter sets
defaultinputParametersCollapsibleButton = ctk.ctkCollapsibleButton()
defaultinputParametersCollapsibleButton.text = "Parameter set"
defaultinputParametersCollapsibleButton.collapsed = True
self.layout.addWidget(defaultinputParametersCollapsibleButton)
defaultParametersLayout = qt.QFormLayout(defaultinputParametersCollapsibleButton)
self.parameterNodeSelector = slicer.qMRMLNodeComboBox()
self.parameterNodeSelector.nodeTypes = ["vtkMRMLScriptedModuleNode"]
self.parameterNodeSelector.addAttribute( "vtkMRMLScriptedModuleNode", "ModuleName", "SegmentMesher" )
self.parameterNodeSelector.selectNodeUponCreation = True
self.parameterNodeSelector.addEnabled = True
self.parameterNodeSelector.renameEnabled = True
self.parameterNodeSelector.removeEnabled = True
self.parameterNodeSelector.noneEnabled = False
self.parameterNodeSelector.showHidden = True
self.parameterNodeSelector.showChildNodeTypes = False
self.parameterNodeSelector.baseName = "SegmentMesher"
self.parameterNodeSelector.setMRMLScene( slicer.mrmlScene )
self.parameterNodeSelector.setToolTip( "Pick parameter set" )
defaultParametersLayout.addRow("Parameter set: ", self.parameterNodeSelector)
#
# Inputs
#
inputParametersCollapsibleButton = ctk.ctkCollapsibleButton()
inputParametersCollapsibleButton.text = "Inputs"
self.layout.addWidget(inputParametersCollapsibleButton)
# Layout within the dummy collapsible button
inputParametersFormLayout = qt.QFormLayout(inputParametersCollapsibleButton)
self.inputModelSelector = slicer.qMRMLNodeComboBox()
self.inputModelSelector.nodeTypes = ["vtkMRMLSegmentationNode"]
self.inputModelSelector.selectNodeUponCreation = True
self.inputModelSelector.addEnabled = False
self.inputModelSelector.removeEnabled = False
self.inputModelSelector.noneEnabled = False
self.inputModelSelector.showHidden = False
self.inputModelSelector.showChildNodeTypes = False
self.inputModelSelector.setMRMLScene( slicer.mrmlScene )
self.inputModelSelector.setToolTip( "Volumetric mesh will be generated for all visible segments in this segmentation node." )
inputParametersFormLayout.addRow("Input segmentation: ", self.inputModelSelector)
self.methodSelectorComboBox = qt.QComboBox()
self.methodSelectorComboBox.addItem("Cleaver", METHOD_CLEAVER)
self.methodSelectorComboBox.addItem("TetGen", METHOD_TETGEN)
inputParametersFormLayout.addRow("Meshing method: ", self.methodSelectorComboBox)
#
# Outputs
#
outputParametersCollapsibleButton = ctk.ctkCollapsibleButton()
outputParametersCollapsibleButton.text = "Outputs"
self.layout.addWidget(outputParametersCollapsibleButton)
outputParametersFormLayout = qt.QFormLayout(outputParametersCollapsibleButton)
#
# output volume selector
#
self.outputModelSelector = slicer.qMRMLNodeComboBox()
self.outputModelSelector.nodeTypes = ["vtkMRMLModelNode"]
self.outputModelSelector.selectNodeUponCreation = True
self.outputModelSelector.addEnabled = True
self.outputModelSelector.renameEnabled = True
self.outputModelSelector.removeEnabled = True
self.outputModelSelector.noneEnabled = False
self.outputModelSelector.showHidden = False
self.outputModelSelector.showChildNodeTypes = False
self.outputModelSelector.setMRMLScene( slicer.mrmlScene )
self.outputModelSelector.setToolTip( "Created volumetric mesh" )
outputParametersFormLayout.addRow("Output model: ", self.outputModelSelector)
#
# Advanced area
#
self.advancedCollapsibleButton = ctk.ctkCollapsibleButton()
self.advancedCollapsibleButton.text = "Advanced"
self.advancedCollapsibleButton.collapsed = True
self.layout.addWidget(self.advancedCollapsibleButton)
advancedFormLayout = qt.QFormLayout(self.advancedCollapsibleButton)
self.cleaverAdditionalParametersWidget = qt.QLineEdit()
self.cleaverAdditionalParametersWidget.setToolTip('See description of parameters in module documentation ')
advancedFormLayout.addRow("Cleaver meshing options:", self.cleaverAdditionalParametersWidget)
self.cleaverAdditionalParametersWidget.text = "--scale 0.2 --multiplier 2 --grading 5"
self.tetGenAdditionalParametersWidget = qt.QLineEdit()
self.tetGenAdditionalParametersWidget.setToolTip('See description of parameters in module documentation ')
advancedFormLayout.addRow("TetGen meshing options:", self.tetGenAdditionalParametersWidget)
self.tetGenAdditionalParametersWidget.text = ""
self.showDetailedLogDuringExecutionCheckBox = qt.QCheckBox(" ")
self.showDetailedLogDuringExecutionCheckBox.checked = False
self.showDetailedLogDuringExecutionCheckBox.setToolTip("Show detailed log during model generation.")
advancedFormLayout.addRow("Show detailed log:", self.showDetailedLogDuringExecutionCheckBox)
self.keepTemporaryFilesCheckBox = qt.QCheckBox(" ")
self.keepTemporaryFilesCheckBox.checked = False
self.keepTemporaryFilesCheckBox.setToolTip("Keep temporary files (inputs, computed outputs, logs) after the model generation is completed.")
self.showTemporaryFilesFolderButton = qt.QPushButton("Show temp folder")
self.showTemporaryFilesFolderButton.toolTip = "Open the folder where temporary files are stored."
self.showTemporaryFilesFolderButton.setSizePolicy(qt.QSizePolicy.MinimumExpanding, qt.QSizePolicy.Preferred)
hbox = qt.QHBoxLayout()
hbox.addWidget(self.keepTemporaryFilesCheckBox)
hbox.addWidget(self.showTemporaryFilesFolderButton)
advancedFormLayout.addRow("Keep temporary files:", hbox)
customCleaverPath = self.logic.getCustomCleaverPath()
self.customCleaverPathSelector = ctk.ctkPathLineEdit()
self.customCleaverPathSelector.setCurrentPath(customCleaverPath)
self.customCleaverPathSelector.nameFilters = [self.logic.cleaverFilename]
self.customCleaverPathSelector.setSizePolicy(qt.QSizePolicy.MinimumExpanding, qt.QSizePolicy.Preferred)
self.customCleaverPathSelector.setToolTip("Set cleaver-cli executable path. "
"If value is empty then cleaver-cli bundled with this extension will be used.")
advancedFormLayout.addRow("Custom Cleaver executable path:", self.customCleaverPathSelector)
customTetGenPath = self.logic.getCustomTetGenPath()
self.customTetGenPathSelector = ctk.ctkPathLineEdit()
self.customTetGenPathSelector.setCurrentPath(customTetGenPath)
self.customTetGenPathSelector.nameFilters = [self.logic.tetGenFilename]
self.customTetGenPathSelector.setSizePolicy(qt.QSizePolicy.MinimumExpanding, qt.QSizePolicy.Preferred)
self.customTetGenPathSelector.setToolTip("Set tetgen executable path. "
"If value is empty then tetgen bundled with this extension will be used.")
advancedFormLayout.addRow("Custom TetGen executable path:", self.customTetGenPathSelector)
#
# Display
#
displayParametersCollapsibleButton = ctk.ctkCollapsibleButton()
displayParametersCollapsibleButton.text = "Display"
displayParametersCollapsibleButton.collapsed = True
self.layout.addWidget(displayParametersCollapsibleButton)
displayParametersFormLayout = qt.QFormLayout(displayParametersCollapsibleButton)
self.clipNodeWidget=slicer.qMRMLClipNodeWidget()
clipNode = slicer.mrmlScene.GetFirstNodeByClass("vtkMRMLClipModelsNode")
self.clipNodeWidget.setMRMLClipNode(clipNode)
displayParametersFormLayout.addRow(self.clipNodeWidget)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = False
self.layout.addWidget(self.applyButton)
self.statusLabel = qt.QPlainTextEdit()
self.statusLabel.setTextInteractionFlags(qt.Qt.TextSelectableByMouse)
self.statusLabel.setCenterOnScroll(True)
self.layout.addWidget(self.statusLabel)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.showTemporaryFilesFolderButton.connect('clicked(bool)', self.onShowTemporaryFilesFolder)
self.inputModelSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.updateMRMLFromGUI)
self.outputModelSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.updateMRMLFromGUI)
self.methodSelectorComboBox.connect("currentIndexChanged(int)", self.updateMRMLFromGUI)
# Immediately update deleteTemporaryFiles in the logic to make it possible to decide to
# keep the temporary file while the model generation is running
self.keepTemporaryFilesCheckBox.connect("toggled(bool)", self.onKeepTemporaryFilesToggled)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.updateMRMLFromGUI()
def _addCustomizationSection(self):
customizationCollapsibleButton = ctk.ctkCollapsibleButton()
customizationCollapsibleButton.text = 'Extraction Customization'
customizationCollapsibleButton.collapsed = True
self.layout.addWidget(customizationCollapsibleButton)
customizationFormLayout = qt.QFormLayout(
customizationCollapsibleButton)
#
# Radiobuttons to select customization Type
#
self.manualCustomizationRadioButton = qt.QRadioButton()
self.manualCustomizationRadioButton.text = 'Manual Customization'
self.manualCustomizationRadioButton.checked = True
customizationFormLayout.layout().addWidget(
self.manualCustomizationRadioButton)
self.parameterFileCustomizationRadioButton = qt.QRadioButton()
self.parameterFileCustomizationRadioButton.text = 'Parameter File Customization'
self.parameterFileCustomizationRadioButton.checked = False
customizationFormLayout.layout().addWidget(
self.parameterFileCustomizationRadioButton)
#
# Manual Customization
#
self.manualCustomizationGroupBox = qt.QGroupBox('Manual Customization')
self.manualCustomizationGroupBox.visible = True
# self.manualCustomizationGroupBox.checkable = True
customizationFormLayout.addWidget(self.manualCustomizationGroupBox)
manualCustomizationFormLayout = qt.QFormLayout(
self.manualCustomizationGroupBox)
# Feature Class section
featureClassCollapsibleButton = ctk.ctkCollapsibleButton()
featureClassCollapsibleButton.text = 'Feature Classes'
featureClassCollapsibleButton.collapsed = False
manualCustomizationFormLayout.addWidget(featureClassCollapsibleButton)
featureClassLayout = qt.QFormLayout(featureClassCollapsibleButton)
self.featuresLayout = qt.QHBoxLayout()
featureClassLayout.addRow('Features:', self.featuresLayout)
self.featuresButtonGroup = qt.QButtonGroup(self.featuresLayout)
self.featuresButtonGroup.exclusive = False
# Get the feature classes dynamically
self.features = list(getFeatureClasses().keys())
# Create a checkbox for each feature
featureButtons = {}
for feature in self.features:
featureButtons[feature] = qt.QCheckBox(feature)
# TODO: decide which features to enable by default
featureButtons[feature].checked = False
if feature == 'firstorder':
featureButtons[feature].checked = True
self.featuresButtonGroup.addButton(featureButtons[feature])
self.featuresLayout.layout().addWidget(featureButtons[feature])
# set the ID to be the index of this feature in the list
self.featuresButtonGroup.setId(featureButtons[feature],
self.features.index(feature))
# Add buttons to select all or none
self.buttonsLayout = qt.QHBoxLayout()
featureClassLayout.addRow('Toggle Features:', self.buttonsLayout)
self.calculateAllFeaturesButton = qt.QPushButton('All Features')
self.calculateAllFeaturesButton.toolTip = 'Calculate all feature classes.'
self.calculateAllFeaturesButton.enabled = True
self.buttonsLayout.addWidget(self.calculateAllFeaturesButton)
self.calculateNoFeaturesButton = qt.QPushButton('No Features')
self.calculateNoFeaturesButton.toolTip = 'Calculate no feature classes.'
self.calculateNoFeaturesButton.enabled = True
self.buttonsLayout.addWidget(self.calculateNoFeaturesButton)
# Resampling and Filtering
filteringCollapsibleButton = ctk.ctkCollapsibleButton()
filteringCollapsibleButton.text = 'Resampling and Filtering'
filteringCollapsibleButton.collapsed = False
manualCustomizationFormLayout.addRow(filteringCollapsibleButton)
# Layout within the dummy collapsible button
filteringFormLayout = qt.QFormLayout(filteringCollapsibleButton)
# Resampling
self.resampledVoxelSize = qt.QLineEdit()
self.resampledVoxelSize.toolTip = 'Three floating-point numbers separated by comma defining the resampled pixel ' \
'size (mm).'
filteringFormLayout.addRow('Resampled voxel size',
self.resampledVoxelSize)
# LoG kernel sizes. default to 5 (?)
self.logKernelSizes = qt.QLineEdit()
self.logKernelSizes.toolTip = 'Laplacian of Gaussian filter kernel sizes (mm), separated by comma. ' \
'If empty, no LoG filtering will be applied.'
filteringFormLayout.addRow('LoG kernel sizes', self.logKernelSizes)
# Wavelet
self.waveletCheckBox = qt.QCheckBox()
self.waveletCheckBox.checked = 0
self.waveletCheckBox.toolTip = 'If checked, PyRadiomics will calculate features on the image after applying ' \
'wavelet transformation'
filteringFormLayout.addRow('Wavelet-based features',
self.waveletCheckBox)
#
# Feature calculation settings
#
settingsCollapsibleButton = ctk.ctkCollapsibleButton()
settingsCollapsibleButton.text = 'Settings'
settingsCollapsibleButton.collapsed = False
manualCustomizationFormLayout.addWidget(settingsCollapsibleButton)
# Layout within the dummy collapsible button
settingsFormLayout = qt.QFormLayout(settingsCollapsibleButton)
# bin width, defaults to 25
self.binWidthSliderWidget = ctk.ctkSliderWidget()
self.binWidthSliderWidget.singleStep = 1
self.binWidthSliderWidget.decimals = 2
self.binWidthSliderWidget.minimum = 0.01
self.binWidthSliderWidget.maximum = 100
self.binWidthSliderWidget.value = 25
self.binWidthSliderWidget.toolTip = 'Set the bin width'
settingsFormLayout.addRow('Bin Width', self.binWidthSliderWidget)
# symmetricalGLCM flag, defaults to false
self.symmetricalGLCMCheckBox = qt.QCheckBox()
self.symmetricalGLCMCheckBox.checked = 1
self.symmetricalGLCMCheckBox.toolTip = 'Use a symmetrical GLCM matrix'
settingsFormLayout.addRow('Enforce Symmetrical GLCM',
self.symmetricalGLCMCheckBox)
#
# Parameter File Customization
#
self.parameterCustomizationGroupBox = qt.QGroupBox(
'Parameter File Customization')
self.parameterCustomizationGroupBox.visible = False
# self.parameterCustomizationGroupBox.checkable = True
customizationFormLayout.addWidget(self.parameterCustomizationGroupBox)
parameterCustomizationFormLayout = qt.QFormLayout(
self.parameterCustomizationGroupBox)
# Path edit to select parameter file
self.parameterFilePathLineEdit = ctk.ctkPathLineEdit()
parameterCustomizationFormLayout.addRow("Parameter File",
self.parameterFilePathLineEdit)
def setup(self):
self.detailsPopup = None
self.setDetailsPopup(self.getSavedDICOMDetailsWidgetType()())
# XXX Slicer 4.5 - Remove these. Here only for backward compatibility.
self.dicomBrowser = self.detailsPopup.dicomBrowser
self.tables = self.detailsPopup.tables
layoutManager = slicer.app.layoutManager()
if layoutManager is not None:
layoutManager.layoutChanged.connect(self.onLayoutChanged)
# connect to the 'Show DICOM Browser' button
self.showBrowserButton = qt.QPushButton('Show DICOM database browser')
self.showBrowserButton.setCheckable(True)
self.layout.addWidget(self.showBrowserButton)
self.showBrowserButton.setStyleSheet("font:Bold;" "font-size:12px")
self.showBrowserButton.connect('clicked()', self.toggleDetailsPopup)
self.loadedDataLabel = qt.QLabel("Loaded data")
self.loadedDataLabel.setSizePolicy(qt.QSizePolicy.Expanding,
qt.QSizePolicy.Fixed)
self.layout.addWidget(self.loadedDataLabel)
font = qt.QFont()
font.setBold(True)
font.setPointSize(12)
self.loadedDataLabel.setFont(font)
self.layout.addWidget(self.loadedDataLabel)
self.subjectHierarchyTree = slicer.qMRMLSubjectHierarchyTreeView()
self.layout.addWidget(self.subjectHierarchyTree)
self.subjectHierarchyTree.setMRMLScene(slicer.mrmlScene)
self.subjectHierarchyTree.currentItemChanged.connect(
self.onCurrentItemChanged)
self.subjectHierarchyTree.currentItemModified.connect(
self.onCurrentItemModified)
self.subjectHierarchyCurrentVisibility = False
self.subjectHierarchyTree.setColumnHidden(
self.subjectHierarchyTree.model().idColumn, True)
self.browserSettingsWidget = ctk.ctkCollapsibleGroupBox()
self.browserSettingsWidget.title = "Browser settings"
self.layout.addWidget(self.browserSettingsWidget)
self.browserSettingsWidget.collapsed = True
self.browserSettingsWidget.setLayout(qt.QFormLayout())
self.directoryButton = ctk.ctkDirectoryButton()
self.browserSettingsWidget.layout().addRow("Local database:",
self.directoryButton)
self.directoryButton.directoryChanged.connect(
self.onDatabaseDirectoryButtonChanged)
self.onDatabaseDirectoryDetailsPopupChanged(
self.detailsPopup.dicomBrowser.databaseDirectory)
self.tableDensityComboBox = qt.QComboBox()
self.browserSettingsWidget.layout().addRow("Table density:",
self.tableDensityComboBox)
self.tableDensityComboBox.currentIndexChanged.connect(
self.onTableDensityChanged)
self.updateTableDensityComboBox()
self.horizontalCheckBox = qt.QCheckBox()
self.horizontalCheckBox.checked = settingsValue(
'DICOM/horizontalTables', 0, converter=int)
self.horizontalCheckBox.stateChanged.connect(
self.onHorizontalStateChanged)
self.browserSettingsWidget.layout().addRow("Horizontal:",
self.horizontalCheckBox)
self.browserPersistentCheckBox = qt.QCheckBox()
self.browserPersistentCheckBox.checked = settingsValue(
'DICOM/BrowserPersistent', False, converter=toBool)
self.browserPersistentCheckBox.stateChanged.connect(
self.onBrowserPersistentStateChanged)
self.browserSettingsWidget.layout().addRow(
"Browser persistent:", self.browserPersistentCheckBox)
self.additionalSettingsLayout = qt.QHBoxLayout()
#
# servers
#
# testing server - not exposed (used for development)
self.localFrame = ctk.ctkCollapsibleButton(self.parent)
self.localFrame.setLayout(qt.QVBoxLayout())
self.localFrame.setText("Servers")
self.layout.addWidget(self.localFrame)
self.localFrame.collapsed = True
self.toggleServer = qt.QPushButton("Start Testing Server")
self.localFrame.layout().addWidget(self.toggleServer)
self.toggleServer.connect('clicked()', self.onToggleServer)
self.verboseServer = qt.QCheckBox("Verbose")
self.localFrame.layout().addWidget(self.verboseServer)
# advanced options - not exposed to end users
# developers can uncomment these lines to access testing server
self.toggleServer.hide()
self.verboseServer.hide()
# Listener
settings = qt.QSettings()
self.toggleListener = qt.QPushButton()
self.toggleListener.checkable = True
if hasattr(slicer, 'dicomListener'):
self.toggleListener.text = "Stop Listener"
slicer.dicomListener.process.connect(
'stateChanged(QProcess::ProcessState)',
self.onListenerStateChanged)
else:
self.toggleListener.text = "Start Listener"
self.localFrame.layout().addWidget(self.toggleListener)
self.toggleListener.connect('clicked()', self.onToggleListener)
self.runListenerAtStart = qt.QCheckBox(
"Start Listener when Slicer Starts")
self.localFrame.layout().addWidget(self.runListenerAtStart)
self.runListenerAtStart.checked = settingsValue(
'DICOM/RunListenerAtStart', False, converter=toBool)
self.runListenerAtStart.connect('clicked()', self.onRunListenerAtStart)
# connect to the main window's dicom button
mw = slicer.util.mainWindow()
if mw:
try:
action = slicer.util.findChildren(mw,
name='LoadDICOMAction')[0]
action.connect('triggered()', self.onOpenDetailsPopup)
except IndexError:
logging.error(
'Could not connect to the main window DICOM button')
if hasattr(slicer, 'dicomListener'):
slicer.dicomListener.fileToBeAddedCallback = self.onListenerToAddFile
slicer.dicomListener.fileAddedCallback = self.onListenerAddedFile
slicer.dicomDatabase.connect('databaseChanged()',
self.onDatabaseChanged)
# the recent activity frame
self.activityFrame = ctk.ctkCollapsibleButton(self.parent)
self.activityFrame.collapsed = True
self.activityFrame.setLayout(qt.QVBoxLayout())
self.activityFrame.setText("Recent DICOM Activity")
self.layout.addWidget(self.activityFrame)
self.recentActivity = DICOMLib.DICOMRecentActivityWidget(
self.activityFrame, detailsPopup=self.detailsPopup)
self.activityFrame.layout().addWidget(self.recentActivity)
self.requestUpdateRecentActivity()
def setupOptionsFrame(self):
self.autoUpdateCheckBox = qt.QCheckBox("Auto-update")
self.autoUpdateCheckBox.setToolTip(
"Auto-update results preview when input segments change.")
self.autoUpdateCheckBox.setChecked(True)
self.autoUpdateCheckBox.setEnabled(False)
self.previewButton = qt.QPushButton("Initialize")
self.previewButton.objectName = self.__class__.__name__ + 'Preview'
self.previewButton.setToolTip("Preview complete segmentation")
# qt.QSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
# fails on some systems, therefore set the policies using separate method calls
qSize = qt.QSizePolicy()
qSize.setHorizontalPolicy(qt.QSizePolicy.Expanding)
self.previewButton.setSizePolicy(qSize)
previewFrame = qt.QHBoxLayout()
previewFrame.addWidget(self.autoUpdateCheckBox)
previewFrame.addWidget(self.previewButton)
self.scriptedEffect.addLabeledOptionsWidget("Preview:", previewFrame)
self.previewOpacitySlider = ctk.ctkSliderWidget()
self.previewOpacitySlider.setToolTip(
"Adjust visibility of results preview.")
self.previewOpacitySlider.minimum = 0
self.previewOpacitySlider.maximum = 1.0
self.previewOpacitySlider.value = 0.0
self.previewOpacitySlider.singleStep = 0.05
self.previewOpacitySlider.pageStep = 0.1
self.previewOpacitySlider.spinBoxVisible = False
self.previewShow3DButton = qt.QPushButton("Show 3D")
self.previewShow3DButton.setToolTip("Preview results in 3D.")
self.previewShow3DButton.setCheckable(True)
displayFrame = qt.QHBoxLayout()
displayFrame.addWidget(qt.QLabel("inputs"))
displayFrame.addWidget(self.previewOpacitySlider)
displayFrame.addWidget(qt.QLabel("results"))
displayFrame.addWidget(self.previewShow3DButton)
self.scriptedEffect.addLabeledOptionsWidget("Display:", displayFrame)
self.cancelButton = qt.QPushButton("Cancel")
self.cancelButton.objectName = self.__class__.__name__ + 'Cancel'
self.cancelButton.setToolTip("Clear preview and cancel auto-complete")
self.applyButton = qt.QPushButton("Apply")
self.applyButton.objectName = self.__class__.__name__ + 'Apply'
self.applyButton.setToolTip("Replace segments by previewed result")
finishFrame = qt.QHBoxLayout()
finishFrame.addWidget(self.cancelButton)
finishFrame.addWidget(self.applyButton)
self.scriptedEffect.addOptionsWidget(finishFrame)
self.previewButton.connect('clicked()', self.onPreview)
self.cancelButton.connect('clicked()', self.onCancel)
self.applyButton.connect('clicked()', self.onApply)
self.previewOpacitySlider.connect("valueChanged(double)",
self.updateMRMLFromGUI)
self.previewShow3DButton.connect("toggled(bool)",
self.updateMRMLFromGUI)
self.autoUpdateCheckBox.connect("stateChanged(int)",
self.updateMRMLFromGUI)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
####################
# For debugging
#
# 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 = "Reload"
reloadFormLayout.addWidget(self.reloadButton)
self.reloadButton.connect('clicked()', self.onReload)
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
#
# input magnitude volume
#
self.magnitudevolume = slicer.qMRMLNodeComboBox()
self.magnitudevolume.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.magnitudevolume.selectNodeUponCreation = True
self.magnitudevolume.addEnabled = True
self.magnitudevolume.removeEnabled = True
self.magnitudevolume.noneEnabled = True
self.magnitudevolume.showHidden = False
self.magnitudevolume.showChildNodeTypes = False
self.magnitudevolume.setMRMLScene(slicer.mrmlScene)
self.magnitudevolume.setToolTip("Select the magnitude image")
parametersFormLayout.addRow("Magnitude Image: ", self.magnitudevolume)
#
# input phase volume
#
self.phasevolume = slicer.qMRMLNodeComboBox()
self.phasevolume.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.phasevolume.selectNodeUponCreation = True
self.phasevolume.addEnabled = True
self.phasevolume.removeEnabled = True
self.phasevolume.noneEnabled = True
self.phasevolume.showHidden = False
self.phasevolume.showChildNodeTypes = False
self.phasevolume.setMRMLScene(slicer.mrmlScene)
self.phasevolume.setToolTip("Select the phase image")
parametersFormLayout.addRow("Phase Image: ", self.phasevolume)
#
# True phase points (vtkMRMLMarkupsFiducialNode)
#
self.truePhasePointSelector = slicer.qMRMLNodeComboBox()
self.truePhasePointSelector.nodeTypes = ((
"vtkMRMLMarkupsFiducialNode"), "")
self.truePhasePointSelector.addEnabled = True
self.truePhasePointSelector.removeEnabled = False
self.truePhasePointSelector.noneEnabled = True
self.truePhasePointSelector.showHidden = False
self.truePhasePointSelector.renameEnabled = True
self.truePhasePointSelector.showChildNodeTypes = False
self.truePhasePointSelector.setMRMLScene(slicer.mrmlScene)
self.truePhasePointSelector.setToolTip(
"Pick up a Markups node listing a true phase point.")
parametersFormLayout.addRow("True Phase Point: ",
self.truePhasePointSelector)
#
# Select which scene view to track
#
self.sceneViewButton_red = qt.QRadioButton('Red')
self.sceneViewButton_yellow = qt.QRadioButton('Yellow')
self.sceneViewButton_green = qt.QRadioButton('Green')
self.sceneViewButton_green.checked = 1
layout = qt.QHBoxLayout(parametersCollapsibleButton)
layout.addWidget(self.sceneViewButton_red)
layout.addWidget(self.sceneViewButton_yellow)
layout.addWidget(self.sceneViewButton_green)
parametersFormLayout.addRow("Scene view:", layout)
# Auto slice selecter
self.autosliceselecterButton = qt.QPushButton("Segment Needle")
self.autosliceselecterButton.toolTip = "Observe slice from scene viewer"
self.autosliceselecterButton.enabled = False
parametersFormLayout.addRow(self.autosliceselecterButton)
realtimebutton = qt.QHBoxLayout()
#
# Start Real-Time Tracking
#
self.trackingButton = qt.QPushButton("Start Simulated Tracking")
self.trackingButton.toolTip = "Observe slice from scene viewer"
self.trackingButton.enabled = False
self.trackingButton.clicked.connect(self.SimStartTimer)
realtimebutton.addWidget(self.trackingButton)
self.SimTimer = qt.QTimer()
self.SimTimer.timeout.connect(self.onRealTimeTracking)
# Stop Real-Time Tracking
self.stopsequence = qt.QPushButton('Stop Simulated Tracking')
self.stopsequence.clicked.connect(self.SimStopTimer)
realtimebutton.addWidget(self.stopsequence)
parametersFormLayout.addRow("", realtimebutton)
# Add vertical spacer
self.layout.addStretch(1)
####################################
## ##
## Scanner Remote Control Protocol##
## ##
####################################
SRCcollapsibleButton = ctk.ctkCollapsibleButton()
SRCcollapsibleButton.text = "Scanner Remote Control Protocol"
self.layout.addWidget(SRCcollapsibleButton)
SRCFormLayout = qt.QFormLayout(SRCcollapsibleButton)
realtimebutton = qt.QHBoxLayout()
# FPS
self.fpsBox = qt.QDoubleSpinBox()
self.fpsBox.setSingleStep(0.1)
self.fpsBox.setMaximum(40)
self.fpsBox.setMinimum(0.1)
self.fpsBox.setSuffix(" FPS")
self.fpsBox.value = 0.5
SRCFormLayout.addRow("Update Rate:", self.fpsBox)
# Start SRC Real-Time Tracking
self.SRCtrackingButton = qt.QPushButton("Start Live Tracking")
self.SRCtrackingButton.toolTip = "Observe slice from scene viewer"
self.SRCtrackingButton.enabled = False
self.SRCtrackingButton.clicked.connect(self.StartTimer)
realtimebutton.addWidget(self.SRCtrackingButton)
self.timer = qt.QTimer()
self.timer.timeout.connect(self.SRCRealTimeTracking)
# Stop Real-Time Tracking
self.stopsequence = qt.QPushButton('Stop Live Tracking')
self.stopsequence.clicked.connect(self.StopTimer)
realtimebutton.addWidget(self.stopsequence)
SRCFormLayout.addRow("", realtimebutton)
# Add vertical spacer
self.layout.addStretch(1)
######################
# Advanced Parameters#
######################
advancedCollapsibleButton = ctk.ctkCollapsibleButton()
advancedCollapsibleButton.text = "Advanced"
advancedCollapsibleButton.collapsed = 1
self.layout.addWidget(advancedCollapsibleButton)
# Layout within the collapsible button
advancedFormLayout = qt.QFormLayout(advancedCollapsibleButton)
#
# 2D slice value
#
self.imageSliceSliderWidget = ctk.ctkSliderWidget()
self.imageSliceSliderWidget.singleStep = 1
self.imageSliceSliderWidget.minimum = 0
self.imageSliceSliderWidget.maximum = 70
self.imageSliceSliderWidget.value = 1
self.imageSliceSliderWidget.setToolTip("Select 2D slice")
advancedFormLayout.addRow("2D Slice ", self.imageSliceSliderWidget)
#
# Mask Threshold
#
self.maskThresholdWidget = ctk.ctkSliderWidget()
self.maskThresholdWidget.singleStep = 1
self.maskThresholdWidget.minimum = 0
self.maskThresholdWidget.maximum = 100
self.maskThresholdWidget.value = 20
self.maskThresholdWidget.setToolTip(
"Set threshold value for computing the output image. Voxels that have intensities lower than this value will set to zero."
)
advancedFormLayout.addRow("Mask Threshold ", self.maskThresholdWidget)
#
# Ridge operator filter
#
self.ridgeOperatorWidget = ctk.ctkSliderWidget()
self.ridgeOperatorWidget.singleStep = 1
self.ridgeOperatorWidget.minimum = 0
self.ridgeOperatorWidget.maximum = 100
self.ridgeOperatorWidget.value = 5
self.ridgeOperatorWidget.setToolTip(
"set up meijering filter threshold")
advancedFormLayout.addRow("Ridge Operator Threshold",
self.ridgeOperatorWidget)
#
# 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)
#
# Manual apply Button
#
self.applyButton = qt.QPushButton("Manual")
self.applyButton.toolTip = "Select slice manually"
self.applyButton.enabled = False
advancedFormLayout.addRow(self.applyButton)
# Refresh Apply button state
self.onSelect()
#
# check box to trigger preview final processed image
#
self.enableprocessedimagecheckbox = qt.QCheckBox()
self.enableprocessedimagecheckbox.checked = 0
self.enableprocessedimagecheckbox.setToolTip(
"If checked, take screen shots for tutorials. Use Save Data to write them to disk."
)
advancedFormLayout.addRow("Enable Processed Image",
self.enableprocessedimagecheckbox)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.trackingButton.connect('clicked(bool)', self.onRealTimeTracking)
self.SRCtrackingButton.connect('clicked(bool)',
self.SRCRealTimeTracking)
self.autosliceselecterButton.connect('clicked(bool)',
self.autosliceselecter)
self.magnitudevolume.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
self.phasevolume.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
self.lastMatrix = vtk.vtkMatrix4x4()
self.timer = qt.QTimer()
self.timer.timeout.connect(self.SRCRealTimeTracking)
self.SimTimer = qt.QTimer()
self.SimTimer.timeout.connect(self.onRealTimeTracking)
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.clearButton = qt.QPushButton("Clear")
buttonLayout.addWidget(self.addByBrowsingButton)
buttonLayout.addWidget(self.clearButton)
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 = slicer.qMRMLCoordinatesWidget()
self.spacing.decimalsOption = ctk.ctkDoubleSpinBox.DecimalsByKey | ctk.ctkDoubleSpinBox.DecimalsByShortcuts | ctk.ctkDoubleSpinBox.DecimalsByValue
self.spacing.minimum = 0.0
self.spacing.maximum = 1000000000.0
self.spacing.quantity = "length"
self.spacing.unitAwareProperties = slicer.qMRMLCoordinatesWidget.Precision | slicer.qMRMLCoordinatesWidget.Prefix | slicer.qMRMLCoordinatesWidget.Scaling | slicer.qMRMLCoordinatesWidget.Suffix
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()
self.archetypePathEdit.filters = ctk.ctkPathLineEdit().Files
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.clearButton.connect('clicked()', self.onClear)
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)
self.logic = MyModuleLogic()
# ------ 1. CREATE LAYOUT AND BUTTONS ------
# Layout setup: 3D Only
self.layoutManager = slicer.app.layoutManager()
self.layoutManager.setLayout(
slicer.vtkMRMLLayoutNode.SlicerLayoutOneUp3DView)
#
# LOAD DATA
#
# Create layout
collapsibleButtonLoad = ctk.ctkCollapsibleButton()
collapsibleButtonLoad.text = "LOAD DATA" # title for layout
self.layout.addWidget(collapsibleButtonLoad)
formLayout_load = qt.QFormLayout(collapsibleButtonLoad)
# Segment 1 Selector
self.segment1_pathSelector = ctk.ctkPathLineEdit()
self.segment1_pathSelector.enabled = True
self.segment1_pathSelector.setMaximumWidth(400)
self.segment1_pathSelector.currentPath = slicer.modules.mymodule.path.replace(
"MyModule.py", "") + 'Data/Liver1.stl'
formLayout_load.addRow("Segment 1: ", self.segment1_pathSelector)
# Segment 1 Selector
self.segment2_pathSelector = ctk.ctkPathLineEdit()
self.segment2_pathSelector.enabled = True
self.segment2_pathSelector.setMaximumWidth(400)
self.segment2_pathSelector.currentPath = slicer.modules.mymodule.path.replace(
"MyModule.py", "") + 'Data/Liver1beforeMM.stl'
formLayout_load.addRow("Segment 2: ", self.segment2_pathSelector)
# Button to load segments
self.loadSegmentsButton = qt.QPushButton(
"LOAD MODELS AS SEGMENTS") # text in button
self.loadSegmentsButton.toolTip = "Load segments as segments" # hint text for button (appears when cursor is above the button for more than one second)
self.loadSegmentsButton.enabled = True # if True it can be clicked
formLayout_load.addRow(
self.loadSegmentsButton) # include button in layout
#
# ALIGNMENT
#
# Create Layout
collapsibleButtonAlignment = ctk.ctkCollapsibleButton()
collapsibleButtonAlignment.text = "ALIGNMENT"
self.layout.addWidget(collapsibleButtonAlignment)
formLayout_alignment = qt.QFormLayout(collapsibleButtonAlignment)
# Button for masks alignment
self.alignSegmentsButton = qt.QPushButton(
"ALIGN MODELS") # text in button
self.alignSegmentsButton.toolTip = "Align segments" # hint text for button (appears when cursor is above the button for more than one second)
self.alignSegmentsButton.enabled = True
formLayout_alignment.addRow(self.alignSegmentsButton)
# COMPARISON BETWEEN MASKS #
# SORENSEN-DICE COEFFICIENT & HOUSDORFF DISTANCE BUTTONS
#
# Create layout
collapsibleButtonComparison = ctk.ctkCollapsibleButton()
collapsibleButtonComparison.text = "COMPARISON" # title for layout
self.layout.addWidget(collapsibleButtonComparison)
formLayout_comparison = qt.QFormLayout(collapsibleButtonComparison)
# Button to obtain the Sorensen-Dice Coefficient
self.diceCoeffButton = qt.QPushButton(
"SORENSEN-DICE COEFFICIENT") # text in button
self.diceCoeffButton.toolTip = "Sorensen-Dice Coefficient" # hint text for button (appears when the cursor is above the button for more than one second)
self.diceCoeffButton.enabled = True # if true it can be clicked
formLayout_comparison.addRow(
self.diceCoeffButton) # include button in layout
#Button to obtain the Hausdorff Distance
self.hausDistButton = qt.QPushButton(
"HAUSDORFF DISTANCE") # text in button
self.hausDistButton.toolTip = qt.QPushButton(
"Hausdorff Distance"
) # hint text for button (appears when the cursor is above the button for more than a second)
self.hausDistButton.enabled = True # if true it can be clicked
formLayout_comparison.addRow(
self.hausDistButton) # include button in layout
#
# VISUALIZATION
#
# Create layout
collapsibleButtonVisualization = ctk.ctkCollapsibleButton()
collapsibleButtonVisualization.text = "VISUALIZATION" # title for layout
self.layout.addWidget(collapsibleButtonVisualization)
formLayout_visualization = qt.QFormLayout(
collapsibleButtonVisualization)
#
# Segment visibility layout
#
# Create collapsible button inside layout
segmentVisibility_GroupBox = ctk.ctkCollapsibleGroupBox()
segmentVisibility_GroupBox.setTitle(
"MODEL VISIBILITY") # title for collapsible button
segmentVisibility_GroupBox.collapsed = False # if True it appears collapsed
formLayout_visualization.addRow(
segmentVisibility_GroupBox) # add collapsible button to layout
# Create layout inside collapsible button
segmentVisibility_GroupBox_Layout = qt.QFormLayout(
segmentVisibility_GroupBox)
# Create horizontal section
segmentVisibilityLayout_1 = qt.QHBoxLayout()
segmentVisibility_GroupBox_Layout.addRow(
segmentVisibilityLayout_1) # insert section in current layout
# Show or Hide Segment 1 in 3D scene
self.segment1_checkBox = qt.QCheckBox('Segment 1') # text in checkbox
self.segment1_checkBox.checked = True # if True it is initially checked
self.segment1_checkBox.enabled = True # if True it can be checked
segmentVisibilityLayout_1.addWidget(
self.segment1_checkBox) # add checkbox to layout
# Show or Hide Segment 2 in 3D scene
self.segment2_checkBox = qt.QCheckBox('Segment 2') # text in checkbox
self.segment2_checkBox.checked = True # if True it is initially checked
self.segment2_checkBox.checked = True # if True it can be checked
segmentVisibilityLayout_1.addWidget(
self.segment2_checkBox) # add checkbox to layout
#
# Segment transparency layout
#
# Create collapsible button inside layout
segmentOpacity_GroupBox = ctk.ctkCollapsibleGroupBox()
segmentOpacity_GroupBox.setTitle(
"MODEL OPACITY") # title for collapsible button
segmentOpacity_GroupBox.collapsed = False # if True it appears collapsed
formLayout_visualization.addRow(
segmentOpacity_GroupBox) # add collapsible button to layout
# Create layout inside collapsible button
segmentOpacity_GroupBox_Layout = qt.QFormLayout(
segmentOpacity_GroupBox)
# Create an opacity Value Slider - Segment 1
self.opacityValueSliderWidget_1 = ctk.ctkSliderWidget()
self.opacityValueSliderWidget_1.singleStep = 5 # step for range of values to be selected
self.opacityValueSliderWidget_1.minimum = 0 # minimum value
self.opacityValueSliderWidget_1.maximum = 100 # maximum value
self.opacityValueSliderWidget_1.value = 100 # initial value
segmentOpacity_GroupBox_Layout.addRow(
"[%]: ", self.opacityValueSliderWidget_1) # add slider to layout
# Create an opacity Value Slider - Segment 2
self.opacityValueSliderWidget_2 = ctk.ctkSliderWidget()
self.opacityValueSliderWidget_2.singleStep = 5 # step for range of values to be selected
self.opacityValueSliderWidget_2.minimum = 0 # minimum value
self.opacityValueSliderWidget_2.maximum = 100 # maximum value
self.opacityValueSliderWidget_2.value = 100 # initial value
segmentOpacity_GroupBox_Layout.addRow(
"[%]: ", self.opacityValueSliderWidget_2) # add slider to layout
#
# COLOR MAP
#
collapsibleButtonColorMap = ctk.ctkCollapsibleButton()
collapsibleButtonColorMap.text = "COLOR MAP"
self.layout.addWidget(collapsibleButtonColorMap)
formLayout_colorMap = qt.QFormLayout(collapsibleButtonColorMap)
self.showColorMapButton = qt.QPushButton(
"SHOW COLOR MAP") # text in button
self.showColorMapButton.toolTip = "Align segments" # hint text for button (appears when cursor is above the button for more than one second)
self.showColorMapButton.enabled = True
formLayout_colorMap.addRow(self.showColorMapButton)
# Displayed Range group box
self.displayedRange_GroupBox = ctk.ctkCollapsibleGroupBox()
self.displayedRange_GroupBox.setTitle("Displayed Range")
self.displayedRange_GroupBox.collapsed = False
self.displayedRange_GroupBox.enabled = False
formLayout_colorMap.addRow(self.displayedRange_GroupBox)
displayedRange_GroupBox_Layout = qt.QFormLayout(
self.displayedRange_GroupBox)
displayedRange_H_Layout = qt.QHBoxLayout()
displayedRange_GroupBox_Layout.addRow(displayedRange_H_Layout)
## Minimum value - displayed range
self.minDisplayedRange_SpinBox = qt.QDoubleSpinBox()
self.minDisplayedRange_SpinBox.setMaximum(40.0)
self.minDisplayedRange_SpinBox.setMinimum(-40.0)
self.minDisplayedRange_SpinBox.setSingleStep(0.1)
self.minDisplayedRange_SpinBox.enabled = True
self.minDisplayedRange_SpinBox.value = 0.0
displayedRange_H_Layout.addWidget(self.minDisplayedRange_SpinBox)
## Displayed range Slider
self.displayedRange_SliderWidget = ctk.ctkDoubleRangeSlider()
self.displayedRange_SliderWidget.setValues(0.0, 10.0)
self.displayedRange_SliderWidget.orientation = 1
self.displayedRange_SliderWidget.singleStep = 0.1
self.displayedRange_SliderWidget.minimum = -40.0
self.displayedRange_SliderWidget.maximum = 40.0
displayedRange_H_Layout.addWidget(self.displayedRange_SliderWidget)
## Maximum value - displayed range
self.maxDisplayedRange_SpinBox = qt.QDoubleSpinBox()
self.maxDisplayedRange_SpinBox.setMaximum(40.0)
self.maxDisplayedRange_SpinBox.setMinimum(-40.0)
self.maxDisplayedRange_SpinBox.setSingleStep(0.1)
self.maxDisplayedRange_SpinBox.enabled = True
self.maxDisplayedRange_SpinBox.value = 10.0
displayedRange_H_Layout.addWidget(self.maxDisplayedRange_SpinBox)
# Scalar Bar Visibility Checkbox
self.ScalarBar_visibility_checkBox = qt.QCheckBox('Scalar Bar Visible')
self.ScalarBar_visibility_checkBox.checked = True
displayedRange_GroupBox_Layout.addRow(
self.ScalarBar_visibility_checkBox)
# Add vertical spacing
self.layout.addStretch(1)
# ------ 2. CONNECT BUTTONS WITH FUNCTIONS ------
# Connect each button with a function
self.loadSegmentsButton.connect(
'clicked(bool)', self.onloadSegmentsButton
) # when the button is pressed we call the function onLoadSegment1Button
self.segment1_checkBox.connect('stateChanged(int)',
self.onupdateSegment1Visibility)
self.segment2_checkBox.connect('stateChanged(int)',
self.onupdateSegment2Visibility)
self.opacityValueSliderWidget_1.connect("valueChanged(double)",
self.onupdateSegment1Opacity)
self.opacityValueSliderWidget_2.connect("valueChanged(double)",
self.onupdateSegment2Opacity)
self.alignSegmentsButton.connect('clicked(bool)',
self.onAlignSegmentsButton)
self.diceCoeffButton.connect('clicked(bool)', self.onDiceCoeffButton)
self.hausDistButton.connect('clicked(bool)',
self.onHausdorffDistButton)
self.showColorMapButton.connect('clicked(bool)',
self.onShowColorMapButton)
self.displayedRange_SliderWidget.connect(
"valuesChanged(double,double)", self.onDisplayedRangeSliderChanged)
self.minDisplayedRange_SpinBox.connect(
"valueChanged(double)", self.onDisplayedRangeSpinBoxChanged)
self.maxDisplayedRange_SpinBox.connect(
"valueChanged(double)", self.onDisplayedRangeSpinBoxChanged)
self.ScalarBar_visibility_checkBox.connect(
'stateChanged(int)', self.onScalarBarVisibilityChecked)
def _createSmall(self):
"""Make the internals of the widget to display in the
Data Probe frame (lower left of slicer main window by default)"""
# this method makes SliceView Annotation
self.sliceAnnotations = DataProbeLib.SliceAnnotations()
# goto module button
self.goToModule = qt.QPushButton('->', self.frame)
self.goToModule.setToolTip(
'Go to the DataProbe module for more information and options')
self.frame.layout().addWidget(self.goToModule)
self.goToModule.connect("clicked()", self.onGoToModule)
# hide this for now - there's not much to see in the module itself
self.goToModule.hide()
# image view
self.showImageBox = qt.QCheckBox('Show Zoomed Slice', self.frame)
self.frame.layout().addWidget(self.showImageBox)
self.showImageBox.connect("toggled(bool)", self.onShowImage)
self.showImageBox.setChecked(False)
self.imageLabel = qt.QLabel()
# qt.QSizePolicy(qt.QSizePolicy.Expanding, qt.QSizePolicy.Expanding)
# fails on some systems, therefore set the policies using separate method calls
qSize = qt.QSizePolicy()
qSize.setHorizontalPolicy(qt.QSizePolicy.Expanding)
qSize.setVerticalPolicy(qt.QSizePolicy.Expanding)
self.imageLabel.setSizePolicy(qSize)
#self.imageLabel.setScaledContents(True)
self.frame.layout().addWidget(self.imageLabel)
self.onShowImage(False)
# top row - things about the viewer itself
self.viewerFrame = qt.QFrame(self.frame)
self.viewerFrame.setLayout(qt.QHBoxLayout())
self.frame.layout().addWidget(self.viewerFrame)
self.viewerColor = qt.QLabel(self.viewerFrame)
self.viewerFrame.layout().addWidget(self.viewerColor)
self.viewInfo = qt.QLabel()
self.viewerFrame.layout().addWidget(self.viewInfo)
self.viewerFrame.layout().addStretch(1)
def _setFixedFontFamily(widget, family='Monospace'):
font = widget.font
font.setFamily(family)
widget.font = font
_setFixedFontFamily(self.viewInfo)
# the grid - things about the layers
# this method makes labels
self.layerGrid = qt.QFrame(self.frame)
layout = qt.QGridLayout()
self.layerGrid.setLayout(layout)
self.frame.layout().addWidget(self.layerGrid)
layers = ('L', 'F', 'B')
self.layerNames = {}
self.layerIJKs = {}
self.layerValues = {}
for (row, layer) in enumerate(layers):
col = 0
layout.addWidget(qt.QLabel(layer), row, col)
col += 1
self.layerNames[layer] = qt.QLabel()
layout.addWidget(self.layerNames[layer], row, col)
col += 1
self.layerIJKs[layer] = qt.QLabel()
layout.addWidget(self.layerIJKs[layer], row, col)
col += 1
self.layerValues[layer] = qt.QLabel()
layout.addWidget(self.layerValues[layer], row, col)
layout.setColumnStretch(col, 100)
_setFixedFontFamily(self.layerNames[layer])
_setFixedFontFamily(self.layerIJKs[layer])
_setFixedFontFamily(self.layerValues[layer])
# goto module button
self.goToModule = qt.QPushButton('->', self.frame)
self.goToModule.setToolTip(
'Go to the DataProbe module for more information and options')
self.frame.layout().addWidget(self.goToModule)
self.goToModule.connect("clicked()", self.onGoToModule)
# hide this for now - there's not much to see in the module itself
self.goToModule.hide()
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 volume selector
#
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.inputSelector.selectNodeUponCreation = True
self.inputSelector.addEnabled = False
self.inputSelector.removeEnabled = False
self.inputSelector.noneEnabled = False
self.inputSelector.showHidden = False
self.inputSelector.showChildNodeTypes = False
self.inputSelector.setMRMLScene(slicer.mrmlScene)
self.inputSelector.setToolTip("Pick the input to the algorithm.")
parametersFormLayout.addRow("Input Volume: ", self.inputSelector)
#
# 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.imageThresholdSliderWidget = ctk.ctkSliderWidget()
self.imageThresholdSliderWidget.singleStep = 0.1
self.imageThresholdSliderWidget.minimum = -100
self.imageThresholdSliderWidget.maximum = 100
self.imageThresholdSliderWidget.value = 0.5
self.imageThresholdSliderWidget.setToolTip(
"Set threshold value for computing the output image. Voxels that have intensities lower than this value will set to zero."
)
parametersFormLayout.addRow("Image threshold",
self.imageThresholdSliderWidget)
#
# 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.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
self.outputSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onSelect()
#Modyfikacja kodu
# Parameters Area
#
parametersCollapsibleButton2 = ctk.ctkCollapsibleButton()
parametersCollapsibleButton2.text = "Adjust"
self.layout.addWidget(parametersCollapsibleButton2)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton2)
#
# input model selector
#
self.inputSelector2 = slicer.qMRMLNodeComboBox()
self.inputSelector2.nodeTypes = ["vtkMRMLModelNode"]
self.inputSelector2.selectNodeUponCreation = True
self.inputSelector2.addEnabled = False
self.inputSelector2.removeEnabled = False
self.inputSelector2.noneEnabled = False
self.inputSelector2.showHidden = False
self.inputSelector2.showChildNodeTypes = False
self.inputSelector2.setMRMLScene(slicer.mrmlScene)
self.inputSelector2.setToolTip("Pick the input to the algorithm.")
parametersFormLayout.addRow("Model: ", self.inputSelector2)
#
# opacity value
#
self.imageOpacitySliderWidget = ctk.ctkSliderWidget()
self.imageOpacitySliderWidget.singleStep = 0.1
self.imageOpacitySliderWidget.minimum = 0
self.imageOpacitySliderWidget.maximum = 100
self.imageOpacitySliderWidget.value = 50
self.imageOpacitySliderWidget.setToolTip("Set opacity value.")
parametersFormLayout.addRow("Image threshold",
self.imageOpacitySliderWidget)
#
# Apply Button
#
self.applyButton1 = qt.QPushButton("Apply")
self.applyButton1.toolTip = "Run the algorithm."
self.applyButton1.enabled = False
parametersFormLayout.addRow(self.applyButton1)
# connections
self.applyButton1.connect('clicked(bool)', self.onApplyButton1)
self.inputSelector2.connect("currentNodeChanged(vtkMRMLNode*)",
self.onSelect2)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onSelect()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.chartOptions = ("Count", "Volume mm^3", "Volume cc", "Min", "Max",
"Mean", "Median", "StdDev")
self.logic = None
self.grayscaleNode = None
self.labelNode = None
self.fileName = None
self.fileDialog = None
# Instantiate and connect widgets ...
#
# the grayscale volume selector
#
self.grayscaleSelectorFrame = qt.QFrame(self.parent)
self.grayscaleSelectorFrame.setLayout(qt.QHBoxLayout())
self.parent.layout().addWidget(self.grayscaleSelectorFrame)
self.grayscaleSelectorLabel = qt.QLabel("Grayscale Volume: ",
self.grayscaleSelectorFrame)
self.grayscaleSelectorLabel.setToolTip(
"Select the grayscale volume (background grayscale scalar volume node) for statistics calculations"
)
self.grayscaleSelectorFrame.layout().addWidget(
self.grayscaleSelectorLabel)
self.grayscaleSelector = slicer.qMRMLNodeComboBox(
self.grayscaleSelectorFrame)
self.grayscaleSelector.nodeTypes = ["vtkMRMLScalarVolumeNode"]
self.grayscaleSelector.selectNodeUponCreation = False
self.grayscaleSelector.addEnabled = False
self.grayscaleSelector.removeEnabled = False
self.grayscaleSelector.noneEnabled = True
self.grayscaleSelector.showHidden = False
self.grayscaleSelector.showChildNodeTypes = False
self.grayscaleSelector.setMRMLScene(slicer.mrmlScene)
# TODO: need to add a QLabel
# self.grayscaleSelector.SetLabelText( "Master Volume:" )
self.grayscaleSelectorFrame.layout().addWidget(self.grayscaleSelector)
#
# the label volume selector
#
self.labelSelectorFrame = qt.QFrame()
self.labelSelectorFrame.setLayout(qt.QHBoxLayout())
self.parent.layout().addWidget(self.labelSelectorFrame)
self.labelSelectorLabel = qt.QLabel()
self.labelSelectorLabel.setText("Label Map: ")
self.labelSelectorFrame.layout().addWidget(self.labelSelectorLabel)
self.labelSelector = slicer.qMRMLNodeComboBox()
self.labelSelector.nodeTypes = ["vtkMRMLLabelMapVolumeNode"]
# todo addAttribute
self.labelSelector.selectNodeUponCreation = False
self.labelSelector.addEnabled = False
self.labelSelector.noneEnabled = True
self.labelSelector.removeEnabled = False
self.labelSelector.showHidden = False
self.labelSelector.showChildNodeTypes = True
self.labelSelector.setMRMLScene(slicer.mrmlScene)
self.labelSelector.setToolTip("Pick the label map to edit")
self.labelSelectorFrame.layout().addWidget(self.labelSelector)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Apply")
self.applyButton.toolTip = "Calculate Statistics."
self.applyButton.enabled = False
self.parent.layout().addWidget(self.applyButton)
# model and view for stats table
self.view = qt.QTableView()
self.view.sortingEnabled = True
self.parent.layout().addWidget(self.view)
# Chart button
self.chartFrame = qt.QFrame()
self.chartFrame.setLayout(qt.QHBoxLayout())
self.parent.layout().addWidget(self.chartFrame)
self.chartButton = qt.QPushButton("Chart")
self.chartButton.toolTip = "Make a chart from the current statistics."
self.chartFrame.layout().addWidget(self.chartButton)
self.chartOption = qt.QComboBox()
self.chartOption.addItems(self.chartOptions)
self.chartFrame.layout().addWidget(self.chartOption)
self.chartIgnoreZero = qt.QCheckBox()
self.chartIgnoreZero.setText('Ignore Zero')
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.chartFrame.enabled = False
# Save button
self.exportToTableButton = qt.QPushButton("Export to table")
self.exportToTableButton.toolTip = "Export statistics to table node"
self.exportToTableButton.enabled = False
self.parent.layout().addWidget(self.exportToTableButton)
# Add vertical spacer
self.parent.layout().addStretch(1)
# connections
self.applyButton.connect('clicked()', self.onApply)
self.chartButton.connect('clicked()', self.onChart)
self.exportToTableButton.connect('clicked()', self.onExportToTable)
self.grayscaleSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onGrayscaleSelect)
self.labelSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onLabelSelect)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Input
inputsCollapsibleButton = ctk.ctkCollapsibleButton()
inputsCollapsibleButton.text = "Inputs"
self.layout.addWidget(inputsCollapsibleButton)
inputsFormLayout = qt.QFormLayout(inputsCollapsibleButton)
self.inputSelector = slicer.qMRMLNodeComboBox()
self.inputSelector.selectNodeUponCreation = True
self.inputSelector.addEnabled = False
self.inputSelector.removeEnabled = True
self.inputSelector.renameEnabled = True
self.inputSelector.noneEnabled = False
self.inputSelector.showHidden = False
self.inputSelector.setMRMLScene(slicer.mrmlScene)
inputsFormLayout.addRow("Input Node: ", self.inputSelector)
self.showHiddenNodesCheckBox = qt.QCheckBox('')
self.showHiddenNodesCheckBox.checked = False
inputsFormLayout.addRow('Show Hidden Nodes: ',
self.showHiddenNodesCheckBox)
# Quick info
quickInfoCollapsibleButton = ctk.ctkCollapsibleButton()
quickInfoCollapsibleButton.text = "Node overview"
self.layout.addWidget(quickInfoCollapsibleButton)
quickInfoFormLayout = qt.QFormLayout(quickInfoCollapsibleButton)
self.nodeNameLabel = qt.QLabel()
quickInfoFormLayout.addRow("Node name: ", self.nodeNameLabel)
self.nodeIdLabel = qt.QLabel()
quickInfoFormLayout.addRow("Node ID: ", self.nodeIdLabel)
self.nodeTypeLabel = qt.QLabel()
quickInfoFormLayout.addRow("Node type: ", self.nodeTypeLabel)
referencedNodeFrame = qt.QFrame()
hbox = qt.QHBoxLayout()
referencedNodeFrame.setLayout(hbox)
self.referencedNodeSelector = qt.QComboBox()
self.referencedNodeSelectButton = qt.QPushButton("Select")
hbox.addWidget(self.referencedNodeSelector)
hbox.addWidget(self.referencedNodeSelectButton)
quickInfoFormLayout.addRow("Referenced nodes: ", referencedNodeFrame)
referencingNodeFrame = qt.QFrame()
hbox = qt.QHBoxLayout()
referencingNodeFrame.setLayout(hbox)
self.referencingNodeSelector = qt.QComboBox()
self.referencingNodeSelectButton = qt.QPushButton("Select")
hbox.addWidget(self.referencingNodeSelector)
hbox.addWidget(self.referencingNodeSelectButton)
quickInfoFormLayout.addRow("Nodes referencing this node: ",
referencingNodeFrame)
self.showInfoButton = qt.QPushButton("Show node information window")
quickInfoFormLayout.addRow(self.showInfoButton)
self.createVariableButtonBaseText = "Create variable in Python console"
self.createVariableButton = qt.QPushButton(
self.createVariableButtonBaseText)
quickInfoFormLayout.addRow(self.createVariableButton)
# connections
self.showInfoButton.connect('clicked(bool)', self.onShowInfoClicked)
self.createVariableButton.connect('clicked(bool)',
self.onCreateVariableClicked)
self.showHiddenNodesCheckBox.connect('stateChanged(int)',
self.onShowHiddenNodesChecked)
self.inputSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onSelectNode)
self.referencedNodeSelectButton.connect(
'clicked(bool)', self.onSelectReferencedNodeClicked)
self.referencingNodeSelectButton.connect(
'clicked(bool)', self.onSelectReferencingNodeClicked)
# Add vertical spacer
self.layout.addStretch(1)
# Initialize
self.onSelectNode()
def setup(self):
#
# servers
#
# testing server - not exposed (used for development)
self.localFrame = ctk.ctkCollapsibleButton(self.parent)
self.localFrame.setLayout(qt.QVBoxLayout())
self.localFrame.setText("Servers")
self.layout.addWidget(self.localFrame)
self.localFrame.collapsed = False
self.toggleServer = qt.QPushButton("Start Testing Server")
self.localFrame.layout().addWidget(self.toggleServer)
self.toggleServer.connect('clicked()', self.onToggleServer)
self.verboseServer = qt.QCheckBox("Verbose")
self.localFrame.layout().addWidget(self.verboseServer)
# advanced options - not exposed to end users
# developers can uncomment these lines to access testing server
self.toggleServer.hide()
self.verboseServer.hide()
# Listener
settings = qt.QSettings()
self.toggleListener = qt.QPushButton()
self.toggleListener.checkable = True
if hasattr(slicer, 'dicomListener'):
self.toggleListener.text = "Stop Listener"
slicer.dicomListener.process.connect(
'stateChanged(QProcess::ProcessState)',
self.onListenerStateChanged)
else:
self.toggleListener.text = "Start Listener"
self.localFrame.layout().addWidget(self.toggleListener)
self.toggleListener.connect('clicked()', self.onToggleListener)
self.runListenerAtStart = qt.QCheckBox(
"Start Listener when Slicer Starts")
self.localFrame.layout().addWidget(self.runListenerAtStart)
self.runListenerAtStart.checked = settingsValue(
'DICOM/RunListenerAtStart', False, converter=toBool)
self.runListenerAtStart.connect('clicked()', self.onRunListenerAtStart)
# the Database frame (home of the ctkDICOM widget)
self.dicomFrame = ctk.ctkCollapsibleButton(self.parent)
self.dicomFrame.setLayout(qt.QVBoxLayout())
self.dicomFrame.setText("DICOM Database and Networking")
self.layout.addWidget(self.dicomFrame)
self.detailsPopup = self.getSavedDICOMDetailsWidgetType()()
# XXX Slicer 4.5 - Remove these. Here only for backward compatibility.
self.dicomBrowser = self.detailsPopup.dicomBrowser
self.tables = self.detailsPopup.tables
# connect to the 'Show DICOM Browser' button
self.showBrowserButton = qt.QPushButton('Show DICOM Browser')
self.dicomFrame.layout().addWidget(self.showBrowserButton)
self.showBrowserButton.connect('clicked()', self.onOpenDetailsPopup)
# connect to the main window's dicom button
mw = slicer.util.mainWindow()
if mw:
try:
action = slicer.util.findChildren(mw,
name='LoadDICOMAction')[0]
action.connect('triggered()', self.onOpenDetailsPopup)
except IndexError:
logging.error(
'Could not connect to the main window DICOM button')
if hasattr(slicer, 'dicomListener'):
slicer.dicomListener.fileToBeAddedCallback = self.onListenerToAddFile
slicer.dicomListener.fileAddedCallback = self.onListenerAddedFile
slicer.dicomDatabase.connect('databaseChanged()',
self.onDatabaseChanged)
# the recent activity frame
self.activityFrame = ctk.ctkCollapsibleButton(self.parent)
self.activityFrame.setLayout(qt.QVBoxLayout())
self.activityFrame.setText("Recent DICOM Activity")
self.layout.addWidget(self.activityFrame)
self.recentActivity = DICOMLib.DICOMRecentActivityWidget(
self.activityFrame, detailsPopup=self.detailsPopup)
self.activityFrame.layout().addWidget(self.recentActivity)
self.requestUpdateRecentActivity()
# Add spacer to layout
self.layout.addStretch(1)
def setupFlicker(self):
self.flickerTimer = self.createTimer(400, self.onFlickerToggled, singleShot=False)
self.flickerCheckBox = qt.QCheckBox("Flicker")
self.flickerCheckBox.checked = False
