def createRegFrame(self):
#
# Parameters Area
#
regCollapsibleButton = ctk.ctkCollapsibleButton()
regCollapsibleButton.text = "Group Registration"
self.layout.addWidget(regCollapsibleButton)
# Layout within the dummy collapsible button
regFormLayout = qt.QFormLayout(regCollapsibleButton)
#
# target volume selector
#
self.regTargetSelector = slicer.qMRMLNodeComboBox()
self.regTargetSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
self.regTargetSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", 0 )
self.set_selector_options(self.regTargetSelector)
self.regTargetSelector.setToolTip( "Pick the input to the algorithm." )
regFormLayout.addRow("Target Volume: ", self.regTargetSelector)
#
# moving volume selector
#
self.regVolumesSelector = slicer.qMRMLCheckableNodeComboBox()
self.regVolumesSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
self.regVolumesSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", 0 )
self.set_selector_options(self.regVolumesSelector)
self.regVolumesSelector.setToolTip( "Pick the input to the algorithm." )
regFormLayout.addRow("Moving Volumes: ", self.regVolumesSelector)
#
# Apply Button
#
self.registerButton = qt.QPushButton("Register")
self.registerButton.toolTip = "Register Images"
self.registerButton.enabled = False
regFormLayout.addRow(self.registerButton)
# Connections before scene
self.registerButton.connect('clicked(bool)', self.onRegisterButton)
self.regTargetSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onTargetSelected)
# Set MRML scenes
self.regVolumesSelector.setMRMLScene( slicer.mrmlScene )
self.regTargetSelector.setMRMLScene( slicer.mrmlScene )
def setup(self):
# Instantiate and connect widgets ...
# Status text
statusCollapsibleButton = ctk.ctkCollapsibleButton()
statusCollapsibleButton.text = "Status"
self.layout.addWidget(statusCollapsibleButton)
self.statusFormLayout = qt.QFormLayout(statusCollapsibleButton)
self.overallStatus = qt.QLabel()
self.overallStatus.text = "Idle"
self.statusFormLayout.addRow("New Process:", self.overallStatus)
self.processes = list()
#
# Volumes
#
self.inputImagesCollapsibleButton = ctk.ctkCollapsibleButton()
self.inputImagesCollapsibleButton.text = "Input Images"
self.layout.addWidget(self.inputImagesCollapsibleButton)
# Layout within the collapsible button
inputImagesFormLayout = qt.QFormLayout(self.inputImagesCollapsibleButton)
# input volume selector
self.fixedVolumeSelector = slicer.qMRMLNodeComboBox()
self.fixedVolumeSelector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.fixedVolumeSelector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap", 0)
self.fixedVolumeSelector.selectNodeUponCreation = True
self.fixedVolumeSelector.addEnabled = True
self.fixedVolumeSelector.removeEnabled = True
self.fixedVolumeSelector.noneEnabled = False
self.fixedVolumeSelector.showHidden = False
self.fixedVolumeSelector.showChildNodeTypes = False
self.fixedVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.fixedVolumeSelector.setToolTip("Pick the fixed input to the algorithm.")
inputImagesFormLayout.addRow("Fixed Image Volume: ", self.fixedVolumeSelector)
# Moving volume selector
self.movingVolumeSelector = slicer.qMRMLCheckableNodeComboBox()
# self.movingVolumeSelector = slicer.qMRMLNodeComboBox()
self.movingVolumeSelector.nodeTypes = (("vtkMRMLScalarVolumeNode"), "")
self.movingVolumeSelector.addAttribute("vtkMRMLScalarVolumeNode", "LabelMap", 0)
self.movingVolumeSelector.selectNodeUponCreation = True
self.movingVolumeSelector.addEnabled = True
self.movingVolumeSelector.removeEnabled = True
self.movingVolumeSelector.noneEnabled = False
self.movingVolumeSelector.showHidden = False
self.movingVolumeSelector.showChildNodeTypes = False
self.movingVolumeSelector.setMRMLScene(slicer.mrmlScene)
self.movingVolumeSelector.setToolTip("Pick the moving volume to the algorithm.")
inputImagesFormLayout.addRow("Moving Volume: ", self.movingVolumeSelector)
#
# Crop parameters
#
self.cropParametersCollapsibleButton = ctk.ctkCollapsibleButton()
self.cropParametersCollapsibleButton.text = "Crop Parameters"
self.layout.addWidget(self.cropParametersCollapsibleButton)
cropParametersFormLayout = qt.QFormLayout(self.cropParametersCollapsibleButton)
cropParametersFormLayout
# Input ROI
self.annotationROISelector = slicer.qMRMLNodeComboBox()
self.annotationROISelector.nodeTypes = (("vtkMRMLAnnotationROINode"), "")
self.annotationROISelector.editEnabled = True
self.annotationROISelector.renameEnabled = True
self.annotationROISelector.setMRMLScene(slicer.mrmlScene)
self.annotationROISelector.setToolTip("Pick the fixed input to the algorithm.")
cropParametersFormLayout.addRow("Input ROI: ", self.annotationROISelector)
# ROI Visibility
self.ROIVisibilityButton = qt.QToolButton()
visibilityIcon = qt.QIcon()
visibilityIcon.addPixmap(qt.QPixmap(":/Icons/VisibleOff.png"), qt.QIcon().Normal, qt.QIcon().Off)
visibilityIcon.addPixmap(qt.QPixmap(":/Icons/VisibleOn.png"), qt.QIcon().Normal, qt.QIcon().On)
self.ROIVisibilityButton.setIcon(visibilityIcon)
self.ROIVisibilityButton.setCheckable(True)
cropParametersFormLayout.addRow("Visibility ROI:", self.ROIVisibilityButton)
# Cropping technique
croppingTechniqueLayout = qt.QHBoxLayout()
self.interpolationButton = qt.QRadioButton("Interpolated cropping")
self.interpolationButton.setChecked(True)
self.voxelBasedButton = qt.QRadioButton("Voxel based cropping")
croppingTechniqueLayout.addWidget(self.interpolationButton)
croppingTechniqueLayout.addWidget(self.voxelBasedButton)
cropParametersFormLayout.addRow("Technique: ", croppingTechniqueLayout)
# Interpolation options
self.interpolationOptionsCollapsibleGroupBox = ctk.ctkCollapsibleGroupBox()
self.interpolationOptionsCollapsibleGroupBox.title = "Interpolation options"
cropParametersFormLayout.addRow("", self.interpolationOptionsCollapsibleGroupBox)
interpolationOptionsLayout = qt.QFormLayout(self.interpolationOptionsCollapsibleGroupBox)
interpolationOptionsLayout.setFieldGrowthPolicy(qt.QFormLayout().ExpandingFieldsGrow)
interpolationOptionsLayout.setRowWrapPolicy(qt.QFormLayout().WrapLongRows)
# Isotropic
self.isotropicCheckBox = qt.QCheckBox()
self.isotropicCheckBox.checked = True
interpolationOptionsLayout.addRow("Isotropic output voxel", self.isotropicCheckBox)
# Input spacing scaling constant
self.inputSpacingScaling = qt.QDoubleSpinBox()
self.inputSpacingScaling.setToolTip(
"In not equal to 1, this will result in upsampling (<1) or downlsampling (>1) relative to the voxel spacing of the input volume."
)
self.inputSpacingScaling.value = 1.000000
interpolationOptionsLayout.addRow("Input spacing scaling constant: ", self.inputSpacingScaling)
# Interpolator technique
interpolatorWidget = qt.QWidget()
sizep = qt.QSizePolicy()
sizep.setHorizontalPolicy(qt.QSizePolicy().Expanding)
sizep.setVerticalPolicy(qt.QSizePolicy().Preferred)
sizep.setHorizontalStretch(0)
sizep.setVerticalStretch(0)
interpolatorWidget.setSizePolicy(sizep)
interpolatorLayout = qt.QGridLayout(interpolatorWidget)
interpolationOptionsLayout.addRow("Technique: ", interpolatorWidget)
self.iNNButton = qt.QRadioButton("Nearest Neighbor")
self.iLinearButton = qt.QRadioButton("Linear")
self.iWindowedSincButton = qt.QRadioButton("WindowedSinc")
self.iBSplineButton = qt.QRadioButton("B-spline")
self.iNNButton.setSizePolicy(qt.QSizePolicy().Minimum, qt.QSizePolicy().Preferred)
self.iLinearButton.setSizePolicy(qt.QSizePolicy().MinimumExpanding, qt.QSizePolicy().Preferred)
self.iWindowedSincButton.setSizePolicy(qt.QSizePolicy().Minimum, qt.QSizePolicy().Preferred)
self.iBSplineButton.setSizePolicy(qt.QSizePolicy().MinimumExpanding, qt.QSizePolicy().Preferred)
self.iLinearButton.setChecked(True)
interpolatorLayout.addWidget(self.iNNButton, 0, 0)
interpolatorLayout.addWidget(self.iLinearButton, 0, 1)
interpolatorLayout.addWidget(self.iWindowedSincButton, 1, 0)
interpolatorLayout.addWidget(self.iBSplineButton, 1, 1)
#
# Crop Button
#
self.cropButton = qt.QPushButton("Crop")
self.cropButton.toolTip = "Crop the fixed volume."
self.cropButton.enabled = False
self.layout.addWidget(self.cropButton)
# Align and crop
self.alignAndCropButton = qt.QPushButton("Align and Crop")
self.alignAndCropButton.toolTip = "Align moving volumes with fixed volume and crop all the images"
self.alignAndCropButton.enabled = False
self.layout.addWidget(self.alignAndCropButton)
self.layout.addStretch(1)
self.cropParametersNode = slicer.modulemrml.vtkMRMLCropVolumeParametersNode()
self.onFixedVolumeSelect()
self.onMovingVolumeSelect()
self.onAnnotationROIChanged()
self.onROIVisibilityChanged()
# connections
self.cropButton.connect("clicked(bool)", self.onCrop)
self.alignAndCropButton.connect("clicked(bool)", self.onAlignAndCrop)
self.fixedVolumeSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onFixedVolumeSelect)
self.movingVolumeSelector.connect("checkedNodesChanged(void)", self.onMovingVolumeSelect)
self.annotationROISelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onAnnotationROIChanged)
self.ROIVisibilityButton.connect("toggled(bool)", self.onROIVisibilityChanged)
self.voxelBasedButton.connect("clicked(bool)", self.onVoxelBasedButtonClicked)
self.interpolationButton.connect("clicked(bool)", self.onInterpolationButtonClicked)
# Display current fixed node
self.displayFixedVolume()
self.updateCropParameters()
self.outputNodes = dict()
self.nreg_completed = 0
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# -------------------------------------------------------------------------------------
self.modelList = list()
self.fieldList = list()
self.ROIList = list()
self.ROIDict = dict() # Key = Name of ROI
# Value = Dictionary of Fields (key = Name of Field
# Value = dictionary of shapes
# key = name of shapes
# value = Statistics store()
self.logic = MeshStatisticsLogic()
# ------------------------------------------------------------------------------------
# SHAPES INPUT
# ------------------------------------------------------------------------------------
self.inputComboBox = slicer.qMRMLCheckableNodeComboBox()
self.inputComboBox.nodeTypes = ['vtkMRMLModelNode']
self.inputComboBox.setMRMLScene(slicer.mrmlScene)
inputLayout = qt.QFormLayout()
inputLayout.addRow(' Models: ', self.inputComboBox)
self.layout.addLayout(inputLayout)
self.inputComboBox.connect('checkedNodesChanged()', self.onInputComboBoxCheckedNodesChanged)
# ------------------------------------------------------------------------------------
# ROI TABLE
# ------------------------------------------------------------------------------------
self.ROIComboBox = ctk.ctkComboBox()
self.ROIComboBox.adjustSize()
self.ROICheckBox = qt.QCheckBox('All')
ROILayout = qt.QHBoxLayout()
ROILayout_0 = qt.QFormLayout()
ROILayout_0.addRow(' Region considered: ', self.ROIComboBox)
ROILayout.addLayout(ROILayout_0)
ROILayout.addWidget(self.ROICheckBox)
self.layout.addLayout(ROILayout)
self.ROICheckBox.connect('stateChanged(int)', self.onROICheckBoxStateChanged)
# ------------------------------------------------------------------------------------
# FIELD TABLE
# ------------------------------------------------------------------------------------
self.tableField = qt.QTableWidget()
self.tableField.setColumnCount(2)
self.tableField.setMinimumHeight(250)
self.tableField.setHorizontalHeaderLabels([' ', ' Field Name '])
self.tableField.setColumnWidth(0, 20)
self.tableField.setColumnWidth(1, 260)
self.tableField.setSizePolicy(qt.QSizePolicy().Expanding, qt.QSizePolicy().Expanding)
label = qt.QLabel(' Select a Field to compute statistics on:')
self.fieldLayout = qt.QVBoxLayout()
self.fieldLayout.addWidget(label)
self.fieldLayout.addWidget(self.tableField)
self.layout.addLayout(self.fieldLayout)
# ------------------------------------------------------------------------------------
# RUN
# ------------------------------------------------------------------------------------
self.runButton = qt.QPushButton(' Run ')
self.runButton.enabled = False
roiLayout = qt.QHBoxLayout()
roiLayout.addWidget(self.runButton)
self.layout.addLayout(roiLayout)
self.runButton.connect('clicked()', self.onRunButton)
# ------------------------------------------------------------------------------------
# Statistics Table - Export
# ------------------------------------------------------------------------------------
self.tabROI = qt.QTabWidget()
self.tabROI.setTabPosition(0)
self.tabROI.adjustSize()
# ---------------------------- Directory - Export Button -----------------------------
self.directoryExport = ctk.ctkDirectoryButton()
self.exportCheckBox = qt.QCheckBox('Separate Files')
self.exportCheckBox.setChecked(True)
self.exportButton = qt.QPushButton(' Export ')
self.exportButton.enabled = True
self.exportPointValueCheckBox = qt.QCheckBox('Export Value on Each Point')
self.exportLayout = qt.QVBoxLayout()
self.directoryAndExportLayout = qt.QHBoxLayout()
self.directoryAndExportLayout.addWidget(self.directoryExport)
self.directoryAndExportLayout.addWidget(self.exportCheckBox)
self.directoryAndExportLayout.addWidget(self.exportPointValueCheckBox)
self.exportButtonsLayout = qt.QHBoxLayout()
self.exportButtonsLayout.addWidget(self.exportButton)
self.exportLayout.addLayout(self.directoryAndExportLayout)
self.exportLayout.addLayout(self.exportButtonsLayout)
self.layout.addStretch(1)
self.logic.updateInterface(self.tableField, self.ROIComboBox, self.ROIList, self.modelList, self.layout)
# ------------------------------------------------------------------------------------
# OBSERVERS
# ------------------------------------------------------------------------------------
def onCloseScene(obj, event):
# initialize Parameters
globals()['MeshStatistics'] = slicer.util.reloadScriptedModule('MeshStatistics')
slicer.mrmlScene.AddObserver(slicer.mrmlScene.EndCloseEvent, onCloseScene)
def createMaskFrame(self):
#
# 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.nodeSelector = slicer.qMRMLCheckableNodeComboBox()
self.nodeSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
self.nodeSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", 0 )
self.set_selector_options(self.nodeSelector)
self.nodeSelector.setMRMLScene( slicer.mrmlScene )
self.nodeSelector.setToolTip( "Pick the input to the algorithm." )
parametersFormLayout.addRow("Input Volumes: ", self.nodeSelector)
#
# annotation ROI selector
#
self.roiSelector = slicer.qMRMLNodeComboBox()
self.roiSelector.nodeTypes = ( ("vtkMRMLAnnotationROINode"), "" )
#self.roiSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", 0 )
self.set_selector_options(self.roiSelector)
self.roiSelector.setMRMLScene( slicer.mrmlScene )
self.roiSelector.setToolTip( "Pick the ROI for the masking." )
parametersFormLayout.addRow("Mask ROI: ", self.roiSelector)
#
# check box to trigger taking screen shots for later use in tutorials
#
self.inPlaceCheckBox = qt.QCheckBox()
self.inPlaceCheckBox.checked = 0
self.inPlaceCheckBox.setToolTip("If checked, will operate in-place.")
# TODO: make option to duplicate nodes
parametersFormLayout.addRow("Mask in-place", self.inPlaceCheckBox)
#
# 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.nodeSelector.connect("checkedNodesChanged()", self.onSelect)
#
# Helper Area
#
helperCollapsibleButton = ctk.ctkCollapsibleButton()
helperCollapsibleButton.text = "Utilities"
self.layout.addWidget(helperCollapsibleButton)
# Layout within the dummy collapsible button
helperFormLayout = qt.QFormLayout(helperCollapsibleButton)
#
# Clear Unmasked Images Button
#
self.clearImagesButton = qt.QPushButton("Remove Unmasked Images From Scene")
self.clearImagesButton.toolTip = "Remove unmasked from scene."
helperFormLayout.addRow(self.clearImagesButton)
self.clearImagesButton.connect('clicked(bool)', self.onClearUnmaskedButton)
#
# Clear Masked Images Button
#
self.clearImagesButton = qt.QPushButton("Remove Masked Images From Scene")
self.clearImagesButton.toolTip = "Remove masked from scene."
helperFormLayout.addRow(self.clearImagesButton)
self.clearImagesButton.connect('clicked(bool)', self.onClearMaskedButton)
