def setup( self ):
self.workflow = ctk.ctkWorkflow()
workflowWidget = ctk.ctkWorkflowStackedWidget()
workflowWidget.setWorkflow( self.workflow )
nNodes = slicer.mrmlScene.GetNumberOfNodesByClass('vtkMRMLScriptedModuleNode')
self.parameterNode = None
for n in xrange(nNodes):
compNode = slicer.mrmlScene.GetNthNodeByClass(n, 'vtkMRMLScriptedModuleNode')
nodeid = None
if compNode.GetModuleName() == 'workflow':
self.parameterNode = compNode
print 'Found existing workflow parameter node'
break
if self.parameterNode == None:
self.parameterNode = slicer.vtkMRMLScriptedModuleNode()
self.parameterNode.SetModuleName('workflow')
slicer.mrmlScene.AddNode(self.parameterNode)
loginStep = WorkflowSteps.LoginStep('Login', self.parameterNode)
approachStep = WorkflowSteps.ApproachStep('Approach', self.parameterNode)
screwStep = WorkflowSteps.ScrewStep('Screw', self.parameterNode)
doneStep = WorkflowSteps.FinalStep('Final', self.parameterNode)
self.workflow.addTransition(loginStep, approachStep, None, ctk.ctkWorkflow.Forward)
self.workflow.addTransition(approachStep, screwStep, None, ctk.ctkWorkflow.Forward)
self.workflow.addTransition(screwStep, doneStep, None, ctk.ctkWorkflow.Forward)
self.workflow.setInitialStep(loginStep)
self.workflow.start()
workflowWidget.visible = True
self.layout.addWidget( workflowWidget )
def compileScript(self, animationNode):
"""Convert the node's script into sequences and a sequence browser node.
Returns the sequenceBrowserNode.
"""
sequenceBrowserNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLSequenceBrowserNode')
sequenceBrowserNode.SetName(animationNode.GetName() + "-Browser")
# TODO: use this when exporting
# sequenceBrowserNode.SetPlaybackItemSkippingEnabled(False)
sequenceNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLSequenceNode')
sequenceNode.SetIndexType(sequenceNode.NumericIndex)
sequenceNode.SetName(animationNode.GetName() + "-TimingSequence")
sequenceBrowserNode.AddSynchronizedSequenceNode(sequenceNode)
# create one data node per frame of the script.
# these are used to synchronize the animation
# but don't hold any other data
script = self.getScript(animationNode)
frames = script['framesPerSecond'] * script['duration']
secondsPerFrame = 1. / script['framesPerSecond']
for frame in range(math.ceil(frames)):
scriptTime = frame * secondsPerFrame
timePointDataNode = slicer.vtkMRMLScriptedModuleNode()
sequenceNode.SetDataNodeAtValue(timePointDataNode, str(scriptTime))
return(sequenceBrowserNode)
def runRegistration(self):
logging.debug("Starting Registration")
self.progress = self.createProgressDialog(value=1, maximum=4)
parameterNode = slicer.vtkMRMLScriptedModuleNode()
parameterNode.SetAttribute(
'FixedImageNodeID',
self.fixedVolumeSelector.currentNode().GetID())
parameterNode.SetAttribute(
'FixedLabelNodeID',
self.fixedLabelSelector.currentNode().GetID())
parameterNode.SetAttribute(
'MovingImageNodeID',
self.movingVolumeSelector.currentNode().GetID())
parameterNode.SetAttribute(
'MovingLabelNodeID',
self.movingLabelSelector.currentNode().GetID())
if self.fiducialSelector.currentNode():
parameterNode.SetAttribute(
'TargetsNodeID',
self.fiducialSelector.currentNode().GetID())
if self.initialTransformSelector.currentNode():
parameterNode.SetAttribute(
'InitialTransformNodeID',
self.initialTransformSelector.currentNode().GetID())
self.logic.runReRegistration(
parameterNode, progressCallback=self.updateProgressBar)
else:
self.logic.run(parameterNode,
progressCallback=self.updateProgressBar)
self.progress.close()
def nodeCheck(self):
"""If there is no parameter node, create one and add it to the scene
"""
if(self.parameterSelector.currentNode() == None):
node = slicer.vtkMRMLScriptedModuleNode()
slicer.mrmlScene.AddNode(node)
self.parameterNodeCreated(node)
self.parameterSelector.setCurrentNode(node)
def createParameterNode(self): """create the Editor parameter node - a singleton in the scene This is used internally by getParameterNode - shouldn't really be called for any other reason. """ node = slicer.vtkMRMLScriptedModuleNode() node.SetModuleName( "Editor" ) slicer.mrmlScene.AddNode(node) return node
def createParameterNode(self):
"""create the Editor parameter node - a singleton in the scene
This is used internally by getParameterNode - shouldn't really
be called for any other reason.
"""
node = slicer.vtkMRMLScriptedModuleNode()
node.SetModuleName("Editor")
slicer.mrmlScene.AddNode(node)
return node
def __init__(self):
ScriptedLoadableModuleLogic.__init__(self)
import serial
self.parameterNode = slicer.vtkMRMLScriptedModuleNode()
self.parameterNode.SetName("arduinoNode")
slicer.mrmlScene.AddNode(self.parameterNode)
self.arduinoConnection = None
def runRegistration(self):
self.progress = self.makeProgressIndicator(4, 1)
parameterNode = slicer.vtkMRMLScriptedModuleNode()
parameterNode.SetAttribute('FixedImageNodeID', self.intraopVolumeSelector.currentNode().GetID())
parameterNode.SetAttribute('FixedLabelNodeID', self.intraopLabelSelector.currentNode().GetID())
parameterNode.SetAttribute('MovingImageNodeID', self.preopVolumeSelector.currentNode().GetID())
parameterNode.SetAttribute('MovingLabelNodeID', self.preopLabelSelector.currentNode().GetID())
if self.fiducialSelector.currentNode():
parameterNode.SetAttribute('TargetsNodeID', self.fiducialSelector.currentNode().GetID())
self.logic.run(parameterNode, progressCallback=self.updateProgressBar)
self.progress.close()
def _createParameterNode(self):
"""create the Editor parameter node - a singleton in the scene
This is used internally by getParameterNode - shouldn't really
be called for any other reason.
"""
node = slicer.vtkMRMLScriptedModuleNode()
node.SetSingletonTag("Editor")
node.SetModuleName("Editor")
node.SetParameter("label", "1")
slicer.mrmlScene.AddNode(node)
# Since we are a singleton, the scene won't add our node into the scene,
# but will instead insert a copy, so we find that and return it
node = self._findParameterNodeInScene()
return node
def _createParameterNode(self): """create the Editor parameter node - a singleton in the scene This is used internally by getParameterNode - shouldn't really be called for any other reason. """ node = slicer.vtkMRMLScriptedModuleNode() node.SetSingletonTag( "Editor" ) node.SetModuleName( "Editor" ) node.SetParameter( "label", "1" ) slicer.mrmlScene.AddNode(node) # Since we are a singleton, the scene won't add our node into the scene, # but will instead insert a copy, so we find that and return it node = self._findParameterNodeInScene() return node
def __init__(self, arduinoNode):
ScriptedLoadableModuleLogic.__init__(self)
self.ArduinoNode = arduinoNode
self.parameterNode = slicer.vtkMRMLScriptedModuleNode()
self.parameterNode.SetName("arduinoNode")
slicer.mrmlScene.AddNode(self.parameterNode)
#Layout Selected (example: Red, Yellow, Green or Complete)
self.selected_view = 0
self.button1 = None
self.button2 = None
self.button3 = None
def runRegistration(fixedVolume, fixedLabel, movingVolume, movingLabel):
registrationLogic = SliceTrackerRegistrationLogic()
data = SessionData()
result = data.createResult(fixedVolume.GetName())
registrationLogic.registrationResult = result
parameterNode = slicer.vtkMRMLScriptedModuleNode()
parameterNode.SetAttribute('FixedImageNodeID', fixedVolume.GetID())
parameterNode.SetAttribute('FixedLabelNodeID', fixedLabel.GetID())
parameterNode.SetAttribute('MovingImageNodeID', movingVolume.GetID())
parameterNode.SetAttribute('MovingLabelNodeID', movingLabel.GetID())
registrationLogic.run(parameterNode)
return result
def createParameterNode(self):
"""
Create a new parameter node
The node is of vtkMRMLScriptedModuleNode class. Module name is added as an attribute to allow filtering
in node selector widgets (attribute name: ModuleName, attribute value: the module's name).
This method can be overridden in derived classes to create a default parameter node with all
parameter values set to their default.
"""
node = slicer.vtkMRMLScriptedModuleNode()
if self.isSingletonParameterNode:
node.SetSingletonTag( self.moduleName )
# Add module name in an attribute to allow filtering in node selector widgets
# Note that SetModuleName is not used anymore as it would be redundant with the ModuleName attribute.
node.SetAttribute( "ModuleName", self.moduleName )
node.SetName(slicer.mrmlScene.GenerateUniqueName(self.moduleName))
return node
def createParameterNode(self):
"""
Create a new parameter node
The node is of vtkMRMLScriptedModuleNode class. Module name is added as an attribute to allow filtering
in node selector widgets (attribute name: ModuleName, attribute value: the module's name).
This method can be overridden in derived classes to create a default parameter node with all
parameter values set to their default.
"""
node = slicer.vtkMRMLScriptedModuleNode()
if self.isSingletonParameterNode:
node.SetSingletonTag(self.moduleName)
# Add module name in an attribute to allow filtering in node selector widgets
# Note that SetModuleName is not used anymore as it would be redundant with the ModuleName attribute.
node.SetAttribute("ModuleName", self.moduleName)
node.SetName(slicer.mrmlScene.GenerateUniqueName(self.moduleName))
return node
def runRegistration(self):
logging.debug("Starting Registration")
self.progress = slicer.util.createProgressDialog(value=1, maximum=4)
parameterNode = slicer.vtkMRMLScriptedModuleNode()
parameterNode.SetAttribute('FixedImageNodeID', self.fixedVolumeSelector.currentNode().GetID())
parameterNode.SetAttribute('FixedLabelNodeID', self.fixedLabelSelector.currentNode().GetID())
parameterNode.SetAttribute('MovingImageNodeID', self.movingVolumeSelector.currentNode().GetID())
parameterNode.SetAttribute('MovingLabelNodeID', self.movingLabelSelector.currentNode().GetID())
if self.fiducialSelector.currentNode():
parameterNode.SetAttribute('TargetsNodeID', self.fiducialSelector.currentNode().GetID())
if self.initialTransformSelector.currentNode():
parameterNode.SetAttribute('InitialTransformNodeID', self.initialTransformSelector.currentNode().GetID())
self.logic.runReRegistration(parameterNode, progressCallback=self.updateProgressBar)
else:
self.logic.run(parameterNode, progressCallback=self.updateProgressBar)
self.progress.close()
def _createParameterNode(): """create the Editor parameter node - a singleton in the scene This is used internally by getParameterNode - shouldn't really be called for any other reason. """ node = slicer.vtkMRMLScriptedModuleNode() node.SetSingletonTag( "Editor" ) node.SetModuleName( "Editor" ) node.SetParameter( "label", "1" ) node.SetParameter( "effect", "DefaultTool" ) node.SetParameter( "propagationMode", str(slicer.vtkMRMLApplicationLogic.BackgroundLayer | slicer.vtkMRMLApplicationLogic.LabelLayer) ) slicer.mrmlScene.AddNode(node) # Since we are a singleton, the scene won't add our node into the scene, # but will instead insert a copy, so we find that and return it node = EditUtil._findParameterNodeInScene() return node
def _createParameterNode(): """create the Editor parameter node - a singleton in the scene This is used internally by getParameterNode - shouldn't really be called for any other reason. """ node = slicer.vtkMRMLScriptedModuleNode() node.SetSingletonTag( "Editor" ) node.SetModuleName( "Editor" ) node.SetParameter( "label", "1" ) node.SetParameter( "effect", "DefaultTool" ) node.SetParameter( "propagationMode", str(slicer.vtkMRMLApplicationLogic.BackgroundLayer | slicer.vtkMRMLApplicationLogic.LabelLayer) ) slicer.mrmlScene.AddNode(node) # Since we are a singleton, the scene won't add our node into the scene, # but will instead insert a copy, so we find that and return it node = EditUtil._findParameterNodeInScene() return node
def _runRegistration(self, fixedVolume, fixedLabel, movingVolume, movingLabel, targets, segmentationData,
progressCallback):
result = self.generateNameAndCreateRegistrationResult(fixedVolume)
result.receivedTime = self.seriesTimeStamps[result.name.replace(result.suffix, "")]
if segmentationData:
result.segmentationData = segmentationData
parameterNode = slicer.vtkMRMLScriptedModuleNode()
parameterNode.SetAttribute('FixedImageNodeID', fixedVolume.GetID())
parameterNode.SetAttribute('FixedLabelNodeID', fixedLabel.GetID())
parameterNode.SetAttribute('MovingImageNodeID', movingVolume.GetID())
parameterNode.SetAttribute('MovingLabelNodeID', movingLabel.GetID())
parameterNode.SetAttribute('TargetsNodeID', targets.GetID())
result.startTime = self.getTime()
self.registrationLogic.run(parameterNode, progressCallback=progressCallback)
result.endTime = self.getTime()
self.addTargetsToMRMLScene(result)
if self.seriesTypeManager.isCoverProstate(self.currentSeries) and self.temporaryIntraopTargets:
self.addTemporaryTargetsToResult(result)
self.invokeEvent(self.InitiateEvaluationEvent)
def main(argv):
try:
parser = argparse.ArgumentParser(description="Slicetracker Registration")
parser.add_argument("-fl", "--fixed-label", dest="fixed_label", metavar="PATH", default="-", required=True,
help="Fixed label to be used for registration")
parser.add_argument("-ml", "--moving-label", dest="moving_label", metavar="PATH", default="-", required=True,
help="Moving label to be used for registration")
parser.add_argument("-fv", "--fixed-volume", dest="fixed_volume", metavar="PATH", default="-", required=True,
help="Fixed volume to be used for registration")
parser.add_argument("-mv", "--moving-volume", dest="moving_volume", metavar="PATH", default="-", required=True,
help="Moving volume to be used for registration")
parser.add_argument("-it", "--initial-transform", dest="initial_transform", metavar="PATH", default="-",
required=False, help="Initial rigid transform for re-registration")
parser.add_argument("-o", "--output-directory", dest="output_directory", metavar="PATH", default="-",
required=False, help="Output directory for registration result")
args = parser.parse_args(argv)
for inputFile in [args.fixed_label, args.moving_label, args.fixed_volume, args.moving_volume]:
if not os.path.isfile(inputFile):
raise AttributeError("File not found: %s" % inputFile)
success, fixedLabel = slicer.util.loadLabelVolume(args.fixed_label, returnNode=True)
success, movingLabel = slicer.util.loadLabelVolume(args.moving_label, returnNode=True)
success, fixedVolume = slicer.util.loadVolume(args.fixed_volume, returnNode=True)
success, movingVolume = slicer.util.loadVolume(args.moving_volume, returnNode=True)
parameterNode = slicer.vtkMRMLScriptedModuleNode()
parameterNode.SetAttribute('FixedImageNodeID', fixedVolume.GetID())
parameterNode.SetAttribute('FixedLabelNodeID', fixedLabel.GetID())
parameterNode.SetAttribute('MovingImageNodeID', movingVolume.GetID())
parameterNode.SetAttribute('MovingLabelNodeID', movingLabel.GetID())
logic = SliceTrackerRegistrationLogic()
logic.run(parameterNode)
if args.output_directory != "-":
logic.registrationResult.save(args.output_directory)
except Exception as e:
print(e)
sys.exit(0)
def main(argv):
try:
parser = argparse.ArgumentParser(description="Slicetracker Registration")
parser.add_argument("-fl", "--fixed-label", dest="fixed_label", metavar="PATH", default="-", required=True,
help="Fixed label to be used for registration")
parser.add_argument("-ml", "--moving-label", dest="moving_label", metavar="PATH", default="-", required=True,
help="Moving label to be used for registration")
parser.add_argument("-fv", "--fixed-volume", dest="fixed_volume", metavar="PATH", default="-", required=True,
help="Fixed volume to be used for registration")
parser.add_argument("-mv", "--moving-volume", dest="moving_volume", metavar="PATH", default="-", required=True,
help="Moving volume to be used for registration")
parser.add_argument("-it", "--initial-transform", dest="initial_transform", metavar="PATH", default="-",
required=False, help="Initial rigid transform for re-registration")
parser.add_argument("-o", "--output-directory", dest="output_directory", metavar="PATH", default="-",
required=False, help="Output directory for registration result")
args = parser.parse_args(argv)
for inputFile in [args.fixed_label, args.moving_label, args.fixed_volume, args.moving_volume]:
if not os.path.isfile(inputFile):
raise AttributeError, "File not found: %s" % inputFile
success, fixedLabel = slicer.util.loadLabelVolume(args.fixed_label, returnNode=True)
success, movingLabel = slicer.util.loadLabelVolume(args.moving_label, returnNode=True)
success, fixedVolume = slicer.util.loadVolume(args.fixed_volume, returnNode=True)
success, movingVolume = slicer.util.loadVolume(args.moving_volume, returnNode=True)
parameterNode = slicer.vtkMRMLScriptedModuleNode()
parameterNode.SetAttribute('FixedImageNodeID', fixedVolume.GetID())
parameterNode.SetAttribute('FixedLabelNodeID', fixedLabel.GetID())
parameterNode.SetAttribute('MovingImageNodeID', movingVolume.GetID())
parameterNode.SetAttribute('MovingLabelNodeID', movingLabel.GetID())
logic = SliceTrackerRegistrationLogic()
logic.run(parameterNode)
if args.output_directory != "-":
logic.registrationResult.save(args.output_directory)
except Exception, e:
print e
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
self.workflow = ctk.ctkWorkflow()
workflowWidget = ctk.ctkWorkflowStackedWidget()
workflowWidget.setWorkflow( self.workflow )
# create all wizard steps
self.loadDataStep = PedicleScrewSimulatorWizard.LoadDataStep( 'LoadData' )
self.defineROIStep = PedicleScrewSimulatorWizard.DefineROIStep( 'DefineROI' )
self.measurementsStep = PedicleScrewSimulatorWizard.MeasurementsStep( 'Measurements' )
self.landmarksStep = PedicleScrewSimulatorWizard.LandmarksStep( 'Landmarks' )
self.screwStep = PedicleScrewSimulatorWizard.ScrewStep( 'Screw' )
self.gradeStep = PedicleScrewSimulatorWizard.GradeStep( 'Grade' )
self.endStep = PedicleScrewSimulatorWizard.EndStep( 'Final' )
# add the wizard steps to an array for convenience
allSteps = []
allSteps.append( self.loadDataStep )
allSteps.append( self.defineROIStep )
allSteps.append( self.landmarksStep)
allSteps.append( self.measurementsStep )
allSteps.append( self.screwStep)
allSteps.append( self.gradeStep)
allSteps.append( self.endStep )
# Add transition
# Check if volume is loaded
self.workflow.addTransition( self.loadDataStep, self.defineROIStep )
self.workflow.addTransition( self.defineROIStep, self.landmarksStep, 'pass', ctk.ctkWorkflow.Bidirectional )
self.workflow.addTransition( self.defineROIStep, self.loadDataStep, 'fail', ctk.ctkWorkflow.Bidirectional )
self.workflow.addTransition( self.landmarksStep, self.measurementsStep, 'pass', ctk.ctkWorkflow.Bidirectional )
self.workflow.addTransition( self.landmarksStep, self.measurementsStep, 'fail', ctk.ctkWorkflow.Bidirectional )
self.workflow.addTransition( self.measurementsStep, self.screwStep, 'pass', ctk.ctkWorkflow.Bidirectional )
self.workflow.addTransition( self.measurementsStep, self.screwStep, 'fail', ctk.ctkWorkflow.Bidirectional )
self.workflow.addTransition( self.screwStep, self.gradeStep, 'pass', ctk.ctkWorkflow.Bidirectional )
self.workflow.addTransition( self.screwStep, self.gradeStep, 'fail', ctk.ctkWorkflow.Bidirectional )
self.workflow.addTransition( self.gradeStep, self.endStep )
nNodes = slicer.mrmlScene.GetNumberOfNodesByClass('vtkMRMLScriptedModuleNode')
self.parameterNode = None
for n in xrange(nNodes):
compNode = slicer.mrmlScene.GetNthNodeByClass(n, 'vtkMRMLScriptedModuleNode')
nodeid = None
if compNode.GetModuleName() == 'PedicleScrewSimulator':
self.parameterNode = compNode
print 'Found existing PedicleScrewSimulator parameter node'
break
if self.parameterNode == None:
self.parameterNode = slicer.vtkMRMLScriptedModuleNode()
self.parameterNode.SetModuleName('PedicleScrewSimulator')
slicer.mrmlScene.AddNode(self.parameterNode)
for s in allSteps:
s.setParameterNode (self.parameterNode)
# restore workflow step
currentStep = self.parameterNode.GetParameter('currentStep')
if currentStep != '':
print 'Restoring workflow step to ', currentStep
if currentStep == 'LoadData':
self.workflow.setInitialStep(self.loadDataStep)
if currentStep == 'DefineROI':
self.workflow.setInitialStep(self.defineROIStep)
if currentStep == 'Measurements':
self.workflow.setInitialStep(self.measurementsStep)
if currentStep == 'Landmarks':
self.workflow.setInitialStep(self.landmarksStep)
if currentStep == 'Screw':
self.workflow.setInitialStep(self.screwStep)
if currentStep == 'Grade':
self.workflow.setInitialStep(self.gradeStep)
if currentStep == 'Final':
self.workflow.setInitialStep(self.endStep)
else:
print 'currentStep in parameter node is empty!'
# start the workflow and show the widget
self.workflow.start()
workflowWidget.visible = True
self.layout.addWidget( workflowWidget )
def _createParameterNode(self):
parameterNode = slicer.vtkMRMLScriptedModuleNode()
slicer.mrmlScene.AddNode(parameterNode)
return parameterNode
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
self.pbucLogic = ImagelessUSCalibrationLogic(
) # Have reference to an instance of the logic
#
# Points group box
#
self.pointGroupBox = qt.QGroupBox()
self.pointGroupBox.setTitle("Points")
self.layout.addWidget(self.pointGroupBox)
# Layout within the group box
self.pointGroupBoxLayout = qt.QVBoxLayout(self.pointGroupBox)
# Marked point frame
self.markedPointFrame = qt.QFrame()
self.pointGroupBoxLayout.addWidget(self.markedPointFrame)
# Layout within the frame
self.markedPointLayout = qt.QHBoxLayout(self.markedPointFrame)
# Select point
self.selectMarkedPointButton = qt.QPushButton("Marked corner")
self.selectMarkedPointButton.setIcon(
qt.QIcon(":/Icons/MarkupsMouseModePlace.png"))
self.selectMarkedPointButton.setToolTip(
"Place points on the corners of the ultrasound probe's foot on the marked side."
)
self.markedPointLayout.addWidget(self.selectMarkedPointButton)
# Reset
self.resetMarkedPointsButton = qt.QPushButton("")
self.resetMarkedPointsButton.setIcon(
qt.QApplication.style().standardIcon(
qt.QStyle.SP_DialogResetButton))
self.resetMarkedPointsButton.setSizePolicy(qt.QSizePolicy.Fixed,
qt.QSizePolicy.Fixed)
self.resetMarkedPointsButton.setToolTip("Clear all points.")
self.markedPointLayout.addWidget(self.resetMarkedPointsButton)
# Unmarked point frame
self.unmarkedPointFrame = qt.QFrame()
self.pointGroupBoxLayout.addWidget(self.unmarkedPointFrame)
# Layout within the frame
self.unmarkedPointLayout = qt.QHBoxLayout(self.unmarkedPointFrame)
# Select point
self.selectUnmarkedPointButton = qt.QPushButton("Unmarked corner")
self.selectUnmarkedPointButton.setIcon(
qt.QIcon(":/Icons/MarkupsMouseModePlace.png"))
self.selectUnmarkedPointButton.setToolTip(
"Place points on the corners of the ultrasound probe's foot on the unmarked side."
)
self.unmarkedPointLayout.addWidget(self.selectUnmarkedPointButton)
# Reset
self.resetUnmarkedPointsButton = qt.QPushButton("")
self.resetUnmarkedPointsButton.setIcon(
qt.QApplication.style().standardIcon(
qt.QStyle.SP_DialogResetButton))
self.resetUnmarkedPointsButton.setSizePolicy(qt.QSizePolicy.Fixed,
qt.QSizePolicy.Fixed)
self.resetUnmarkedPointsButton.setToolTip("Clear all points.")
self.unmarkedPointLayout.addWidget(self.resetUnmarkedPointsButton)
#
# Depth group box
#
self.depthGroupBox = qt.QGroupBox()
self.depthGroupBox.setTitle("Depth")
self.layout.addWidget(self.depthGroupBox)
# Layout within the group box
self.depthGroupBoxLayout = qt.QHBoxLayout(self.depthGroupBox)
# Depth label
self.depthLabel = qt.QLabel("Depth \t")
self.depthLabel.setSizePolicy(qt.QSizePolicy.Fixed,
qt.QSizePolicy.Fixed)
self.depthGroupBoxLayout.addWidget(self.depthLabel)
# Depth spin box
self.depthSpinBox = qt.QSpinBox()
self.depthSpinBox.setRange(0, 1000)
self.depthSpinBox.setSingleStep(1)
self.depthSpinBox.setSuffix("mm")
self.depthSpinBox.setToolTip("Ultrasound imaging depth.")
self.depthGroupBoxLayout.addWidget(self.depthSpinBox)
#
# 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)
#
# 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.usCalibrationNodeSelector = slicer.qMRMLNodeComboBox()
self.usCalibrationNodeSelector.nodeTypes = [
"vtkMRMLScriptedModuleNode"
]
self.usCalibrationNodeSelector.addEnabled = True
self.usCalibrationNodeSelector.removeEnabled = True
self.usCalibrationNodeSelector.noneEnabled = False
self.usCalibrationNodeSelector.showHidden = True # Since scripted module nodes are hidden by default
self.usCalibrationNodeSelector.showChildNodeTypes = False
self.usCalibrationNodeSelector.baseName = "UltrasoundCalibration"
self.usCalibrationNodeSelector.setMRMLScene(slicer.mrmlScene)
self.usCalibrationNodeSelector.setToolTip(
"Select the ultrasound calibration parameters node.")
self.parametersLayout.addWidget(self.usCalibrationNodeSelector)
#
# 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.selectMarkedPointButton.connect(
"clicked(bool)", self.onSelectMarkedPointButtonClicked)
self.resetMarkedPointsButton.connect(
"clicked(bool)", self.onResetMarkedPointsButtonClicked)
self.selectUnmarkedPointButton.connect(
"clicked(bool)", self.onSelectUnmarkedPointButtonClicked)
self.resetUnmarkedPointsButton.connect(
"clicked(bool)", self.onResetUnmarkedPointsButtonClicked)
self.depthSpinBox.connect("valueChanged(int)", self.onDepthChanged)
self.usCalibrationNodeSelector.connect(
"currentNodeChanged(vtkMRMLNode*)", self.onCalibrationNodeChanged)
self.usImageNodeSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onUSImageNodeChanged)
self.stylusTipToProbeNodeSelector.connect(
"currentNodeChanged(vtkMRMLNode*)",
self.onStylusTipToProbeNodeChanged)
self.imageToProbeNodeSelector.connect(
"currentNodeChanged(vtkMRMLNode*)", self.onImageToProbeNodeChanged)
self.applyButton.connect("clicked(bool)",
self.onApplyOutputTransformToImageClicked)
#
# Create a parameters node by default
#
defaultUSCalibrationNode = slicer.vtkMRMLScriptedModuleNode()
defaultUSCalibrationNode.SetName("UltrasoundCalibration")
defaultUSCalibrationNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(defaultUSCalibrationNode)
self.usCalibrationNodeSelector.setCurrentNodeID(
defaultUSCalibrationNode.GetID())
# Add vertical spacer
self.layout.addStretch(1)
def updateWidgetFromMRML(self):
"""Changes the displayed inputs to match the current parameter node
If an attribute has not been set, it is set from the currently
displayed attribute
"""
# If there is no parameter node, create one and add it to the scene
if self.parameterSelector.currentNode() is None:
node = slicer.vtkMRMLScriptedModuleNode()
slicer.mrmlScene.AddNode(node)
self.parameterNodeCreated(node)
self.parameterSelector.setCurrentNode(node)
paramNode = self.parameterSelector.currentNode()
if paramNode is not None:
# DVH Array 1
dvh1Node = paramNode.GetNodeReferenceID(self.dvh1NodeReference)
self.dvh1Selector.blockSignals(True)
self.dvh1Selector.setCurrentNodeID(dvh1Node)
self.dvh1Selector.blockSignals(False)
# DVH Array 2
dvh2Node = paramNode.GetNodeReferenceID(self.dvh2NodeReference)
self.dvh2Selector.blockSignals(True)
self.dvh2Selector.setCurrentNodeID(dvh2Node)
self.dvh2Selector.blockSignals(False)
# Dose Volume
doseVolumeNode = paramNode.GetNodeReferenceID(self.doseVolumeNodeReference)
self.doseVolumeSelector.blockSignals(True)
self.doseVolumeSelector.setCurrentNodeID(doseVolumeNode)
self.doseVolumeSelector.blockSignals(False)
# Dose Volume Only Checkbox
doseVolumeOnlyChecked = paramNode.GetAttribute(self.doseVolumeOnlyCheckedAttrName)
if doseVolumeOnlyChecked is not None:
checkedState = int(doseVolumeOnlyChecked)
self.showDoseVolumeOnlyCheckbox.blockSignals(True)
if checkedState:
self.showDoseVolumeOnlyCheckbox.setCheckState(2)
else:
self.showDoseVolumeOnlyCheckbox.setCheckState(0)
self.showDoseVolumeOnlyCheckbox.blockSignals(False)
else:
self.parameterSelector.currentNode().SetAttribute(self.doseVolumeOnlyCheckedAttrName, str(self.showDoseVolumeOnlyCheckbox.checkState()))
# Dose To Agreement Criterion
doseToAgreementCriterion = paramNode.GetAttribute(self.doseToAgreementCriterionAttrName)
if doseToAgreementCriterion is not None:
self.doseToAgreementSpinbox.blockSignals(True)
self.doseToAgreementSpinbox.setValue(float(doseToAgreementCriterion))
self.doseToAgreementSpinbox.blockSignals(False)
else:
paramNode.SetAttribute(self.doseToAgreementCriterionAttrName, str(self.doseToAgreementSpinbox.value))
# Volume Difference Criterion
volumeDifferenceCriterion = paramNode.GetAttribute(self.volumeDifferenceCriterionAttrName)
if volumeDifferenceCriterion is not None:
self.volumeDifferenceSpinbox.blockSignals(True)
self.volumeDifferenceSpinbox.setValue(float(volumeDifferenceCriterion))
self.volumeDifferenceSpinbox.blockSignals(False)
else:
paramNode.SetAttribute(self.volumeDifferenceCriterionAttrName, str(self.volumeDifferenceSpinbox.value))
# Agreement Acceptance % (use previously stored one if availiable)
agreementAcceptancePercentage = paramNode.GetAttribute(self.agreementAcceptanceAttrName)
if agreementAcceptancePercentage is not None:
self.agreementAcceptanceOutput.text = agreementAcceptancePercentage
else:
self.agreementAcceptanceOutput.text = ''
def updateWidgetFromMRML(self):
"""Changes the displayed inputs to match the current parameter node
If an attribute has not been set, it is set from the currently
displayed attribute
"""
# If there is no parameter node, create one and add it to the scene
if self.parameterSelector.currentNode() is None:
node = slicer.vtkMRMLScriptedModuleNode()
slicer.mrmlScene.AddNode(node)
self.parameterNodeCreated(node)
self.parameterSelector.setCurrentNode(node)
paramNode = self.parameterSelector.currentNode()
if paramNode is not None:
# DVH Table 1
dvh1Node = paramNode.GetNodeReferenceID(self.dvh1NodeReference)
self.dvh1Selector.blockSignals(True)
self.dvh1Selector.setCurrentNodeID(dvh1Node)
self.dvh1Selector.blockSignals(False)
# DVH Table 2
dvh2Node = paramNode.GetNodeReferenceID(self.dvh2NodeReference)
self.dvh2Selector.blockSignals(True)
self.dvh2Selector.setCurrentNodeID(dvh2Node)
self.dvh2Selector.blockSignals(False)
# Dose Volume
doseVolumeNode = paramNode.GetNodeReferenceID(self.doseVolumeNodeReference)
self.doseVolumeSelector.blockSignals(True)
self.doseVolumeSelector.setCurrentNodeID(doseVolumeNode)
self.doseVolumeSelector.blockSignals(False)
# Dose Volume Only Checkbox
doseVolumeOnlyChecked = paramNode.GetAttribute(self.doseVolumeOnlyCheckedAttrName)
if doseVolumeOnlyChecked is not None:
checkedState = int(doseVolumeOnlyChecked)
self.showDoseVolumeOnlyCheckbox.blockSignals(True)
if checkedState:
self.showDoseVolumeOnlyCheckbox.setCheckState(2)
else:
self.showDoseVolumeOnlyCheckbox.setCheckState(0)
self.showDoseVolumeOnlyCheckbox.blockSignals(False)
else:
self.parameterSelector.currentNode().SetAttribute(self.doseVolumeOnlyCheckedAttrName, str(self.showDoseVolumeOnlyCheckbox.checkState()))
# Dose To Agreement Criterion
doseToAgreementCriterion = paramNode.GetAttribute(self.doseToAgreementCriterionAttrName)
if doseToAgreementCriterion is not None:
self.doseToAgreementSpinbox.blockSignals(True)
self.doseToAgreementSpinbox.setValue(float(doseToAgreementCriterion))
self.doseToAgreementSpinbox.blockSignals(False)
else:
paramNode.SetAttribute(self.doseToAgreementCriterionAttrName, str(self.doseToAgreementSpinbox.value))
# Volume Difference Criterion
volumeDifferenceCriterion = paramNode.GetAttribute(self.volumeDifferenceCriterionAttrName)
if volumeDifferenceCriterion is not None:
self.volumeDifferenceSpinbox.blockSignals(True)
self.volumeDifferenceSpinbox.setValue(float(volumeDifferenceCriterion))
self.volumeDifferenceSpinbox.blockSignals(False)
else:
paramNode.SetAttribute(self.volumeDifferenceCriterionAttrName, str(self.volumeDifferenceSpinbox.value))
# Agreement Acceptance % (use previously stored one if availiable)
agreementAcceptancePercentage = paramNode.GetAttribute(self.agreementAcceptanceAttrName)
if agreementAcceptancePercentage is not None:
self.agreementAcceptanceOutput.text = agreementAcceptancePercentage
else:
self.agreementAcceptanceOutput.text = ''
def setup(self):
ScriptedLoadableModuleWidget.setup(self)
# Instantiate and connect widgets ...
self.workflow = ctk.ctkWorkflow()
workflowWidget = ctk.ctkWorkflowStackedWidget()
workflowWidget.setWorkflow(self.workflow)
# create all wizard steps
self.loadDataStep = PedicleScrewSimulatorWizard.LoadDataStep(
'LoadData')
self.defineROIStep = PedicleScrewSimulatorWizard.DefineROIStep(
'DefineROI')
self.measurementsStep = PedicleScrewSimulatorWizard.MeasurementsStep(
'Measurements')
self.landmarksStep = PedicleScrewSimulatorWizard.LandmarksStep(
'Landmarks')
self.screwStep = PedicleScrewSimulatorWizard.ScrewStep('Screw')
self.gradeStep = PedicleScrewSimulatorWizard.GradeStep('Grade')
self.endStep = PedicleScrewSimulatorWizard.EndStep('Final')
# add the wizard steps to an array for convenience
allSteps = []
allSteps.append(self.loadDataStep)
allSteps.append(self.defineROIStep)
allSteps.append(self.landmarksStep)
allSteps.append(self.measurementsStep)
allSteps.append(self.screwStep)
allSteps.append(self.gradeStep)
allSteps.append(self.endStep)
# Add transition
# Check if volume is loaded
self.workflow.addTransition(self.loadDataStep, self.defineROIStep)
self.workflow.addTransition(self.defineROIStep, self.landmarksStep,
'pass', ctk.ctkWorkflow.Bidirectional)
self.workflow.addTransition(self.defineROIStep, self.loadDataStep,
'fail', ctk.ctkWorkflow.Bidirectional)
self.workflow.addTransition(self.landmarksStep, self.measurementsStep,
'pass', ctk.ctkWorkflow.Bidirectional)
self.workflow.addTransition(self.landmarksStep, self.measurementsStep,
'fail', ctk.ctkWorkflow.Bidirectional)
self.workflow.addTransition(self.measurementsStep, self.screwStep,
'pass', ctk.ctkWorkflow.Bidirectional)
self.workflow.addTransition(self.measurementsStep, self.screwStep,
'fail', ctk.ctkWorkflow.Bidirectional)
self.workflow.addTransition(self.screwStep, self.gradeStep, 'pass',
ctk.ctkWorkflow.Bidirectional)
self.workflow.addTransition(self.screwStep, self.gradeStep, 'fail',
ctk.ctkWorkflow.Bidirectional)
self.workflow.addTransition(self.gradeStep, self.endStep)
nNodes = slicer.mrmlScene.GetNumberOfNodesByClass(
'vtkMRMLScriptedModuleNode')
self.parameterNode = None
for n in xrange(nNodes):
compNode = slicer.mrmlScene.GetNthNodeByClass(
n, 'vtkMRMLScriptedModuleNode')
nodeid = None
if compNode.GetModuleName() == 'PedicleScrewSimulator':
self.parameterNode = compNode
print 'Found existing PedicleScrewSimulator parameter node'
break
if self.parameterNode == None:
self.parameterNode = slicer.vtkMRMLScriptedModuleNode()
self.parameterNode.SetModuleName('PedicleScrewSimulator')
slicer.mrmlScene.AddNode(self.parameterNode)
for s in allSteps:
s.setParameterNode(self.parameterNode)
# restore workflow step
currentStep = self.parameterNode.GetParameter('currentStep')
if currentStep != '':
print 'Restoring workflow step to ', currentStep
if currentStep == 'LoadData':
self.workflow.setInitialStep(self.loadDataStep)
if currentStep == 'DefineROI':
self.workflow.setInitialStep(self.defineROIStep)
if currentStep == 'Measurements':
self.workflow.setInitialStep(self.measurementsStep)
if currentStep == 'Landmarks':
self.workflow.setInitialStep(self.landmarksStep)
if currentStep == 'Screw':
self.workflow.setInitialStep(self.screwStep)
if currentStep == 'Grade':
self.workflow.setInitialStep(self.gradeStep)
if currentStep == 'Final':
self.workflow.setInitialStep(self.endStep)
else:
print 'currentStep in parameter node is empty!'
# start the workflow and show the widget
self.workflow.start()
workflowWidget.visible = True
self.layout.addWidget(workflowWidget)
def _getParameterNode(self): parameterNode = slicer.vtkMRMLScriptedModuleNode() slicer.mrmlScene.AddNode(parameterNode) return parameterNode