def setup(self):
ScriptedLoadableModuleWidget.setup(self)
self.logic = CNN_Image_ClassifierLogic()
self.moduleDir = os.path.dirname(
slicer.modules.collect_training_images.path)
# 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.modelSelector = qt.QComboBox()
self.modelSelector.addItems(["Select model"])
modelDirectoryContents = os.listdir(
os.path.join(self.moduleDir, os.pardir, "Models"))
modelNames = [
dir for dir in modelDirectoryContents
if dir.find(".") == -1 and dir != "Dockerfile"
]
self.modelSelector.addItems(["Create new model"])
self.modelSelector.addItems(modelNames)
parametersFormLayout.addRow(self.modelSelector)
#
# Apply Button
#
self.applyButton = qt.QPushButton("Start")
self.applyButton.toolTip = "Run the algorithm."
self.applyButton.enabled = False
parametersFormLayout.addRow(self.applyButton)
'''
self.classifyAllFramesButton = qt.QPushButton("Classify all frames")
self.classifyAllFramesButton.toolTip = "classify all frames in a sequence"
parametersFormLayout.addRow(self.classifyAllFramesButton)
'''
#
# Object table
#
self.objectTable = qt.QTableWidget()
self.objectTable.setColumnCount(3)
self.objectTable.setHorizontalHeaderLabels(
["Name", "Found", "Confidence"])
parametersFormLayout.addRow(self.objectTable)
#
# Adjust Confidence Thresholds
#
confidenceThresholdsCollapsibleButton = ctk.ctkCollapsibleButton()
confidenceThresholdsCollapsibleButton.text = "Confidence Thresholds"
self.layout.addWidget(confidenceThresholdsCollapsibleButton)
confidenceFormLayout = qt.QFormLayout(
confidenceThresholdsCollapsibleButton)
self.confidenceSlider = qt.QSlider(0x1) #horizontal slider
self.confidenceSlider.setRange(0, 100)
self.confidenceSlider.setTickInterval(5)
self.confidenceSlider.setTickPosition(2) #Ticks appear below slider
self.confidenceSlider.setSliderPosition(80)
self.confidenceSlider.setToolTip(
"Set the minimum degree of confidence that must be met for an object to be considered found"
)
confidenceFormLayout.addRow("Confidence: ", self.confidenceSlider)
self.confidenceLabel = qt.QLabel("80%")
confidenceFormLayout.addRow(self.confidenceLabel)
self.recordingPlayWidget = slicer.qMRMLSequenceBrowserPlayWidget()
parametersFormLayout.addRow(self.recordingPlayWidget)
self.recordingSeekWidget = slicer.qMRMLSequenceBrowserSeekWidget()
parametersFormLayout.addRow(self.recordingSeekWidget)
# connections
self.applyButton.connect('clicked(bool)', self.onApplyButton)
#self.classifyAllFramesButton.connect('clicked(bool)', self.onClassifyAllFramesClicked)
self.modelSelector.connect('currentIndexChanged(int)',
self.onModelSelected)
self.confidenceSlider.connect('sliderMoved(int)',
self.onConfidenceChanged)
# Add vertical spacer
self.layout.addStretch(1)
# Refresh Apply button state
self.onSelect()
try:
self.webcamReference = slicer.util.getNode('Webcam_Reference')
except slicer.util.MRMLNodeNotFoundException:
#if not self.webcamReference:
imageSpacing = [0.2, 0.2, 0.2]
imageData = vtk.vtkImageData()
imageData.SetDimensions(640, 480, 1)
imageData.AllocateScalars(vtk.VTK_UNSIGNED_CHAR, 1)
thresholder = vtk.vtkImageThreshold()
thresholder.SetInputData(imageData)
thresholder.SetInValue(0)
thresholder.SetOutValue(0)
# Create volume node
self.webcamReference = slicer.vtkMRMLVectorVolumeNode()
self.webcamReference.SetName('Webcam_Reference')
self.webcamReference.SetSpacing(imageSpacing)
self.webcamReference.SetImageDataConnection(
thresholder.GetOutputPort())
# Add volume to scene
slicer.mrmlScene.AddNode(self.webcamReference)
displayNode = slicer.vtkMRMLVectorVolumeDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
self.webcamReference.SetAndObserveDisplayNodeID(
displayNode.GetID())
self.webcamConnectorNode = self.createWebcamPlusConnector()
self.webcamConnectorNode.Start()
self.setupWebcamResliceDriver()
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# tracks the modified event observer on the currently
# selected sequence browser node
self.sequenceBrowserObserverRecord = None
self.animatorActionsGUI = None
self.logic = AnimatorLogic()
# Instantiate and connect widgets ...
#
# Parameters Area
#
parametersCollapsibleButton = ctk.ctkCollapsibleButton()
parametersCollapsibleButton.text = "Animation Parameters"
self.layout.addWidget(parametersCollapsibleButton)
# Layout within the dummy collapsible button
parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)
self.durationBox = ctk.ctkDoubleSpinBox()
self.durationBox.suffix = " seconds"
self.durationBox.decimals = 1
self.durationBox.minimum = 1
self.durationBox.value = 5
self.durationBox.toolTip = "Duration cannot be changed after animation created"
parametersFormLayout.addRow("New animation duration", self.durationBox)
#
# animation selector
#
self.animationSelector = slicer.qMRMLNodeComboBox()
self.animationSelector.nodeTypes = ["vtkMRMLScriptedModuleNode"]
self.animationSelector.setNodeTypeLabel("Animation", "vtkMRMLScriptedModuleNode")
self.animationSelector.selectNodeUponCreation = True
self.animationSelector.addEnabled = True
self.animationSelector.addAttribute("vtkMRMLScriptedModuleNode", "ModuleName", "Animation")
self.animationSelector.baseName = "Animation"
self.animationSelector.removeEnabled = True
self.animationSelector.noneEnabled = True
self.animationSelector.showHidden = True
self.animationSelector.showChildNodeTypes = False
self.animationSelector.setMRMLScene( slicer.mrmlScene )
self.animationSelector.setToolTip( "Pick the animation description." )
parametersFormLayout.addRow("Animation Node: ", self.animationSelector)
self.sequencePlay = slicer.qMRMLSequenceBrowserPlayWidget()
self.sequencePlay.setMRMLScene(slicer.mrmlScene)
self.sequenceSeek = slicer.qMRMLSequenceBrowserSeekWidget()
self.sequenceSeek.setMRMLScene(slicer.mrmlScene)
parametersFormLayout.addRow(self.sequencePlay)
parametersFormLayout.addRow(self.sequenceSeek)
self.actionsMenuButton = qt.QPushButton("Add Action")
self.actionsMenuButton.enabled = False
self.actionsMenu = qt.QMenu()
self.actionsMenuButton.setMenu(self.actionsMenu)
for actionName in slicer.modules.animatorActionPlugins.keys():
qAction = qt.QAction(actionName, self.actionsMenu)
qAction.connect('triggered()', lambda actionName=actionName: self.onAddAction(actionName))
self.actionsMenu.addAction(qAction)
parametersFormLayout.addWidget(self.actionsMenuButton)
#
# Actions Area
#
self.actionsCollapsibleButton = ctk.ctkCollapsibleButton()
self.actionsCollapsibleButton.text = "Actions"
self.layout.addWidget(self.actionsCollapsibleButton)
# Layout within the dummy collapsible button
self.actionsFormLayout = qt.QFormLayout(self.actionsCollapsibleButton)
#
# Export Area
#
self.exportCollapsibleButton = ctk.ctkCollapsibleButton()
self.exportCollapsibleButton.text = "Export"
self.layout.addWidget(self.exportCollapsibleButton)
self.exportCollapsibleButton.enabled = False
self.exportFormLayout = qt.QFormLayout(self.exportCollapsibleButton)
self.sizeSelector = qt.QComboBox()
for size in self.sizes.keys():
self.sizeSelector.addItem(size)
self.sizeSelector.currentText = self.defaultSize
self.exportFormLayout.addRow("Animation size", self.sizeSelector)
self.fileFormatSelector = qt.QComboBox()
for format in self.fileFormats.keys():
self.fileFormatSelector.addItem(format)
self.fileFormatSelector.currentText = self.defaultFileFormat
self.exportFormLayout.addRow("Animation format", self.fileFormatSelector)
self.outputFileButton = qt.QPushButton("Select a file...")
self.exportFormLayout.addRow("Output file", self.outputFileButton)
self.exportButton = qt.QPushButton("Export")
self.exportButton.enabled = False
self.exportFormLayout.addRow("", self.exportButton)
# connections
self.animationSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
self.outputFileButton.connect("clicked()", self.selectExportFile)
self.exportButton.connect("clicked()", self.onExport)
# Add vertical spacer
self.layout.addStretch(1)
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
self.pbucLogic = PointerBasedUSCalibrationLogic() # Have reference to an instance of the logic
#
# Tracked ultrasound playback toolbox
#
self.playToolBox = qt.QToolBox()
self.layout.addWidget( self.playToolBox )
#
# Real-time playback
#
self.realTimeFrame = qt.QFrame( self.playToolBox )
self.realTimeLayout = qt.QVBoxLayout( self.realTimeFrame )
self.connectorNodeSelector = slicer.qMRMLNodeComboBox()
self.connectorNodeSelector.nodeTypes = [ "vtkMRMLIGTLConnectorNode" ]
self.connectorNodeSelector.addEnabled = False
self.connectorNodeSelector.removeEnabled = False
self.connectorNodeSelector.noneEnabled = False
self.connectorNodeSelector.showHidden = False
self.connectorNodeSelector.showChildNodeTypes = False
self.connectorNodeSelector.setMRMLScene( slicer.mrmlScene )
self.connectorNodeSelector.setToolTip( "Select the connector node for playback." )
self.realTimeLayout.addWidget( self.connectorNodeSelector )
self.freezeButton = qt.QPushButton( "Freeze" )
self.freezeButton.setToolTip( "Freeze the connection." )
self.realTimeLayout.addWidget( self.freezeButton )
#
# Recorded sequence playback
#
self.sequenceFrame = qt.QFrame( self.playToolBox )
self.sequenceLayout = qt.QVBoxLayout( self.sequenceFrame )
self.sequenceBrowserNodeSelector = slicer.qMRMLNodeComboBox()
self.sequenceBrowserNodeSelector.nodeTypes = [ "vtkMRMLSequenceBrowserNode" ]
self.sequenceBrowserNodeSelector.addEnabled = False
self.sequenceBrowserNodeSelector.removeEnabled = False
self.sequenceBrowserNodeSelector.noneEnabled = False
self.sequenceBrowserNodeSelector.showHidden = False
self.sequenceBrowserNodeSelector.showChildNodeTypes = False
self.sequenceBrowserNodeSelector.setMRMLScene( slicer.mrmlScene )
self.sequenceBrowserNodeSelector.setToolTip( "Select the sequence browser node for playback." )
self.sequenceLayout.addWidget( self.sequenceBrowserNodeSelector )
self.sequenceBrowserPlayWidget = slicer.qMRMLSequenceBrowserPlayWidget() # TODO: Somehow disable the recording button without changing sequences' recording states
self.sequenceBrowserPlayWidget.setMRMLSequenceBrowserNode( self.sequenceBrowserNodeSelector.currentNode() )
self.sequenceLayout.addWidget( self.sequenceBrowserPlayWidget )
self.sequenceBrowserSeekWidget = slicer.qMRMLSequenceBrowserSeekWidget()
self.sequenceBrowserSeekWidget.setMRMLSequenceBrowserNode( self.sequenceBrowserNodeSelector.currentNode() )
self.sequenceLayout.addWidget( self.sequenceBrowserSeekWidget )
# Add the playback modes to the tool box
self.playToolBox.addItem( self.realTimeFrame, "Real-time" )
self.playToolBox.addItem( self.sequenceFrame, "Sequence" )
#
# Points group box
#
self.pointGroupBox = qt.QGroupBox()
self.pointGroupBox.setTitle( "Points" )
self.layout.addWidget( self.pointGroupBox )
# Layout within the group box
self.pointGroupBoxLayout = qt.QHBoxLayout( self.pointGroupBox )
# Mark point
self.markPointButton = qt.QPushButton( "Mark Point" )
self.markPointButton.setIcon( qt.QIcon( ":/Icons/MarkupsMouseModePlace.png" ) )
self.markPointButton.setToolTip( "Start placing a point on the ultrasound image." )
self.pointGroupBoxLayout.addWidget( self.markPointButton )
# Undo
self.undoPointsButton = qt.QPushButton( "" )
self.undoPointsButton.setIcon( qt.QIcon( ":/Icons/Small/SlicerUndo.png" ) )
self.undoPointsButton.setSizePolicy( qt.QSizePolicy.Fixed, qt.QSizePolicy.Fixed )
self.undoPointsButton.setToolTip( "Remove the most recently placed point." )
self.pointGroupBoxLayout.addWidget( self.undoPointsButton )
# Reset
self.resetPointsButton = qt.QPushButton( "" )
self.resetPointsButton.setIcon( qt.QApplication.style().standardIcon( qt.QStyle.SP_DialogResetButton ) )
self.resetPointsButton.setSizePolicy( qt.QSizePolicy.Fixed, qt.QSizePolicy.Fixed )
self.resetPointsButton.setToolTip( "Clear all points." )
self.pointGroupBoxLayout.addWidget( self.resetPointsButton )
#
# Result label
#
self.calibrationResultLabel = qt.QLabel()
self.calibrationResultLabel.setText( "No calibration parameters selected." )
self.calibrationResultLabel.setToolTip( "Output from the calibration." )
self.layout.addWidget( self.calibrationResultLabel )
#
# Advanced area
#
self.advancedCollapsibleButton = ctk.ctkCollapsibleButton()
self.advancedCollapsibleButton.setText( "Advanced" )
self.advancedCollapsibleButton.collapsed = True
self.layout.addWidget( self.advancedCollapsibleButton )
# Layout within the collapsible button
self.advancedLayout = qt.QFormLayout( self.advancedCollapsibleButton )
# Mark point
self.applyButton = qt.QPushButton( "Apply" )
self.applyButton.setToolTip( "Apply the ImageToProbe transform to the ultrasound image." )
self.advancedLayout.addWidget( self.applyButton )
#
# Results area
#
self.resultsCollapsibleButton = ctk.ctkCollapsibleButton()
self.resultsCollapsibleButton.setText( "Results" )
self.resultsCollapsibleButton.collapsed = True
self.advancedLayout.addWidget( self.resultsCollapsibleButton )
# Layout within the collapsible button
self.resultsLayout = qt.QFormLayout( self.resultsCollapsibleButton )
# Results table
self.resultsTable = qt.QTableWidget( self.resultsCollapsibleButton )
self.resultsTable.setColumnCount( self.RESULTS_NUM_INDICES )
self.resultsTable.setHorizontalHeaderLabels( [ "Image Points", "Probe Points", "Error", "Delete" ] )
self.resultsTable.horizontalHeader().setResizeMode( qt.QHeaderView.Stretch )
self.resultsTable.horizontalHeader().setResizeMode( self.RESULTS_DELETE_INDEX, qt.QHeaderView.Fixed )
self.resultsLayout.addRow( self.resultsTable )
#
# Parameters area
#
self.parametersCollapsibleButton = ctk.ctkCollapsibleButton()
self.parametersCollapsibleButton.setText( "Parameters" )
self.parametersCollapsibleButton.collapsed = True
self.advancedLayout.addWidget( self.parametersCollapsibleButton )
# Layout within the collapsible button
self.parametersLayout = qt.QVBoxLayout( self.parametersCollapsibleButton )
# Parameters node
self.frwNodeSelector = slicer.qMRMLNodeComboBox()
self.frwNodeSelector.nodeTypes = [ "vtkMRMLFiducialRegistrationWizardNode" ]
self.frwNodeSelector.addEnabled = True
self.frwNodeSelector.removeEnabled = True
self.frwNodeSelector.noneEnabled = False
self.frwNodeSelector.showHidden = False
self.frwNodeSelector.showChildNodeTypes = False
self.frwNodeSelector.baseName = "UltrasoundCalibration"
self.frwNodeSelector.setMRMLScene( slicer.mrmlScene )
self.frwNodeSelector.setToolTip( "Select the ultrasound calibration parameters node." )
self.parametersLayout.addWidget( self.frwNodeSelector )
#
# Input group box
#
self.inputGroupBox = qt.QGroupBox( self.parametersCollapsibleButton )
self.inputGroupBox.setTitle( "Input" )
self.parametersLayout.addWidget( self.inputGroupBox )
# Layout within the group box
self.inputGroupBoxLayout = qt.QFormLayout( self.inputGroupBox )
# US image selector
self.usImageNodeSelector = slicer.qMRMLNodeComboBox()
self.usImageNodeSelector.nodeTypes = [ "vtkMRMLVolumeNode" ]
self.usImageNodeSelector.addEnabled = False
self.usImageNodeSelector.removeEnabled = False
self.usImageNodeSelector.noneEnabled = True
self.usImageNodeSelector.showHidden = False
self.usImageNodeSelector.showChildNodeTypes = True
self.usImageNodeSelector.setMRMLScene( slicer.mrmlScene )
self.usImageNodeSelector.setToolTip( "Select the ultrasound image node." )
self.inputGroupBoxLayout.addRow( "Ultrasound image ", self.usImageNodeSelector )
# StylusTipToProbe selector
self.stylusTipToProbeNodeSelector = slicer.qMRMLNodeComboBox()
self.stylusTipToProbeNodeSelector.nodeTypes = [ "vtkMRMLLinearTransformNode" ]
self.stylusTipToProbeNodeSelector.addEnabled = False
self.stylusTipToProbeNodeSelector.removeEnabled = False
self.stylusTipToProbeNodeSelector.noneEnabled = True
self.stylusTipToProbeNodeSelector.showHidden = False
self.stylusTipToProbeNodeSelector.showChildNodeTypes = True
self.stylusTipToProbeNodeSelector.setMRMLScene( slicer.mrmlScene )
self.stylusTipToProbeNodeSelector.setToolTip( "Select the StylusTipToProbe node (parent transforms will be applied)." )
self.inputGroupBoxLayout.addRow( "StylusTipToProbe ", self.stylusTipToProbeNodeSelector )
#
# Output group box
#
self.outputGroupBox = qt.QGroupBox( self.parametersCollapsibleButton )
self.outputGroupBox.setTitle( "Output" )
self.parametersLayout.addWidget( self.outputGroupBox )
# Layout within the group box
self.outputGroupBoxLayout = qt.QFormLayout( self.outputGroupBox )
# ImageToProbe selector
self.imageToProbeNodeSelector = slicer.qMRMLNodeComboBox()
self.imageToProbeNodeSelector.nodeTypes = [ "vtkMRMLLinearTransformNode" ]
self.imageToProbeNodeSelector.addEnabled = True
self.imageToProbeNodeSelector.removeEnabled = False
self.imageToProbeNodeSelector.noneEnabled = True
self.imageToProbeNodeSelector.renameEnabled = True
self.imageToProbeNodeSelector.showHidden = False
self.imageToProbeNodeSelector.showChildNodeTypes = True
self.imageToProbeNodeSelector.setMRMLScene( slicer.mrmlScene )
self.imageToProbeNodeSelector.setToolTip( "Select the ImageToProbe output node (stores the result of the calibration)." )
self.outputGroupBoxLayout.addRow( "ImageToProbe ", self.imageToProbeNodeSelector )
#
# Set up connections
#
self.freezeButton.connect( "clicked(bool)", self.onFreezeButtonClicked )
self.sequenceBrowserNodeSelector.connect( "currentNodeChanged(vtkMRMLNode*)", self.onSequenceBrowserNodeChanged )
self.frwNodeSelector.connect( "currentNodeChanged(vtkMRMLNode*)", self.onCalibrationNodeChanged )
self.usImageNodeSelector.connect( "currentNodeChanged(vtkMRMLNode*)", self.onUSImageNodeChanged )
self.stylusTipToProbeNodeSelector.connect( "currentNodeChanged(vtkMRMLNode*)", self.onStylusTipToProbeNodeChanged )
self.markPointButton.connect( "clicked(bool)", self.onMarkPointButtonClicked )
self.undoPointsButton.connect( "clicked(bool)", self.onUndoPointsButtonClicked )
self.resetPointsButton.connect( "clicked(bool)", self.onResetPointsButtonClicked )
self.imageToProbeNodeSelector.connect( "currentNodeChanged(vtkMRMLNode*)", self.onImageToProbeNodeChanged )
self.applyButton.connect( "clicked(bool)", self.onApplyOutputTransformToImageClicked )
#
# Create a parameters node by default
#
defaultFRWNode = slicer.vtkMRMLFiducialRegistrationWizardNode()
defaultFRWNode.SetName( "UltrasoundCalibration" )
defaultFRWNode.SetScene( slicer.mrmlScene )
slicer.mrmlScene.AddNode( defaultFRWNode )
self.frwNodeSelector.setCurrentNodeID( defaultFRWNode.GetID() )
# Add vertical spacer
self.layout.addStretch(1)