def __init__(self, ModuleNodeName):
VTKObservationMixin.__init__(self)
self.InputCases = list()
self.allCaseStartTime = 0
# Dictionaries
self.pipeline = {}
self.completed = {}
# Status
self.Node = slicer.vtkMRMLCommandLineModuleNode()
self.Node.SetStatus(self.Node.Idle)
self.Node.SetName(ModuleNodeName)
self.ProgressBar = slicer.qSlicerCLIProgressBar()
self.ProgressBar.setCommandLineModuleNode(self.Node)
self.ProgressBar.setNameVisibility(slicer.qSlicerCLIProgressBar.AlwaysVisible)
self.ErrorMessage = 'Unexpected error'
def __init__(self, pipelineID, CaseInput, interface):
VTKObservationMixin.__init__(self)
self.pipelineID = pipelineID
self.strPipelineID = "_" + str(self.pipelineID)
self.CaseInput = CaseInput
# Pipeline computation time
self.pipelineStartTime = 0
self.pipelineEndTime = 0
# Status
self.StatusModifiedEvent = slicer.vtkMRMLCommandLineModuleNode().StatusModifiedEvent
self.Node = slicer.vtkMRMLCommandLineModuleNode()
self.Node.SetStatus(self.Node.Idle)
self.Node.SetName('Case ' + str(self.pipelineID))
self.currentCLINode = None
self.ProgressBar = slicer.qSlicerCLIProgressBar()
self.ProgressBar.setCommandLineModuleNode(self.Node)
self.ProgressBar.setNameVisibility(slicer.qSlicerCLIProgressBar.AlwaysVisible)
self.ErrorMessage = 'Unexpected error'
def __init__(self, pipelineID, CaseInput, interface):
VTKObservationMixin.__init__(self)
self.pipelineID = pipelineID
self.strPipelineID = "_" + str(self.pipelineID)
self.CaseInput = CaseInput
# Pipeline computation time
self.pipelineStartTime = 0
self.pipelineEndTime = 0
# Status
self.StatusModifiedEvent = slicer.vtkMRMLCommandLineModuleNode(
).StatusModifiedEvent
self.Node = slicer.vtkMRMLCommandLineModuleNode()
self.Node.SetStatus(self.Node.Idle)
self.Node.SetName('Case ' + str(self.pipelineID))
self.currentCLINode = None
self.ProgressBar = slicer.qSlicerCLIProgressBar()
self.ProgressBar.setCommandLineModuleNode(self.Node)
self.ProgressBar.setNameVisibility(
slicer.qSlicerCLIProgressBar.AlwaysVisible)
self.ErrorMessage = 'Unexpected error'
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
#
# input/output collapsible area
#
inputOutputCollapsibleButton = ctk.ctkCollapsibleButton()
inputOutputCollapsibleButton.text = "Input/Output"
self.layout.addWidget(inputOutputCollapsibleButton)
# Layout within the i/o collapsible button
ioFormLayout = qt.QFormLayout(inputOutputCollapsibleButton)
#
# input volume selector
#
self.inputSelector = ctk.ctkPathLineEdit()
self.inputSelector.filters = ctk.ctkPathLineEdit.Files
self.inputSelector.setToolTip("Specify the input dwi")
ioFormLayout.addRow("Input Volume: ", self.inputSelector)
#
# input mask selector
#
self.maskSelector = ctk.ctkPathLineEdit()
self.maskSelector.filters = ctk.ctkPathLineEdit.Files
self.maskSelector.setToolTip("Specify the mask of input dwi")
ioFormLayout.addRow("Input Volume Mask: ", self.maskSelector)
#
# Create Mask
#
self.createMaskCheckBox = qt.QCheckBox('Create the mask')
self.createMaskCheckBox.toolTip = "Check if you don't have a mask or would like to create one"
self.createMaskCheckBox.enabled = True
self.createMaskCheckBox.checked = False
ioFormLayout.addWidget(self.createMaskCheckBox)
self.createMask = False
#
# output directory selector
#
self.outputDirSelector = ctk.ctkPathLineEdit()
self.outputDirSelector.filters = ctk.ctkPathLineEdit.Dirs
self.outputDirSelector.setToolTip(
"Specify the output directory, default: same as input dwi directory"
)
ioFormLayout.addRow("Output Directory:", self.outputDirSelector)
#
# processing collapsible area
#
processCollapsibleButton = ctk.ctkCollapsibleButton()
processCollapsibleButton.text = "Processing"
self.layout.addWidget(processCollapsibleButton)
# Layout within the processing collapsible button
processFormLayout = qt.QFormLayout(processCollapsibleButton)
processFormLayout.setSpacing(10)
#
# Visual Mode
#
self.visualMode = qt.QCheckBox('Slicer Visual Mode')
self.visualMode.toolTip = '''Uncheck for auto processing w/o
Slicer visualization and user interaction'''
self.visualMode.enabled = True
self.visualMode.checked = True
processFormLayout.addWidget(self.visualMode)
self.autoMode = True # Default initialization, used to trigger Slicer GUI
#
# Process Button
#
self.applyButton = qt.QPushButton("Process")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = False
processFormLayout.addRow(self.applyButton)
#
# Progress Bar
#
self.progressBar = slicer.qSlicerCLIProgressBar()
self.progressBar.setToolTip("Progress of the algorithm")
processFormLayout.addWidget(self.progressBar)
#
# Decision Labelling
#
self.decisionLabel = qt.QLabel("Gradient information")
self.decisionLabel.setToolTip(
"Machine learning decision for current gradient on display")
self.decisionLabel.setStyleSheet("font: bold")
processFormLayout.addWidget(self.decisionLabel)
#
# Summary Labelling
#
self.summaryLabel = qt.QLabel("QC summary")
self.summaryLabel.setToolTip("Quality check summary")
self.summaryLabel.setStyleSheet("font: bold")
processFormLayout.addWidget(self.summaryLabel)
#
# Reset Result Button
#
self.resetResultsButton = qt.QPushButton("Reset Results")
self.resetResultsButton.toolTip = "Reset to machine learning results."
self.resetResultsButton.enabled = True
processFormLayout.addRow(self.resetResultsButton)
#
# Decision collapsible area
#
processCollapsibleButton = ctk.ctkCollapsibleButton()
processCollapsibleButton.text = "Decision"
self.layout.addWidget(processCollapsibleButton)
# Layout within the processing collapsible button
decisionFormLayout = qt.QFormLayout(processCollapsibleButton)
decisionFormLayout.setSpacing(10)
# -------------------------------------------------------------------------
qualityPanel = qt.QHBoxLayout()
#
# Keep Gradient Button
#
self.keepButton = qt.QPushButton("Keep")
self.keepButton.toolTip = "Keep the current gradient."
self.keepButton.enabled = True
qualityPanel.addWidget(self.keepButton)
#
# Discard Gradient Button
#
self.discardButton = qt.QPushButton("Discard")
self.discardButton.toolTip = "Discard the current gradient."
self.discardButton.enabled = True
self.discardButton.setStyleSheet("background-color: red")
qualityPanel.addWidget(self.discardButton)
decisionFormLayout.addRow(qualityPanel)
# -------------------------------------------------------------------------
# -------------------------------------------------------------------------
confidencePanel = qt.QHBoxLayout()
#
# Make it sure Button
#
self.sureButton = qt.QPushButton("Sure")
self.sureButton.toolTip = "Make it sure."
self.sureButton.enabled = True
confidencePanel.addWidget(self.sureButton)
# Make it unsure Button
#
self.unsureButton = qt.QPushButton("Unsure")
self.unsureButton.toolTip = "Make it unsure."
self.unsureButton.enabled = True
self.unsureButton.setStyleSheet("background-color: yellow")
confidencePanel.addWidget(self.unsureButton)
decisionFormLayout.addRow(confidencePanel)
# -------------------------------------------------------------------------
#
# Next Review Button
#
self.nextReviewButton = qt.QPushButton("Next Review")
self.nextReviewButton.toolTip = "Pull up the next gradient for review."
self.nextReviewButton.enabled = True
decisionFormLayout.addRow(self.nextReviewButton)
#
# Finish collapsible area
#
processCollapsibleButton = ctk.ctkCollapsibleButton()
processCollapsibleButton.text = "Finish"
self.layout.addWidget(processCollapsibleButton)
# Layout within the processing collapsible button
finishFormLayout = qt.QFormLayout(processCollapsibleButton)
#
# Save Result Button
#
self.saveResultsButton = qt.QPushButton("Save")
self.saveResultsButton.toolTip = "Save the results."
self.saveResultsButton.enabled = True
finishFormLayout.addRow(self.saveResultsButton)
# Add vertical spacer
self.layout.addStretch(1)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
self.inputSelector.connect("currentPathChanged(QString)",
self.onSelectInput)
self.maskSelector.connect("currentPathChanged(QString)",
self.onSelectMask)
self.outputDirSelector.connect("currentPathChanged(QString)",
self.onSelectOutput)
self.visualMode.connect('toggled(bool)', self.onVisualMode)
self.createMaskCheckBox.connect('toggled(bool)', self.withoutMask)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.logic = CreateMeshLogic()
# Inputs
inputsCollapsibleButton = ctk.ctkCollapsibleButton()
inputsCollapsibleButton.text = 'Inputs'
self.layout.addWidget(inputsCollapsibleButton)
inputsFormLayout = qt.QFormLayout(inputsCollapsibleButton)
# Segmentation selector
self.segmentationSelector = slicer.qMRMLNodeComboBox()
self.segmentationSelector.nodeTypes = ['vtkMRMLSegmentationNode']
self.segmentationSelector.addEnabled = False
self.segmentationSelector.removeEnabled = False
self.segmentationSelector.renameEnabled = False
self.segmentationSelector.setMRMLScene(slicer.mrmlScene)
self.segmentationSelector.setToolTip(
'Pick the segmentation to compute a mesh from')
inputsFormLayout.addRow('Segmentation:', self.segmentationSelector)
# Fiducials selector
self.fiducialsSelector = slicer.qMRMLNodeComboBox()
self.fiducialsSelector.nodeTypes = ['vtkMRMLMarkupsFiducialNode']
self.fiducialsSelector.addEnabled = False
self.fiducialsSelector.removeEnabled = False
self.fiducialsSelector.renameEnabled = False
self.fiducialsSelector.setMRMLScene(slicer.mrmlScene)
self.fiducialsSelector.setToolTip(
'Select the fiducials that will define the light sources and detectors position'
)
inputsFormLayout.addRow('Fiducials:', self.fiducialsSelector)
# Outputs
outputsCollapsibleButton = ctk.ctkCollapsibleButton()
outputsCollapsibleButton.text = 'Outputs'
self.layout.addWidget(outputsCollapsibleButton)
outputsFormLayout = qt.QFormLayout(outputsCollapsibleButton)
# Mesh directory
self.meshPathLineEdit = ctk.ctkPathLineEdit()
self.meshPathLineEdit.filters = ctk.ctkPathLineEdit.Dirs
self.meshPathLineEdit.currentPath = self.cachedPathFor(
'CreateMeshOutputPath')
outputsFormLayout.addRow('Mesh directory:', self.meshPathLineEdit)
# Mesh name
self.meshNameField = qt.QLineEdit()
outputsFormLayout.addRow('Mesh name:', self.meshNameField)
# Meshing
meshingCollapsibleButton = ctk.ctkCollapsibleButton()
meshingCollapsibleButton.text = 'Meshing'
self.layout.addWidget(meshingCollapsibleButton)
meshingFormLayout = qt.QFormLayout(meshingCollapsibleButton)
# Mesh type
self.meshTypeComboBox = ctk.ctkComboBox()
for meshType in self.logic.meshTypes:
self.meshTypeComboBox.addItem(meshType)
meshingFormLayout.addRow('Mesh type:', self.meshTypeComboBox)
# Cell size
self.cellSizeSpinBox = slicer.qMRMLSpinBox()
self.cellSizeSpinBox.setValue(1.5)
self.cellSizeSpinBox.setMRMLScene(slicer.mrmlScene)
meshingFormLayout.addRow('Cell size:', self.cellSizeSpinBox)
# Cell radius edge
self.cellRadiusSpinBox = slicer.qMRMLSpinBox()
self.cellRadiusSpinBox.setValue(3.0)
self.cellRadiusSpinBox.setMRMLScene(slicer.mrmlScene)
meshingFormLayout.addRow('Cell radius edge:', self.cellRadiusSpinBox)
# Facet size
self.facetSizeSpinBox = slicer.qMRMLSpinBox()
self.facetSizeSpinBox.setValue(1.5)
self.facetSizeSpinBox.setMRMLScene(slicer.mrmlScene)
meshingFormLayout.addRow('Facet size:', self.facetSizeSpinBox)
# Facet angle
self.facetAngleSpinBox = slicer.qMRMLSpinBox()
self.facetAngleSpinBox.setValue(25.0)
self.facetAngleSpinBox.setMRMLScene(slicer.mrmlScene)
meshingFormLayout.addRow('Facet angle:', self.facetAngleSpinBox)
# Facet distance
self.facetDistanceSpinBox = slicer.qMRMLSpinBox()
self.facetDistanceSpinBox.setValue(3.0)
self.facetDistanceSpinBox.setMRMLScene(slicer.mrmlScene)
meshingFormLayout.addRow('Facet distance:', self.facetDistanceSpinBox)
# Optimize mesh
self.optimizeCheckBox = qt.QCheckBox()
meshingFormLayout.addRow('Optimize mesh:', self.optimizeCheckBox)
# NIRFAST
nirfastCollapsibleButton = ctk.ctkCollapsibleButton()
nirfastCollapsibleButton.text = 'NIRFAST Matlab'
self.layout.addWidget(nirfastCollapsibleButton)
nirfastFormLayout = qt.QFormLayout(nirfastCollapsibleButton)
# NIRFAST-Matlab
self.nirfastMatlabPathLineEdit = ctk.ctkPathLineEdit()
self.nirfastMatlabPathLineEdit.filters = ctk.ctkPathLineEdit.Dirs
self.nirfastMatlabPathLineEdit.currentPath = self.cachedPathFor(
'NIRFASTMatlabPath')
nirfastFormLayout.addRow('NIRFAST Matlab:',
self.nirfastMatlabPathLineEdit)
# Run
self.runButton = qt.QPushButton()
self.runButton.setCheckable(True)
self.setRunning(False)
self.layout.addWidget(self.runButton)
# Progress
self.progressBar = slicer.qSlicerCLIProgressBar()
self.logic.setProgressBar(self.progressBar)
self.layout.addWidget(self.progressBar)
# Add vertical spacer
self.layout.addStretch(1)
# Connections
self.segmentationSelector.connect('currentNodeChanged(vtkMRMLNode*)',
self.onSegmentationNodeChanged)
self.onSegmentationNodeChanged(self.segmentationSelector.currentNode())
self.meshPathLineEdit.connect('currentPathChanged(QString)',
self.logic.cacheOutputMeshDir)
self.nirfastMatlabPathLineEdit.connect(
'currentPathChanged(QString)', self.logic.cacheNirfastMatlabDir)
self.runButton.connect('clicked()', self.onRun)
self.logic.setBusy = self.setRunning
self.logic.setError = self.showError