def registerCustomLayouts(self):
Guidelet.registerCustomLayouts(self)
layoutLogic = self.layoutManager.layoutLogic()
customLayout = (
"<layout type=\"horizontal\" split=\"false\" >"
" <item>"
" <view class=\"vtkMRMLViewNode\" singletontag=\"1\">"
" <property name=\"viewlabel\" action=\"default\">1</property>"
" </view>"
" </item>"
" <item>"
" <layout type=\"vertical\" split=\"false\" >"
" <item>"
" <view class=\"vtkMRMLSliceNode\" singletontag=\"Red\">"
" <property name=\"orientation\" action=\"default\">Axial</property>"
" <property name=\"viewlabel\" action=\"default\">R</property>"
" <property name=\"viewcolor\" action=\"default\">#F34A33</property>"
" </view>"
" </item>"
" <item>"
" <view class=\"vtkMRMLViewNode\" singletontag=\"2\">"
" <property name=\"viewlabel\" action=\"default\">1</property>"
" </view>"
" </item>"
" </layout>"
" </item>"
"</layout>")
layoutLogic.GetLayoutNode().AddLayoutDescription(
self.slice3DChartCustomLayoutId, customLayout)
def setupConnections(self):
logging.debug('ScoliUs.setupConnections()')
Guidelet.setupConnections(self)
self.calibrationCollapsibleButton.connect(
'toggled(bool)', self.onPatientSetupPanelToggled)
self.exampleButton.connect('clicked(bool)',
self.onExampleButtonClicked)
def disconnect(self):
logging.debug('USRegistrationGuidelet.disconnect')
Guidelet.disconnect(self)
# panels
self.ui.captureCollapsibleButton.disconnect('clicked(bool)',
self.onCapturePanelToggled)
self.ui.registerCollapsibleButton.disconnect(
'clicked(bool)', self.onRegisterPanelToggled)
self.ui.segmentCollapsibleButton.disconnect('clicked(bool)',
self.onSegmentPanelToggled)
# load & segment panel
self.ui.loadPatientDataButton.disconnect('clicked(bool)',
self.onLoadPatientDataClicked)
self.ui.createModelButton.disconnect('clicked(bool)',
self.onCreateModelClicked)
# capture panel
self.ui.deleteSeqButton.disconnect('clicked(bool)',
self.onDeleteSeqClicked)
self.ui.loadTFModelButton.disconnect('clicked(bool)',
self.onLoadTFModelClicked)
self.ui.pauseRecButton.disconnect('clicked(bool)',
self.onPauseRecClicked)
self.ui.startStopRecButton.disconnect('clicked(bool)',
self.onStartStopRec)
# register panel
self.ui.performRegButton.disconnect('clicked(bool)',
self.onPerformRegClicked)
def __init__(self, parent, logic, configurationName='Default'):
self.calibrationCollapsibleButton = None
Guidelet.__init__(self, parent, logic, configurationName)
logging.debug('ExampleGuideletGuidelet.__init__')
self.logic.addValuesToDefaultConfiguration()
moduleDirectoryPath = slicer.modules.exampleguidelet.path.replace(
'ExampleGuidelet.py', '')
# Set up main frame.
self.sliceletDockWidget.setObjectName('ExampleGuideletPanel')
self.sliceletDockWidget.setWindowTitle('Example guidelet')
self.mainWindow.setWindowTitle('ExampleGuidelet')
self.mainWindow.windowIcon = qt.QIcon(
moduleDirectoryPath + '/Resources/Icons/ExampleGuidelet.png')
self.setupScene()
self.navigationView = self.VIEW_ULTRASOUND_3D
# Setting button open on startup.
self.calibrationCollapsibleButton.setProperty('collapsed', False)
def __init__(self, parent, logic, configurationName='Default'):
# init guidelet
Guidelet.__init__(self, parent, logic, configurationName)
# module intrinsics
self.logic.addValuesToDefaultConfiguration()
self.modulePath = os.path.dirname(slicer.modules.usregistration.path)
self.moduleTransformsPath = os.path.join(self.modulePath,
'Resources/Transforms')
self.moduleModelsPath = os.path.join(self.modulePath,
'Resources/Models')
self.moduleIconsPath = os.path.join(self.modulePath, 'Resources/Icons')
self.referenceInView = False
self.probeInView = False
self.stylusInView = False
# set up main frame
self.sliceletDockWidget.setObjectName('USRegistration')
self.sliceletDockWidget.setWindowTitle('Skull US Registration')
self.mainWindow.setWindowTitle('Skull US Registration')
self.mainWindow.windowIcon = qt.QIcon(
os.path.join(self.moduleIconsPath, 'USRegistration.png'))
# hide slicer status bar
slicer.util.mainWindow().statusBar().hide()
# setup
self.setupScene()
# tool visibility icons
self.setupToolWatchdog()
def setupConnections(self):
logging.debug('EpiGuide.setupConnections()')
Guidelet.setupConnections(self)
self.navigationCollapsibleButton.connect('toggled(bool)',
self.onNavigationPanelToggled)
# Add our own behaviour (in addition to the default behavior) of the Ultrasound record button
self.ultrasound.startStopRecordingButton.connect(
'clicked(bool)', self.onStartStopRecordingButtonClicked)
def disconnect(self):
# see setupConnections
logging.debug('EpiGuide.disconnect()')
Guidelet.disconnect(self)
# Remove observer
self.navigationCollapsibleButton.disconnect(
'toggled(bool)', self.onNavigationPanelToggled)
self.ultrasound.startStopRecordingButton.disconnect(
'clicked(bool)', self.onStartStopRecordingButtonClicked)
def disconnect(self): #TODO see connect
logging.debug('ScoliUs.disconnect()')
Guidelet.disconnect(self)
# Remove observer to old parameter node
self.calibrationCollapsibleButton.disconnect(
'toggled(bool)', self.onPatientSetupPanelToggled)
self.exampleButton.disconnect('clicked(bool)',
self.onExampleButtonClicked)
def disconnect(self):#TODO see connect
logging.debug('ScoliUs.disconnect()')
Guidelet.disconnect(self)
# Remove observer to old parameter node
if self.patientSLandmarks_Reference and self.patientSLandmarks_ReferenceObserver:
self.patientSLandmarks_Reference.RemoveObserver(self.patientSLandmarks_ReferenceObserver)
self.patientSLandmarks_ReferenceObserver = None
self.calibrationCollapsibleButton.disconnect('toggled(bool)', self.onPatientSetupPanelToggled)
self.exampleButton.disconnect('clicked(bool)', self.onExampleButtonClicked)
def disconnect(self): #TODO see connect
logging.debug('ScoliUs.disconnect()')
Guidelet.disconnect(self)
# Remove observer to old parameter node
if self.patientSLandmarks_Reference and self.patientSLandmarks_ReferenceObserver:
self.patientSLandmarks_Reference.RemoveObserver(
self.patientSLandmarks_ReferenceObserver)
self.patientSLandmarks_ReferenceObserver = None
self.calibrationCollapsibleButton.disconnect(
'toggled(bool)', self.onPatientSetupPanelToggled)
self.exampleButton.disconnect('clicked(bool)',
self.onExampleButtonClicked)
def __init__(self, parent, logic, configurationName='Default'):
Guidelet.__init__(self, parent, logic, configurationName)
logging.debug('UltrasoundTrainingSystemGuidelet.__init__')
self.logic.addValuesToDefaultConfiguration()
# Set default layout name to the simulator training layout
self.defaultLayoutName = self.VIEW_US_SIMULATOR_TRAINING
# Set up main frame
self.sliceletDockWidget.setObjectName('UltrasoundTrainingSystemPanel')
self.sliceletDockWidget.setWindowTitle('UltrasoundTrainingSystem')
self.mainWindow.setWindowTitle('UltrasoundTrainingSystem')
self.selectView(self.VIEW_US_SIMULATOR_TRAINING)
def setupScene(self): #applet specific
parameterNode = self.logic.getParameterNode()
Guidelet.setupScene(self)
moduleDir = os.path.dirname(slicer.modules.usneedleguide.path)
# Load transform
probeModelToImageFullpath = os.path.join(
moduleDir, 'Resources', self.PROBEMODEL_TO_IMAGE_FILENAME)
probeModelToImageNode = slicer.mrmlScene.GetFirstNodeByName(
self.PROBEMODEL_TO_IMAGE)
if probeModelToImageNode is None:
probeModelToImageNode = slicer.util.loadTransform(
probeModelToImageFullpath)
probeModelToImageNode.SetName(self.PROBEMODEL_TO_IMAGE)
parameterNode.SetNodeReferenceID(self.PROBEMODEL_TO_IMAGE,
probeModelToImageNode.GetID())
# Load models
modelFileNames = ['Guide06cm', 'Guide08cm', 'Guide10cm', 'Guide12cm']
for i in range(len(modelFileNames)):
modelNode = parameterNode.GetNodeReference(modelFileNames[i])
if modelNode is None:
fileName = modelFileNames[i]
modelFullpath = os.path.join(moduleDir, 'Resources',
fileName + '.vtk')
modelNode = slicer.util.loadModel(modelFullpath)
displayNode = modelNode.GetDisplayNode()
displayNode.SetVisibility(True)
displayNode.SetColor(self.GUIDECOLORS[i][0],
self.GUIDECOLORS[i][1],
self.GUIDECOLORS[i][2])
displayNode.SetSliceIntersectionVisibility(True)
displayNode.SetSliceIntersectionThickness(2)
modelNode.SetAndObserveTransformNodeID(
probeModelToImageNode.GetID())
parameterNode.SetNodeReferenceID(modelFileNames[i],
modelNode.GetID())
# Hide slice view annotations (patient name, scale, color bar, etc.) as they
# decrease reslicing performance by 20%-100%
import DataProbe
dataProbeUtil = DataProbe.DataProbeLib.DataProbeUtil()
dataProbeParameterNode = dataProbeUtil.getParameterNode()
dataProbeParameterNode.SetParameter('showSliceViewAnnotations', '0')
def createFeaturePanels(self):
logging.debug('USRegistrationGuidelet.createFeaturePanels')
moduleDirectoryPath = slicer.modules.usregistration.path.replace(
'USRegistration.py', '')
self.uiWidget = slicer.util.loadUI(moduleDirectoryPath +
'Resources/UI/USRegistration.ui')
self.sliceletPanelLayout.addWidget(self.uiWidget)
self.ui = slicer.util.childWidgetVariables(self.uiWidget)
self.ui.line.setFrameShadow(qt.QFrame.Plain)
self.ui.line_2.setFrameShadow(qt.QFrame.Plain)
featurePanelList = [
self.ui.captureCollapsibleButton,
self.ui.segmentCollapsibleButton,
self.ui.registerCollapsibleButton,
]
featurePanelList[len(featurePanelList
):] = Guidelet.createFeaturePanels(self)
self.sliceletPanelLayout.addItem(
qt.QSpacerItem(20, 40, qt.QSizePolicy.Minimum,
qt.QSizePolicy.Expanding))
return featurePanelList
def onViewSelect(self, layoutIndex):
# Check out layout request first, then pass on to parent to handle the existing ones
text = self.viewSelectorComboBox.currentText
if text == self.VIEW_ULTRASOUND_3D_3DCHART:
# self.layoutManager.setLayout(self.slice3DChartCustomLayoutId)
# self.delayedFitUltrasoundImageToView() # (8.30.17) may want to add this, but no change:
# self.showUltrasoundIn3dView(True)
# ####### this should keep the 2 panel
self.layoutManager.setLayout(self.red3dCustomLayoutId)
self.delayedFitUltrasoundImageToView()
self.showUltrasoundIn3dView(True)
# ######
self.populateChart()
return
Guidelet.onViewSelect(self, layoutIndex)
def setupScene(self):
logging.debug('USRegistrationGuidelet.setupScene')
Guidelet.setupScene(self)
self.setupTransforms()
self.setupModels()
self.setupTransformTree()
self.setupSegmentEditor()
# hide slice view annotations (patient name, scale, color bar, etc.) as they
# decrease reslicing performance by 20%-100%
logging.debug('USRegistrationGuidelet: Hide slice view annotations')
import DataProbe
dataProbeUtil = DataProbe.DataProbeLib.DataProbeUtil()
dataProbeParameterNode = dataProbeUtil.getParameterNode()
dataProbeParameterNode.SetParameter('showSliceViewAnnotations', '0')
def setupScene(self):
logging.debug('setupScene')
Guidelet.setupScene(self)
logging.debug('Create transforms')
algiaCervicalModuleDataPath = slicer.modules.zalgiacervical.path.replace("zAlgiaCervical.py","") + 'Data/'
self.AlgiaCervicalLogic = zAlgiaCervicalLogic()
self.AlgiaCervicalLogic.variableSetUp()
# Cameras
'''logging.debug('Create cameras')
self.LeftCamera = slicer.util.getNode('Left Camera')
if not self.LeftCamera:
self.LeftCamera=slicer.vtkMRMLCameraNode()
self.LeftCamera.SetName("Left Camera")
slicer.mrmlScene.AddNode(self.LeftCamera)
self.RightCamera = slicer.util.getNode('Right Camera')
if not self.RightCamera:
self.RightCamera=slicer.vtkMRMLCameraNode()
self.RightCamera.SetName("Right Camera")
slicer.mrmlScene.AddNode(self.RightCamera)'''
# Models
logging.debug('Create models')
# Load head model
self.headModel = slicer.util.getNode('head')
if not self.headModel:
slicer.util.loadModel(algiaCervicalModuleDataPath + 'head.stl')
self.headModel = slicer.util.getNode(pattern="head")
# Views
self.registerCustomLayoutsAlgia()
self.layoutManager.setLayout(self.dual3dcuantitativeCustomLayoutId)
#Delete Ultrasound created by Guidelet by default
scene = slicer.mrmlScene
red = scene.GetNodeByID('vtkMRMLSliceNodeRed')
red.SetSliceVisible(False)
def __init__(self, parent, logic, configurationName='Default'):
Guidelet.__init__(self, parent, logic, configurationName)
logging.debug('AlgiaCervicalGuidelet.__init__')
#Init del logic zAlgiaCervical
# Member variables
self.m = vtk.vtkMatrix4x4()
self.transform=numpy.zeros((4,4), dtype=numpy.float64)
self.observedNode = None
self.outputObserverTag = -1
self.record = False
self.timerActive=False
self.recordingTime_mode1=5 # 5 seconds to record initial position
self.recordingTime_mode2=20 # 5 seconds to record initial position
self.mode=0
self.myTimer=Timer()
self.translation_x=numpy.array([])
self.translation_y=numpy.array([])
self.translation_z=numpy.array([])
self.rotation_x=numpy.array([])
self.rotation_y=numpy.array([])
self.rotation_z=numpy.array([])
self.timeStamp=numpy.array([])
# Set up main frame.
self.sliceletDockWidget.setObjectName('AlgiaCervicalPanel')
self.sliceletDockWidget.setWindowTitle('AlgiaCervical')
self.mainWindow.setWindowTitle('Algia Cervical')
#self.mainWindow.windowIcon = qt.QIcon(moduleDirectoryPath + '/Resources/Icons/zAlgiaCervical.png')
self.setupScene()
#self.showChart()
#sliceletPanelLayout = self.sliceletPanelLayout
#sliceletPanelLayout.removeWidget(self.ultrasoundCollapsibleButton)
# self.ultrasound.cleanup()
self.ultrasoundCollapsibleButton.setProperty('collapsed', True)
self.ultrasoundCollapsibleButton.setVisible(False)
self.advancedCollapsibleButton.setProperty('collapsed', True)
def createFeaturePanels(self):
# Create GUI panels.
featurePanelList = Guidelet.createFeaturePanels(self)
self.navigationCollapsibleButton = ctk.ctkCollapsibleButton()
featurePanelList[len(featurePanelList):] = [
self.navigationCollapsibleButton
]
return featurePanelList
def createFeaturePanels(self):
# Create GUI panels.
self.calibrationCollapsibleButton = ctk.ctkCollapsibleButton()
self.patientSetupPanel()
featurePanelList = Guidelet.createFeaturePanels(self)
featurePanelList[len(featurePanelList):] = [self.calibrationCollapsibleButton]
return featurePanelList
def createFeaturePanels(self):
# Create GUI panels.
self.transformsCollapsibleButton = ctk.ctkCollapsibleButton()
self.setupMainPanel()
featurePanelList = Guidelet.createFeaturePanels(self)
#Due to this, Transforms collapsible button can't be collapsed...
featurePanelList = [self.transformsCollapsibleButton]
return featurePanelList
def createFeaturePanels(self):
# Create GUI panels.
self.calibrationCollapsibleButton = ctk.ctkCollapsibleButton()
self.patientSetupPanel()
featurePanelList = Guidelet.createFeaturePanels(self)
featurePanelList[len(featurePanelList):] = [
self.calibrationCollapsibleButton
]
return featurePanelList
def createFeaturePanels(self):
# Create GUI panels.
logging.debug('UltrasoundTrainingSystem.createFeaturePanels()')
self.LoadSceneCollapsibleButton = ctk.ctkCollapsibleButton()
self.SetupLoadSceneCollapsibleButton()
featurePanelList = Guidelet.createFeaturePanels(self)
featurePanelList[len(featurePanelList):] = [
self.LoadSceneCollapsibleButton
]
return featurePanelList
def __init__(self, parent, logic, configurationName='Default'):
self.calibrationCollapsibleButton = None
Guidelet.__init__(self, parent, logic, configurationName)
logging.debug('ExampleGuideletGuidelet.__init__')
self.logic.addValuesToDefaultConfiguration()
moduleDirectoryPath = slicer.modules.exampleguidelet.path.replace('ExampleGuidelet.py', '')
# Set up main frame.
self.sliceletDockWidget.setObjectName('ExampleGuideletPanel')
self.sliceletDockWidget.setWindowTitle('Example guidelet')
self.mainWindow.setWindowTitle('ExampleGuidelet')
self.mainWindow.windowIcon = qt.QIcon(moduleDirectoryPath + '/Resources/Icons/ExampleGuidelet.png')
self.setupScene()
self.navigationView = self.VIEW_ULTRASOUND_3D
# Setting button open on startup.
self.calibrationCollapsibleButton.setProperty('collapsed', False)
def __init__(self, parent, logic, configurationName='Default'):
self.slice3DChartCustomLayoutId = 5000 # Must come before Guidelet.__init__
Guidelet.__init__(self, parent, logic, configurationName)
logging.debug('EpiGuideGuidelet.__init__')
self.logic.addValuesToDefaultConfiguration()
# for debugging purposes only, to be removed
slicer.epi = self
self.navigationCollapsibleButton = None
self.imageData = None
self.imageDimensions = None
self.line = None
self.table = None
self.chart = None
self.view = None
self.signalArray = None
self.distanceArray = None
self.boundsRecalculated = False
self.fitUltrasoundImageToViewOnConnect = True
self.firstPeakToSETTipTransformNode = None
self.secondPeakToSETTipTransformNode = None
self.thirdPeakToSETTipTransformNode = None
self.firstPeakModelNode = None
self.secondPeakModelNode = None
self.thirdPeakModelNode = None
self.needleWithTipModel = None
self.trajectoryModel_needleModel = None
self.trajectoryModel_needleTip = None
self.referenceToRasTransform = None
self.needleTipToNeedleTransform = None
self.needleModelToNeedleTipTransform = None
self.trajModelToNeedleTipTransform = None
self.needleToReferenceTransform = None
self.setTipToReferenceTransformNode = None
self.aModeImageNode = None
self.timer = qt.QTimer()
self.agilentCommandLogic = PlusRemoteLogic()
self.agilentConnectorNode = slicer.mrmlScene.AddNode(
slicer.vtkMRMLIGTLConnectorNode())
self.agilentConnectorNode.SetLogErrorIfServerConnectionFailed(False)
hostNamePort = self.parameterNode.GetParameter(
'AgilentServerHostNamePort') # example: "localhost:18944"
[hostName, port] = hostNamePort.split(':')
self.agilentConnectorNode.SetTypeClient(hostName, int(port))
self.agilentConnectorNode.Start()
self.needleModelTipRadius = 0.0
# Set up main frame
self.sliceletDockWidget.setObjectName('EpiGuidePanel')
self.sliceletDockWidget.setWindowTitle('EpiGuideNav')
self.mainWindow.setWindowTitle('Epidural injection navigation')
self.navigationView = self.VIEW_TRIPLE_3D # should we change to VIEW_ULTRASOUND_3D_3DCHART ???
def setupScene(self): #applet specific
logging.debug('setupScene')
'''
ReferenceToRas transform is used in almost all IGT applications. Reference is the coordinate system
of a tool fixed to the patient. Tools are tracked relative to Reference, to compensate for patient
motion. ReferenceToRas makes sure that everything is displayed in an anatomical coordinate system, i.e.
R, A, and S (Right, Anterior, and Superior) directions in Slicer are correct relative to any
images or tracked tools displayed.
ReferenceToRas is needed for initialization, so we need to set it up before calling Guidelet.setupScene().
'''
self.referenceToRas = slicer.util.getNode('ReferenceToRas')
if not self.referenceToRas:
self.referenceToRas=slicer.vtkMRMLLinearTransformNode()
self.referenceToRas.SetName("ReferenceToRas")
m = self.logic.readTransformFromSettings('ReferenceToRas', self.configurationName)
if m is None:
m = self.logic.createMatrixFromString('1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1')
self.referenceToRas.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.referenceToRas)
Guidelet.setupScene(self)
# Transforms
logging.debug('Create transforms')
'''
In this example we assume that there is a tracked needle in the system. The needle is not
tracked at its tip, so we need a NeedleTipToNeedle transform to define where the needle tip is.
In your application Needle may be called Stylus, or maybe you don't need such a tool at all.
'''
self.needleToReference = slicer.util.getNode('NeedleToReference')
if not self.needleToReference:
self.needleToReference = slicer.vtkMRMLLinearTransformNode()
self.needleToReference.SetName('NeedleToReference')
slicer.mrmlScene.AddNode(self.needleToReference)
self.needleTipToNeedle = slicer.util.getNode('NeedleTipToNeedle')
if not self.needleTipToNeedle:
self.needleTipToNeedle = slicer.vtkMRMLLinearTransformNode()
self.needleTipToNeedle.SetName('NeedleTipToNeedle')
m = self.logic.readTransformFromSettings('NeedleTipToNeedle', self.configurationName)
if m:
self.needleTipToNeedle.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.needleTipToNeedle)
# Models
logging.debug('Create models')
self.needleModel = slicer.util.getNode('NeedleModel')
if not self.needleModel:
self.needleModel = slicer.modules.createmodels.logic().CreateNeedle(80, 1.0, 2.5, 0)
self.needleModel.SetName('NeedleModel')
# Build transform tree
logging.debug('Set up transform tree')
self.needleToReference.SetAndObserveTransformNodeID(self.referenceToRas.GetID())
self.needleTipToNeedle.SetAndObserveTransformNodeID(self.needleToReference.GetID())
self.needleModel.SetAndObserveTransformNodeID(self.needleTipToNeedle.GetID())
# Hide slice view annotations (patient name, scale, color bar, etc.) as they
# decrease reslicing performance by 20%-100%
logging.debug('Hide slice view annotations')
import DataProbe
dataProbeUtil=DataProbe.DataProbeLib.DataProbeUtil()
dataProbeParameterNode=dataProbeUtil.getParameterNode()
dataProbeParameterNode.SetParameter('showSliceViewAnnotations', '0')
def setupViewerLayouts(self):
Guidelet.setupViewerLayouts(self)
# Now we can add our own layout to the drop down list
self.viewSelectorComboBox.addItem(self.VIEW_ULTRASOUND_3D_3DCHART)
def preCleanup(self):#common
Guidelet.preCleanup(self)
logging.debug('preCleanup')
def setupConnections(self):
logging.debug('ScoliUs.setupConnections()')
Guidelet.setupConnections(self)
self.calibrationCollapsibleButton.connect('toggled(bool)', self.onPatientSetupPanelToggled)
self.exampleButton.connect('clicked(bool)', self.onExampleButtonClicked)
def disconnect(self): #TODO: see connect
logging.debug('UsSimulatorTraining.disconnect()')
Guidelet.disconnect(self)
def setupScene(self): #applet specific
logging.debug('setupScene')
'''
ReferenceToRas transform is used in almost all IGT applications. Reference is the coordinate system
of a tool fixed to the patient. Tools are tracked relative to Reference, to compensate for patient
motion. ReferenceToRas makes sure that everything is displayed in an anatomical coordinate system, i.e.
R, A, and S (Right, Anterior, and Superior) directions in Slicer are correct relative to any
images or tracked tools displayed.
ReferenceToRas is needed for initialization, so we need to set it up before calling Guidelet.setupScene().
'''
self.referenceToRas = slicer.util.getNode('ReferenceToRas')
if not self.referenceToRas:
self.referenceToRas = slicer.vtkMRMLLinearTransformNode()
self.referenceToRas.SetName("ReferenceToRas")
m = self.logic.readTransformFromSettings('ReferenceToRas',
self.configurationName)
if m is None:
m = self.logic.createMatrixFromString(
'1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1')
self.referenceToRas.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.referenceToRas)
Guidelet.setupScene(self)
# Transforms
logging.debug('Create transforms')
'''
In this example we assume that there is a tracked needle in the system. The needle is not
tracked at its tip, so we need a NeedleTipToNeedle transform to define where the needle tip is.
In your application Needle may be called Stylus, or maybe you don't need such a tool at all.
'''
self.needleToReference = slicer.util.getNode('NeedleToReference')
if not self.needleToReference:
self.needleToReference = slicer.vtkMRMLLinearTransformNode()
self.needleToReference.SetName('NeedleToReference')
slicer.mrmlScene.AddNode(self.needleToReference)
self.needleTipToNeedle = slicer.util.getNode('NeedleTipToNeedle')
if not self.needleTipToNeedle:
self.needleTipToNeedle = slicer.vtkMRMLLinearTransformNode()
self.needleTipToNeedle.SetName('NeedleTipToNeedle')
m = self.logic.readTransformFromSettings('NeedleTipToNeedle',
self.configurationName)
if m:
self.needleTipToNeedle.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.needleTipToNeedle)
# Models
logging.debug('Create models')
self.needleModel = slicer.util.getNode('NeedleModel')
if not self.needleModel:
self.needleModel = slicer.modules.createmodels.logic(
).CreateNeedle(80, 1.0, 2.5, 0)
self.needleModel.SetName('NeedleModel')
# Build transform tree
logging.debug('Set up transform tree')
self.needleToReference.SetAndObserveTransformNodeID(
self.referenceToRas.GetID())
self.needleTipToNeedle.SetAndObserveTransformNodeID(
self.needleToReference.GetID())
self.needleModel.SetAndObserveTransformNodeID(
self.needleTipToNeedle.GetID())
# Hide slice view annotations (patient name, scale, color bar, etc.) as they
# decrease reslicing performance by 20%-100%
logging.debug('Hide slice view annotations')
import DataProbe
dataProbeUtil = DataProbe.DataProbeLib.DataProbeUtil()
dataProbeParameterNode = dataProbeUtil.getParameterNode()
dataProbeParameterNode.SetParameter('showSliceViewAnnotations', '0')
def setupConnections(self):
logging.debug('UltrasoundTrainingSystem.setupConnections()')
Guidelet.setupConnections(self)
self.LoadSceneButton.connect('clicked()', self.openLoadSceneDialog)
def disconnect(self): #TODO: see connect
logging.debug('UltrasoundTrainingSystem.disconnect()')
Guidelet.disconnect(self)
def cleanup(self):#common
Guidelet.cleanup(self)
logging.debug('cleanup')
def preCleanup(self): #common
Guidelet.preCleanup(self)
logging.debug('preCleanup')
def cleanup(self): #common
Guidelet.cleanup(self)
logging.debug('cleanup')
def preCleanup(self):
logging.debug('USRegistrationGuidelet.preCleanup')
Guidelet.preCleanup(self)
def setupConnections(self):
logging.debug('UsSimulatorTraining.setupConnections()')
Guidelet.setupConnections(self)
self.LoadSceneButton.connect('clicked()', self.openLoadSceneDialog)
def preCleanup(self):
Guidelet.preCleanup(self)
logging.debug('precleanup')
def setupConnectorNode(self):
Guidelet.setupConnectorNode(self)
self.connectorNode.SetLogErrorIfServerConnectionFailed(False)
def setupScene(self): #applet specific
logging.debug('setupScene')
# ReferenceToRas is needed for ultrasound initialization, so we need to
# set it up before calling Guidelet.setupScene().
self.referenceToRas = slicer.util.getNode('ReferenceToRas')
if not self.referenceToRas:
self.referenceToRas=slicer.vtkMRMLLinearTransformNode()
self.referenceToRas.SetName("ReferenceToRas")
m = self.logic.readTransformFromSettings('ReferenceToRas', self.configurationName)
if m is None:
# The following line should not be needed.
m = self.logic.createMatrixFromString('1 0 0 0 0 1 0 0 0 0 1 0 0 0 0 1')
self.referenceToRas.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.referenceToRas)
Guidelet.setupScene(self)
# Transforms
logging.debug('Create transforms')
moduleDir = os.path.dirname(slicer.modules.exampleguidelet.path)
self.transdToReference = slicer.util.getNode('TransdToReference')
if not self.transdToReference:
self.transdToReference = slicer.vtkMRMLLinearTransformNode()
self.transdToReference.SetName("TransdToReference")
m = self.logic.readTransformFromSettings('TransdToReference', self.configurationName)
if m:
self.transdToReference.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.transdToReference)
self.probeToReference = slicer.util.getNode('ProbeToReference')
if not self.probeToReference:
self.probeToReference = slicer.vtkMRMLLinearTransformNode()
self.probeToReference.SetName("ProbeToReference")
slicer.mrmlScene.AddNode(self.probeToReference)
self.needleToReference = slicer.util.getNode('NeedleToReference')
if not self.needleToReference:
self.needleToReference = slicer.vtkMRMLLinearTransformNode()
self.needleToReference.SetName('NeedleToReference')
slicer.mrmlScene.AddNode(self.needleToReference)
self.needleTipToNeedle = slicer.util.getNode('NeedleTipToNeedle')
if not self.needleTipToNeedle:
self.needleTipToNeedle = slicer.vtkMRMLLinearTransformNode()
self.needleTipToNeedle.SetName('NeedleTipToNeedle')
m = self.logic.readTransformFromSettings('NeedleTipToNeedle', self.configurationName)
if m:
self.needleTipToNeedle.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.needleTipToNeedle)
# Models
logging.debug('Create models')
self.needleModel = slicer.util.getNode('NeedleModel')
if not self.needleModel:
self.needleModel = slicer.modules.createmodels.logic().CreateNeedle(80, 1.0, 2.5, 0)
self.needleModel.SetName('NeedleModel')
# Build transform tree
logging.debug('Set up transform tree')
self.transdToReference.SetAndObserveTransformNodeID(self.referenceToRas.GetID())
self.probeToReference.SetAndObserveTransformNodeID(self.referenceToRas.GetID())
self.needleToReference.SetAndObserveTransformNodeID(self.referenceToRas.GetID())
self.needleTipToNeedle.SetAndObserveTransformNodeID(self.needleToReference.GetID())
self.needleModel.SetAndObserveTransformNodeID(self.needleTipToNeedle.GetID())
# Hide slice view annotations (patient name, scale, color bar, etc.) as they
# decrease reslicing performance by 20%-100%
logging.debug('Hide slice view annotations')
import DataProbe
dataProbeUtil=DataProbe.DataProbeLib.DataProbeUtil()
dataProbeParameterNode=dataProbeUtil.getParameterNode()
dataProbeParameterNode.SetParameter('showSliceViewAnnotations', '0')
def setupAdvancedPanel(self):
Guidelet.setupAdvancedPanel(self)
self.registerCustomLayouts()