def createUserInterface(self):
'''
'''
# TODO: might make sense to hide the button for the last step at this
# point, but the widget does not have such option
self.__layout = self.__parent.createUserInterface()
# # Place Tracker Position
# placeTrackerPositionButton = qt.QPushButton("Add tracker position")
# placeTrackerPositionButton.toolTip = "Add a tracker position to the list"
# self.__layout.addWidget(placeTrackerPositionButton)
# placeTrackerPositionButton.connect('clicked(bool)', self.onPlaceTrackerPositionButtonClicked)
#
# # Load a tracker list
# loadTrackerListButton = qt.QPushButton("Test spatial points lists creation")
# loadTrackerListButton.toolTip = "Load spatial points to test registration"
# self.__layout.addWidget(loadTrackerListButton)
# loadTrackerListButton.connect('clicked(bool)', self.onLoadSpatialPointsListClicked)
self.fiducialsList = FiducialsList()
self.fiducialsList.setModuleLogic(self.logic)
self.__layout.addWidget(self.fiducialsList.getFiducialsWidget())
self.fiducialsWidget = self.fiducialsList.getFiducialsWidget()
#customize the UI
self.fiducialsWidget.placeSpatialButton.setVisible(True)
self.fiducialsWidget.placeFiducialButton.setVisible(False)
self.fiducialsWidget.fiducialsList.setColumnHidden(2, True)
self.fiducialsWidget.fiducialsList.setColumnHidden(4, True)
#connect signals and slots
self.fiducialsWidget.placeSpatialButton.connect(
'clicked(bool)', self.onPlaceTrackerPositionButtonClicked)
self.updateWidgetFromParameters(self.parameterNode())
self.updateGeometry()
qt.QTimer.singleShot(0, self.killButton)
print("Fiducials Widget size Hint:")
self.fiducialsWidget.sizeHint
print("Fiducials Widget size :")
self.fiducialsWidget.size
print("Spatial fiducials step size Hint:")
print self.sizeHint
print("Spatial fiducials step size")
print self.size
def createUserInterface( self ):
'''
'''
# TODO: might make sense to hide the button for the last step at this
# point, but the widget does not have such option
self.__layout = self.__parent.createUserInterface()
# # BUTTONS --------------------------------------------------------------------
# This is commented out and the buttons are in the UI from the designer
#
# #layout for the buttons
# self.buttonsLayout = qt.QHBoxLayout()
# self.__layout.addLayout(self.buttonsLayout, 1)
#
# # Place fiducial
# placeFiducialButtom = qt.QPushButton("Place fiducial")
# placeFiducialButtom.toolTip = "Add a fiducial to the list"
# self.buttonsLayout.addWidget(placeFiducialButtom)
# placeFiducialButtom.connect('clicked(bool)', self.onPlaceFiducialButtomClicked)
#
# # Spacer
# self.buttonsLayout.addStretch()
self.fiducialsList = FiducialsList()
self.fiducialsList.setModuleLogic(self.logic)
self.__layout.addWidget(self.fiducialsList.getFiducialsWidget())
self.fiducialsWidget = self.fiducialsList.getFiducialsWidget()
#customize the UI
self.fiducialsWidget.placeSpatialButton.setVisible(False)
self.fiducialsWidget.placeFiducialButton.setVisible(True)
self.fiducialsWidget.fiducialsList.setColumnHidden(2, True)
self.fiducialsWidget.fiducialsList.setColumnHidden(4, True)
qt.QTimer.singleShot(0, self.killButton)
print("Fiducials Widget size Hint:")
print self.fiducialsWidget.sizeHint
print("Fiducials Widget size :")
print self.fiducialsWidget.size
print("Image fiducials step size Hint:")
print self.sizeHint
print("Image fiducials step size")
print self.size
def createUserInterface( self ):
'''
'''
# TODO: might make sense to hide the button for the last step at this
# point, but the widget does not have such option
self.__layout = self.__parent.createUserInterface()
# # BUTTONS --------------------------------------------------------------------
# This is commented out and the buttons are in the UI from the designer
#
# #layout for the buttons
# self.buttonsLayout = qt.QHBoxLayout()
# self.__layout.addLayout(self.buttonsLayout, 1)
#
# # Place fiducial
# placeFiducialButtom = qt.QPushButton("Place fiducial")
# placeFiducialButtom.toolTip = "Add a fiducial to the list"
# self.buttonsLayout.addWidget(placeFiducialButtom)
# placeFiducialButtom.connect('clicked(bool)', self.onPlaceFiducialButtomClicked)
#
# # Spacer
# self.buttonsLayout.addStretch()
self.fiducialsList = FiducialsList()
self.fiducialsList.setPlaceImageFiducialStep(True)
self.fiducialsList.setModuleLogic(self.logic)
self.__layout.addWidget(self.fiducialsList.getFiducialsWidget())
self.fiducialsWidget = self.fiducialsList.getFiducialsWidget()
#customize the UI
self.fiducialsWidget.placeSpatialButton.setVisible(False)
self.fiducialsWidget.placeFiducialButton.setVisible(True)
self.fiducialsWidget.fiducialsList.setColumnHidden(2, True)
self.fiducialsWidget.fiducialsList.setColumnHidden(3, True)
self.fiducialsWidget.fiducialsList.setColumnHidden(4, True)
qt.QTimer.singleShot(0, self.killButton)
print("Fiducials Widget size Hint:")
print self.fiducialsWidget.sizeHint
print("Fiducials Widget size :")
print self.fiducialsWidget.size
print("Image fiducials step size Hint:")
print self.sizeHint
print("Image fiducials step size")
print self.size
def createUserInterface( self ):
'''
'''
# TODO: might make sense to hide the button for the last step at this
# point, but the widget does not have such option
self.__layout = self.__parent.createUserInterface()
# # Place Tracker Position
# placeTrackerPositionButton = qt.QPushButton("Add tracker position")
# placeTrackerPositionButton.toolTip = "Add a tracker position to the list"
# self.__layout.addWidget(placeTrackerPositionButton)
# placeTrackerPositionButton.connect('clicked(bool)', self.onPlaceTrackerPositionButtonClicked)
#
# # Load a tracker list
# loadTrackerListButton = qt.QPushButton("Test spatial points lists creation")
# loadTrackerListButton.toolTip = "Load spatial points to test registration"
# self.__layout.addWidget(loadTrackerListButton)
# loadTrackerListButton.connect('clicked(bool)', self.onLoadSpatialPointsListClicked)
self.fiducialsList = FiducialsList()
self.fiducialsList.setModuleLogic(self.logic)
self.__layout.addWidget(self.fiducialsList.getFiducialsWidget())
self.fiducialsWidget = self.fiducialsList.getFiducialsWidget()
#customize the UI
self.fiducialsWidget.placeSpatialButton.setVisible(True)
self.fiducialsWidget.placeFiducialButton.setVisible(False)
self.fiducialsWidget.fiducialsList.setColumnHidden(2, True)
self.fiducialsWidget.fiducialsList.setColumnHidden(4, True)
#connect signals and slots
self.fiducialsWidget.placeSpatialButton.connect('clicked(bool)', self.onPlaceTrackerPositionButtonClicked)
self.updateWidgetFromParameters(self.parameterNode())
self.updateGeometry()
qt.QTimer.singleShot(0, self.killButton)
print("Fiducials Widget size Hint:")
self.fiducialsWidget.sizeHint
print("Fiducials Widget size :")
self.fiducialsWidget.size
print("Spatial fiducials step size Hint:")
print self.sizeHint
print("Spatial fiducials step size")
print self.size
class CaptureSpatialPositionsStep(USGuidedStep):
def __init__(self, stepid):
self.initialize(stepid)
self.setName('2. Capture spatial positions step')
#self.setDescription( 'Place fiducials using the tracker' )
self.__parent = super(CaptureSpatialPositionsStep, self)
self.numberOfAcquiredSpatialPositions = 0
def createUserInterface(self):
'''
'''
# TODO: might make sense to hide the button for the last step at this
# point, but the widget does not have such option
self.__layout = self.__parent.createUserInterface()
# # Place Tracker Position
# placeTrackerPositionButton = qt.QPushButton("Add tracker position")
# placeTrackerPositionButton.toolTip = "Add a tracker position to the list"
# self.__layout.addWidget(placeTrackerPositionButton)
# placeTrackerPositionButton.connect('clicked(bool)', self.onPlaceTrackerPositionButtonClicked)
#
# # Load a tracker list
# loadTrackerListButton = qt.QPushButton("Test spatial points lists creation")
# loadTrackerListButton.toolTip = "Load spatial points to test registration"
# self.__layout.addWidget(loadTrackerListButton)
# loadTrackerListButton.connect('clicked(bool)', self.onLoadSpatialPointsListClicked)
self.fiducialsList = FiducialsList()
self.fiducialsList.setModuleLogic(self.logic)
self.__layout.addWidget(self.fiducialsList.getFiducialsWidget())
self.fiducialsWidget = self.fiducialsList.getFiducialsWidget()
#customize the UI
self.fiducialsWidget.placeSpatialButton.setVisible(True)
self.fiducialsWidget.placeFiducialButton.setVisible(False)
self.fiducialsWidget.fiducialsList.setColumnHidden(2, True)
self.fiducialsWidget.fiducialsList.setColumnHidden(4, True)
#connect signals and slots
self.fiducialsWidget.placeSpatialButton.connect(
'clicked(bool)', self.onPlaceTrackerPositionButtonClicked)
self.updateWidgetFromParameters(self.parameterNode())
self.updateGeometry()
qt.QTimer.singleShot(0, self.killButton)
print("Fiducials Widget size Hint:")
self.fiducialsWidget.sizeHint
print("Fiducials Widget size :")
self.fiducialsWidget.size
print("Spatial fiducials step size Hint:")
print self.sizeHint
print("Spatial fiducials step size")
print self.size
def killButton(self):
# hide useless button
bl = slicer.util.findChildren(text='ReportROI')
if len(bl):
bl[0].hide()
def validate(self, desiredBranchId):
'''
'''
self.__parent.validationSucceeded(desiredBranchId)
print(
"We are in the validate function of CaptureSpatialPositionsStepStep"
)
def onEntry(self, comingFrom, transitionType):
super(CaptureSpatialPositionsStep,
self).onEntry(comingFrom, transitionType)
self.updateWidgetFromParameters(self.parameterNode())
pNode = self.parameterNode()
pNode.SetParameter('currentStep', self.stepid)
print(
"We are in the onEntry function of CaptureSpatialPositionsStepStep coming from:"
)
print comingFrom.name()
qt.QTimer.singleShot(0, self.killButton)
def onExit(self, goingTo, transitionType):
self.doStepProcessing()
super(CaptureSpatialPositionsStep,
self).onExit(goingTo, transitionType)
print(
"We are in the onExit function of CaptureSpatialPositionsStepStep")
def updateWidgetFromParameters(self, parameterNode):
print("We are in the place fiducials step")
self.fiducialsList.updateSpatialFiducialsList()
#self.updateTrackerPointsList()
def doStepProcessing(self):
# calculate the transform to align the ROI in the next step with the
# baseline volume
pNode = self.parameterNode()
# def onPlaceTrackerPositionButtonClicked(self):
# self.logic.recordTrackerPosition()
#
def onLoadSpatialPointsListClicked(self):
self.logic.addFiducialsToTrackerList()
def onPlaceTrackerPositionButtonClicked(self):
fiducialName = "F" + str(self.numberOfAcquiredSpatialPositions)
positionRecorded = self.logic.captureSpatialsPositions(fiducialName)
path = slicer.modules.stylusbasedusprobecalibration.path
modulePath = os.path.dirname(path)
if positionRecorded == True:
#get the most recent node (the last) in the Tracker Points List
#trackerNode = slicer.util.getNode(fiducialName+"-Tracker")
# trackerNode = self.logic.getFiducialNode('Tracker Points List', -1)
#
#
# # Associate the fiducial and the tracker position
# # We remove the previous (if exist) tracker node
# # and we put the new tracker node ID in the table and check the row
# currentItem = self.fiducialsWidget.fiducialsList.item(self.numberOfAcquiredSpatialPositions , 4)
# if currentItem is None:
# self.fiducialsList.addNewEmptyRow(self.numberOfAcquiredSpatialPositions)
#
# currentItem = self.fiducialsWidget.fiducialsList.item(self.numberOfAcquiredSpatialPositions , 4)
#
# self.fiducialsWidget.fiducialsList.item(self.numberOfAcquiredSpatialPositions , 3).setText(trackerNode.GetName())
# self.fiducialsWidget.fiducialsList.item(self.numberOfAcquiredSpatialPositions , 4).setText(trackerNode.GetID())
# self.fiducialsWidget.fiducialsList.item(self.numberOfAcquiredSpatialPositions , 0).setCheckState(2)
self.fiducialsList.updateFiducialsList("Tracker Points List")
soundFile = os.path.join(modulePath, "sounds/notify.wav")
sound = qt.QSound(soundFile)
sound.play()
self.numberOfAcquiredSpatialPositions += 1
else:
soundFile = os.path.join(modulePath, "sounds/critico.wav")
#sound=qt.QSound("C:\Users\Usuario\devel\slicelets\USGuidedProcedure\sounds\critico.wav")
sound = qt.QSound(soundFile)
sound.play()
def updateTrackerPointsList(self):
#clear list
#self.fiducialsWidget.fiducialsList.clear()
#raise this flag to ignore change events in the table, the flag is lowered at the end of this method
self.updatingList = True
# get the nodes
fiducialListNode = slicer.util.getNode("Fiducials List")
trackerListNode = slicer.util.getNode("Tracker Points List")
# clear the list of tracker points
trackerListNode.RemoveChildrenNodes()
# create as many tracker nodes as fiducials
saml = slicer.modules.annotations.logic()
saml.SetActiveHierarchyNodeID(trackerListNode.GetID())
for childrenIndex in xrange(
fiducialListNode.GetNumberOfChildrenNodes()):
fidHierarchyNode = fiducialListNode.GetNthChildNode(childrenIndex)
fidNode = fidHierarchyNode.GetAssociatedNode()
fidPos = [0, 0, 0]
dummy = fidNode.GetFiducialCoordinates(fidPos)
fidName = fidNode.GetName()
fidID = fidNode.GetID()
trackerNode = slicer.vtkMRMLAnnotationFiducialNode()
trackerNode.SetFiducialWorldCoordinates(fidPos)
trackerNode.SetName(fidName + '-Tracker')
slicer.mrmlScene.AddNode(trackerNode)
self.updatingList = False
class PlaceSpatialFiducialsStep( USGuidedStep ) :
def __init__( self, stepid ):
self.initialize( stepid )
self.setName( '3. Place spatial Fiducials' )
#self.setDescription( 'Place fiducials using the tracker' )
self.__parent = super( PlaceSpatialFiducialsStep, self )
def createUserInterface( self ):
'''
'''
# TODO: might make sense to hide the button for the last step at this
# point, but the widget does not have such option
self.__layout = self.__parent.createUserInterface()
# # Place Tracker Position
# placeTrackerPositionButton = qt.QPushButton("Add tracker position")
# placeTrackerPositionButton.toolTip = "Add a tracker position to the list"
# self.__layout.addWidget(placeTrackerPositionButton)
# placeTrackerPositionButton.connect('clicked(bool)', self.onPlaceTrackerPositionButtonClicked)
#
# # Load a tracker list
# loadTrackerListButton = qt.QPushButton("Test spatial points lists creation")
# loadTrackerListButton.toolTip = "Load spatial points to test registration"
# self.__layout.addWidget(loadTrackerListButton)
# loadTrackerListButton.connect('clicked(bool)', self.onLoadSpatialPointsListClicked)
self.fiducialsList = FiducialsList()
self.fiducialsList.setModuleLogic(self.logic)
self.__layout.addWidget(self.fiducialsList.getFiducialsWidget())
self.fiducialsWidget = self.fiducialsList.getFiducialsWidget()
#customize the UI
self.fiducialsWidget.placeSpatialButton.setVisible(True)
self.fiducialsWidget.placeFiducialButton.setVisible(False)
self.fiducialsWidget.fiducialsList.setColumnHidden(2, True)
self.fiducialsWidget.fiducialsList.setColumnHidden(4, True)
#connect signals and slots
self.fiducialsWidget.placeSpatialButton.connect('clicked(bool)', self.onPlaceTrackerPositionButtonClicked)
self.updateWidgetFromParameters(self.parameterNode())
self.updateGeometry()
qt.QTimer.singleShot(0, self.killButton)
print("Fiducials Widget size Hint:")
self.fiducialsWidget.sizeHint
print("Fiducials Widget size :")
self.fiducialsWidget.size
print("Spatial fiducials step size Hint:")
print self.sizeHint
print("Spatial fiducials step size")
print self.size
def killButton(self):
# hide useless button
bl = slicer.util.findChildren(text='ReportROI')
if len(bl):
bl[0].hide()
def validate( self, desiredBranchId ):
'''
'''
self.__parent.validationSucceeded(desiredBranchId)
print("We are in the validate function of PlaceSpatialFiducialsStep")
def onEntry(self, comingFrom, transitionType):
super(PlaceSpatialFiducialsStep, self).onEntry(comingFrom, transitionType)
self.updateWidgetFromParameters(self.parameterNode())
pNode = self.parameterNode()
pNode.SetParameter('currentStep', self.stepid)
print("We are in the onEntry function of PlaceSpatialFiducialsStep coming from:" )
print comingFrom.name()
qt.QTimer.singleShot(0, self.killButton)
def onExit(self, goingTo, transitionType):
self.doStepProcessing()
super(PlaceSpatialFiducialsStep, self).onExit(goingTo, transitionType)
print("We are in the onExit function of PlaceSpatialFiducialsStep")
def updateWidgetFromParameters(self, parameterNode):
print("We are in the place fiducials step")
self.fiducialsList.updateSpatialFiducialsList()
#self.updateTrackerPointsList()
def doStepProcessing(self):
# calculate the transform to align the ROI in the next step with the
# baseline volume
pNode = self.parameterNode()
self.updateListNodesForRegistration()
# def onPlaceTrackerPositionButtonClicked(self):
# self.logic.recordTrackerPosition()
#
def onLoadSpatialPointsListClicked(self):
self.logic.addFiducialsToTrackerList()
def onPlaceTrackerPositionButtonClicked(self):
if self.fiducialsWidget.fiducialsList.rowCount ==0:
ret=qt.QMessageBox.warning(self.fiducialsWidget, 'Fiducials List', 'You must have image fiducials to match with tracker positions.', qt.QMessageBox.Ok , qt.QMessageBox.Ok )
return
currentRow = self.fiducialsWidget.fiducialsList.currentRow()
print("Current row is: " + str(currentRow))
if currentRow==-1:
ret=qt.QMessageBox.warning(self.fiducialsWidget, 'Fiducials List', 'You must select an image fiducials to match with the tracker position.', qt.QMessageBox.Ok , qt.QMessageBox.Ok )
return
fiducialListNode=slicer.util.getNode("Fiducials List")
# TODO uncomment this line and comment all the following TOD
fidHierarchyNode=fiducialListNode.GetNthChildNode(currentRow)
fidNode=fidHierarchyNode.GetAssociatedNode()
fidName = fidNode.GetName()
positionRecorded= self.logic.recordTrackerPosition()
path=slicer.modules.usguidedprocedure.path
modulePath=os.path.dirname(path)
if positionRecorded==True:
#get the most recent node (the last) in the Tracker Points List
trackerNode = self.logic.getFiducialNode('Tracker Points List', -1)
trackerNode.SetName(fidName + '-Tracker')
# Associate the fiducial and the tracker position
# We remove the previous (if exist) tracker node
# and we put the new tracker node ID in the table and check the row
previousTrackerID = self.fiducialsWidget.fiducialsList.item(currentRow, 4).text()
previousTrackerNode = slicer.mrmlScene.GetNodeByID(previousTrackerID)
if previousTrackerNode:
logic = slicer.modules.annotations.logic()
logic.RemoveAnnotationNode(previousTrackerNode)
self.fiducialsWidget.fiducialsList.item(currentRow, 3).setText(trackerNode.GetName())
self.fiducialsWidget.fiducialsList.item(currentRow, 4).setText(trackerNode.GetID())
self.fiducialsWidget.fiducialsList.item(currentRow, 0).setCheckState(2)
soundFile=os.path.join(modulePath,"sounds/notify.wav")
sound=qt.QSound(soundFile)
sound.play()
else:
soundFile=os.path.join(modulePath,"sounds/critico.wav")
#sound=qt.QSound("C:\Users\Usuario\devel\slicelets\USGuidedProcedure\sounds\critico.wav")
sound=qt.QSound(soundFile)
sound.play()
def updateTrackerPointsList(self):
#clear list
#self.fiducialsWidget.fiducialsList.clear()
#raise this flag to ignore change events in the table, the flag is lowered at the end of this method
self.updatingList = True
# get the nodes
fiducialListNode=slicer.util.getNode("Fiducials List")
trackerListNode=slicer.util.getNode("Tracker Points List")
# clear the list of tracker points
trackerListNode.RemoveChildrenNodes()
# create as many tracker nodes as fiducials
saml = slicer.modules.annotations.logic()
saml.SetActiveHierarchyNodeID(trackerListNode.GetID())
for childrenIndex in xrange(fiducialListNode.GetNumberOfChildrenNodes()):
fidHierarchyNode=fiducialListNode.GetNthChildNode(childrenIndex)
fidNode=fidHierarchyNode.GetAssociatedNode()
fidPos=[0,0,0]
dummy=fidNode.GetFiducialCoordinates(fidPos)
fidName = fidNode.GetName()
fidID = fidNode.GetID()
trackerNode=slicer.vtkMRMLAnnotationFiducialNode()
trackerNode.SetFiducialWorldCoordinates(fidPos)
trackerNode.SetName(fidName + '-Tracker')
slicer.mrmlScene.AddNode(trackerNode)
self.updatingList = False
def updateListNodesForRegistration(self):
#raise this flag to ignore change events in the table, the flag is lowered at the end of this method
self.updatingList = True
# get the nodes
fiducialListNode=slicer.util.getNode("Fiducials List")
trackerListNode=slicer.util.getNode("Tracker Points List")
fiducialListNodeForRegistration=slicer.util.getNode("Fiducials List (for registration)")
trackerListNodeForRegistration=slicer.util.getNode("Tracker Points List (for registration)")
# clear the lists (for registration)
fiducialListNodeForRegistration.RemoveChildrenNodes()
trackerListNodeForRegistration.RemoveChildrenNodes()
saml=slicer.modules.annotations.logic()
for row in range(self.fiducialsWidget.fiducialsList.rowCount):
fidID = self.fiducialsWidget.fiducialsList.item(row, 2).text()
trackerID = self.fiducialsWidget.fiducialsList.item(row, 4).text()
#print row
#print fidID
#print trackerID
fidNode = slicer.mrmlScene.GetNodeByID(fidID)
trackerNode = slicer.mrmlScene.GetNodeByID(trackerID)
#print fidNode
#print trackerNode
#if the row is selected to be used in the registration
if self.fiducialsWidget.fiducialsList.item(row, 0).checkState()==2:
#print 'Checked row'
fidPos=[0,0,0]
dummy=fidNode.GetFiducialCoordinates(fidPos)
fidName = fidNode.GetName()
trackerPos=[0,0,0]
dummy=trackerNode.GetFiducialCoordinates(trackerPos)
trackerName = trackerNode.GetName()
#create the new nodes copying the data
fidNodeForRegistration=slicer.vtkMRMLAnnotationFiducialNode()
fidNodeForRegistration.SetFiducialWorldCoordinates(fidPos)
fidNodeForRegistration.SetName(fidName)
trackerNodeForRegistration=slicer.vtkMRMLAnnotationFiducialNode()
trackerNodeForRegistration.SetFiducialWorldCoordinates(trackerPos)
trackerNodeForRegistration.SetName(trackerName)
# add the nodes to the lists for registration
saml.SetActiveHierarchyNodeID(fiducialListNodeForRegistration.GetID())
slicer.mrmlScene.AddNode(fidNodeForRegistration)
saml.SetActiveHierarchyNodeID(trackerListNodeForRegistration.GetID())
slicer.mrmlScene.AddNode(trackerNodeForRegistration)
class PlaceImageFiducialsStep( USGuidedStep ) :
def __init__( self, stepid ):
self.initialize( stepid )
self.setName( '1. PlaceImageFiducials' )
#self.setDescription( 'Place fiducials in the image' )
self.__parent = super( PlaceImageFiducialsStep, self )
def createUserInterface( self ):
'''
'''
# TODO: might make sense to hide the button for the last step at this
# point, but the widget does not have such option
self.__layout = self.__parent.createUserInterface()
# # BUTTONS --------------------------------------------------------------------
# This is commented out and the buttons are in the UI from the designer
#
# #layout for the buttons
# self.buttonsLayout = qt.QHBoxLayout()
# self.__layout.addLayout(self.buttonsLayout, 1)
#
# # Place fiducial
# placeFiducialButtom = qt.QPushButton("Place fiducial")
# placeFiducialButtom.toolTip = "Add a fiducial to the list"
# self.buttonsLayout.addWidget(placeFiducialButtom)
# placeFiducialButtom.connect('clicked(bool)', self.onPlaceFiducialButtomClicked)
#
# # Spacer
# self.buttonsLayout.addStretch()
self.fiducialsList = FiducialsList()
self.fiducialsList.setPlaceImageFiducialStep(True)
self.fiducialsList.setModuleLogic(self.logic)
self.__layout.addWidget(self.fiducialsList.getFiducialsWidget())
self.fiducialsWidget = self.fiducialsList.getFiducialsWidget()
#customize the UI
self.fiducialsWidget.placeSpatialButton.setVisible(False)
self.fiducialsWidget.placeFiducialButton.setVisible(True)
self.fiducialsWidget.fiducialsList.setColumnHidden(2, True)
self.fiducialsWidget.fiducialsList.setColumnHidden(3, True)
self.fiducialsWidget.fiducialsList.setColumnHidden(4, True)
qt.QTimer.singleShot(0, self.killButton)
print("Fiducials Widget size Hint:")
print self.fiducialsWidget.sizeHint
print("Fiducials Widget size :")
print self.fiducialsWidget.size
print("Image fiducials step size Hint:")
print self.sizeHint
print("Image fiducials step size")
print self.size
def killButton(self):
# hide useless button
bl = slicer.util.findChildren(text='ReportROI')
if len(bl):
bl[0].hide()
def validate( self, desiredBranchId ):
'''
'''
self.__parent.validationSucceeded(desiredBranchId)
print("We are in the validate function of PlaceImageFiducialsStep")
def onEntry(self, comingFrom, transitionType):
super(PlaceImageFiducialsStep, self).onEntry(comingFrom, transitionType)
self.logic.createRegistrationLists()
self.logic.createTargetList()
self.logic.createPlusCommandsList()
self.fiducialsList.listenToListModifications()
#self.logic.crosshairEnable()
self.updateWidgetFromParameters(self.parameterNode())
pNode = self.parameterNode()
pNode.SetParameter('currentStep', self.stepid)
print("We are in the onEntry function of PlaceImageFiducialsStep")
""" # For debugging
import sys
sys.path.append('C:/Users/Usuario/devel/eclipse/plugins/org.python.pydev_2.7.1.2012100913/pysrc')
import pydevd
pydevd.settrace()
"""
qt.QTimer.singleShot(0, self.killButton)
def onExit(self, goingTo, transitionType):
self.doStepProcessing()
super(PlaceImageFiducialsStep, self).onExit(goingTo, transitionType)
#crosshairNode=slicer.util.getNode("Crosshair")
#crosshairNode.SetCrosshairMode(1)
#self.logic.crosshairDisable()
self.fiducialsList.doNotListenToListModifications()
print("We are in the onExit function of PlaceImageFiducialsStep")
def updateWidgetFromParameters(self, parameterNode):
self.fiducialsList.updateFiducialsList()
print("We are in the place fiducials step")
def doStepProcessing(self):
# calculate the transform to align the ROI in the next step with the
# baseline volume
pNode = self.parameterNode()
class CaptureSpatialPositionsStep( USGuidedStep ) :
def __init__( self, stepid ):
self.initialize( stepid )
self.setName( '2. Capture spatial positions step' )
#self.setDescription( 'Place fiducials using the tracker' )
self.__parent = super( CaptureSpatialPositionsStep, self )
self.numberOfAcquiredSpatialPositions = 0
def createUserInterface( self ):
'''
'''
# TODO: might make sense to hide the button for the last step at this
# point, but the widget does not have such option
self.__layout = self.__parent.createUserInterface()
# # Place Tracker Position
# placeTrackerPositionButton = qt.QPushButton("Add tracker position")
# placeTrackerPositionButton.toolTip = "Add a tracker position to the list"
# self.__layout.addWidget(placeTrackerPositionButton)
# placeTrackerPositionButton.connect('clicked(bool)', self.onPlaceTrackerPositionButtonClicked)
#
# # Load a tracker list
# loadTrackerListButton = qt.QPushButton("Test spatial points lists creation")
# loadTrackerListButton.toolTip = "Load spatial points to test registration"
# self.__layout.addWidget(loadTrackerListButton)
# loadTrackerListButton.connect('clicked(bool)', self.onLoadSpatialPointsListClicked)
self.fiducialsList = FiducialsList()
self.fiducialsList.setModuleLogic(self.logic)
self.__layout.addWidget(self.fiducialsList.getFiducialsWidget())
self.fiducialsWidget = self.fiducialsList.getFiducialsWidget()
#customize the UI
self.fiducialsWidget.placeSpatialButton.setVisible(True)
self.fiducialsWidget.placeFiducialButton.setVisible(False)
self.fiducialsWidget.fiducialsList.setColumnHidden(2, True)
self.fiducialsWidget.fiducialsList.setColumnHidden(4, True)
#connect signals and slots
self.fiducialsWidget.placeSpatialButton.connect('clicked(bool)', self.onPlaceTrackerPositionButtonClicked)
self.updateWidgetFromParameters(self.parameterNode())
self.updateGeometry()
qt.QTimer.singleShot(0, self.killButton)
print("Fiducials Widget size Hint:")
self.fiducialsWidget.sizeHint
print("Fiducials Widget size :")
self.fiducialsWidget.size
print("Spatial fiducials step size Hint:")
print self.sizeHint
print("Spatial fiducials step size")
print self.size
def killButton(self):
# hide useless button
bl = slicer.util.findChildren(text='ReportROI')
if len(bl):
bl[0].hide()
def validate( self, desiredBranchId ):
'''
'''
self.__parent.validationSucceeded(desiredBranchId)
print("We are in the validate function of CaptureSpatialPositionsStepStep")
def onEntry(self, comingFrom, transitionType):
super(CaptureSpatialPositionsStep, self).onEntry(comingFrom, transitionType)
self.updateWidgetFromParameters(self.parameterNode())
pNode = self.parameterNode()
pNode.SetParameter('currentStep', self.stepid)
print("We are in the onEntry function of CaptureSpatialPositionsStepStep coming from:" )
print comingFrom.name()
qt.QTimer.singleShot(0, self.killButton)
def onExit(self, goingTo, transitionType):
self.doStepProcessing()
super(CaptureSpatialPositionsStep, self).onExit(goingTo, transitionType)
print("We are in the onExit function of CaptureSpatialPositionsStepStep")
def updateWidgetFromParameters(self, parameterNode):
print("We are in the place fiducials step")
self.fiducialsList.updateSpatialFiducialsList()
#self.updateTrackerPointsList()
def doStepProcessing(self):
# calculate the transform to align the ROI in the next step with the
# baseline volume
pNode = self.parameterNode()
# def onPlaceTrackerPositionButtonClicked(self):
# self.logic.recordTrackerPosition()
#
def onLoadSpatialPointsListClicked(self):
self.logic.addFiducialsToTrackerList()
def onPlaceTrackerPositionButtonClicked(self):
fiducialName = "F" + str(self.numberOfAcquiredSpatialPositions)
positionRecorded= self.logic.captureSpatialsPositions(fiducialName)
path=slicer.modules.stylusbasedusprobecalibration.path
modulePath=os.path.dirname(path)
if positionRecorded==True:
#get the most recent node (the last) in the Tracker Points List
#trackerNode = slicer.util.getNode(fiducialName+"-Tracker")
# trackerNode = self.logic.getFiducialNode('Tracker Points List', -1)
#
#
# # Associate the fiducial and the tracker position
# # We remove the previous (if exist) tracker node
# # and we put the new tracker node ID in the table and check the row
# currentItem = self.fiducialsWidget.fiducialsList.item(self.numberOfAcquiredSpatialPositions , 4)
# if currentItem is None:
# self.fiducialsList.addNewEmptyRow(self.numberOfAcquiredSpatialPositions)
#
# currentItem = self.fiducialsWidget.fiducialsList.item(self.numberOfAcquiredSpatialPositions , 4)
#
# self.fiducialsWidget.fiducialsList.item(self.numberOfAcquiredSpatialPositions , 3).setText(trackerNode.GetName())
# self.fiducialsWidget.fiducialsList.item(self.numberOfAcquiredSpatialPositions , 4).setText(trackerNode.GetID())
# self.fiducialsWidget.fiducialsList.item(self.numberOfAcquiredSpatialPositions , 0).setCheckState(2)
self.fiducialsList.updateFiducialsList("Tracker Points List")
soundFile=os.path.join(modulePath,"sounds/notify.wav")
sound=qt.QSound(soundFile)
sound.play()
self.numberOfAcquiredSpatialPositions += 1
else:
soundFile=os.path.join(modulePath,"sounds/critico.wav")
#sound=qt.QSound("C:\Users\Usuario\devel\slicelets\USGuidedProcedure\sounds\critico.wav")
sound=qt.QSound(soundFile)
sound.play()
def updateTrackerPointsList(self):
#clear list
#self.fiducialsWidget.fiducialsList.clear()
#raise this flag to ignore change events in the table, the flag is lowered at the end of this method
self.updatingList = True
# get the nodes
fiducialListNode=slicer.util.getNode("Fiducials List")
trackerListNode=slicer.util.getNode("Tracker Points List")
# clear the list of tracker points
trackerListNode.RemoveChildrenNodes()
# create as many tracker nodes as fiducials
saml = slicer.modules.annotations.logic()
saml.SetActiveHierarchyNodeID(trackerListNode.GetID())
for childrenIndex in xrange(fiducialListNode.GetNumberOfChildrenNodes()):
fidHierarchyNode=fiducialListNode.GetNthChildNode(childrenIndex)
fidNode=fidHierarchyNode.GetAssociatedNode()
fidPos=[0,0,0]
dummy=fidNode.GetFiducialCoordinates(fidPos)
fidName = fidNode.GetName()
fidID = fidNode.GetID()
trackerNode=slicer.vtkMRMLAnnotationFiducialNode()
trackerNode.SetFiducialWorldCoordinates(fidPos)
trackerNode.SetName(fidName + '-Tracker')
slicer.mrmlScene.AddNode(trackerNode)
self.updatingList = False
class PlaceStylusTipInTheImageStep( USGuidedStep ) :
def __init__( self, stepid ):
self.initialize( stepid )
self.setName( '3. PlaceStylusTipInTheImage' )
#self.setDescription( 'Place fiducials in the image' )
self.__parent = super( PlaceStylusTipInTheImageStep, self )
def createUserInterface( self ):
'''
'''
# TODO: might make sense to hide the button for the last step at this
# point, but the widget does not have such option
self.__layout = self.__parent.createUserInterface()
# # BUTTONS --------------------------------------------------------------------
# This is commented out and the buttons are in the UI from the designer
#
# #layout for the buttons
# self.buttonsLayout = qt.QHBoxLayout()
# self.__layout.addLayout(self.buttonsLayout, 1)
#
# # Place fiducial
# placeFiducialButtom = qt.QPushButton("Place fiducial")
# placeFiducialButtom.toolTip = "Add a fiducial to the list"
# self.buttonsLayout.addWidget(placeFiducialButtom)
# placeFiducialButtom.connect('clicked(bool)', self.onPlaceFiducialButtomClicked)
#
# # Spacer
# self.buttonsLayout.addStretch()
self.fiducialsList = FiducialsList()
self.fiducialsList.setModuleLogic(self.logic)
self.__layout.addWidget(self.fiducialsList.getFiducialsWidget())
self.fiducialsWidget = self.fiducialsList.getFiducialsWidget()
#customize the UI
self.fiducialsWidget.placeSpatialButton.setVisible(False)
self.fiducialsWidget.placeFiducialButton.setVisible(True)
self.fiducialsWidget.fiducialsList.setColumnHidden(2, True)
self.fiducialsWidget.fiducialsList.setColumnHidden(4, True)
qt.QTimer.singleShot(0, self.killButton)
print("Fiducials Widget size Hint:")
print self.fiducialsWidget.sizeHint
print("Fiducials Widget size :")
print self.fiducialsWidget.size
print("Image fiducials step size Hint:")
print self.sizeHint
print("Image fiducials step size")
print self.size
def killButton(self):
# hide useless button
bl = slicer.util.findChildren(text='ReportROI')
if len(bl):
bl[0].hide()
def validate( self, desiredBranchId ):
'''
'''
self.__parent.validationSucceeded(desiredBranchId)
print("We are in the validate function of PlaceStylusTipInTheImageStep")
def onEntry(self, comingFrom, transitionType):
super(PlaceStylusTipInTheImageStep, self).onEntry(comingFrom, transitionType)
self.fiducialsList.listenToListModifications()
#self.logic.crosshairEnable()
self.fiducialsList.setPlaceImageFiducialStep(True)
self.updateWidgetFromParameters(self.parameterNode())
pNode = self.parameterNode()
pNode.SetParameter('currentStep', self.stepid)
if self.fiducialsWidget.fiducialsList.rowCount > 0:
item = self.fiducialsWidget.fiducialsList.item(0, 0)
self.fiducialsWidget.fiducialsList.itemClicked(item)
print("We are in the onEntry function of PlaceStylusTipInTheImageStep")
qt.QTimer.singleShot(0, self.killButton)
def onExit(self, goingTo, transitionType):
self.doStepProcessing()
super(PlaceStylusTipInTheImageStep, self).onExit(goingTo, transitionType)
#crosshairNode=slicer.util.getNode("Crosshair")
#crosshairNode.SetCrosshairMode(1)
#self.logic.crosshairDisable()
self.fiducialsList.setPlaceImageFiducialStep(False)
self.fiducialsList.doNotListenToListModifications()
print("We are in the onExit function of PlaceStylusTipInTheImageStep")
def updateWidgetFromParameters(self, parameterNode):
self.fiducialsList.updateFiducialsList("Tracker Points List")
print("We are in the place fiducials step")
def doStepProcessing(self):
# calculate the transform to align the ROI in the next step with the
# baseline volume
pNode = self.parameterNode()
self.updateListNodesForRegistration()
def updateListNodesForRegistration(self):
#raise this flag to ignore change events in the table, the flag is lowered at the end of this method
self.updatingList = True
# get the nodes
fiducialListNode=slicer.util.getNode("Fiducials List")
trackerListNode=slicer.util.getNode("Tracker Points List")
fiducialListNodeForRegistration=slicer.util.getNode("Fiducials List (for registration)")
trackerListNodeForRegistration=slicer.util.getNode("Tracker Points List (for registration)")
# clear the lists (for registration)
fiducialListNodeForRegistration.RemoveChildrenNodes()
trackerListNodeForRegistration.RemoveChildrenNodes()
saml=slicer.modules.annotations.logic()
for row in range(self.fiducialsWidget.fiducialsList.rowCount):
fidID = self.fiducialsWidget.fiducialsList.item(row, 2).text()
trackerID = self.fiducialsWidget.fiducialsList.item(row, 4).text()
#print row
#print fidID
#print trackerID
fidNode = slicer.mrmlScene.GetNodeByID(fidID)
trackerNode = slicer.mrmlScene.GetNodeByID(trackerID)
#print fidNode
#print trackerNode
#if the row is selected to be used in the registration
if self.fiducialsWidget.fiducialsList.item(row, 0).checkState()==2:
#print 'Checked row'
fidPos=[0,0,0]
dummy=fidNode.GetFiducialCoordinates(fidPos)
fidName = fidNode.GetName()
trackerPos=[0,0,0]
dummy=trackerNode.GetFiducialCoordinates(trackerPos)
trackerName = trackerNode.GetName()
#create the new nodes copying the data
fidNodeForRegistration=slicer.vtkMRMLAnnotationFiducialNode()
fidNodeForRegistration.SetFiducialWorldCoordinates(fidPos)
fidNodeForRegistration.SetName(fidName)
trackerNodeForRegistration=slicer.vtkMRMLAnnotationFiducialNode()
trackerNodeForRegistration.SetFiducialWorldCoordinates(trackerPos)
trackerNodeForRegistration.SetName(trackerName)
# add the nodes to the lists for registration
saml.SetActiveHierarchyNodeID(fiducialListNodeForRegistration.GetID())
slicer.mrmlScene.AddNode(fidNodeForRegistration)
saml.SetActiveHierarchyNodeID(trackerListNodeForRegistration.GetID())
slicer.mrmlScene.AddNode(trackerNodeForRegistration)
self.logic.hideAllTheFiducialsNode("Fiducials List (for registration)")
self.logic.hideAllTheFiducialsNode("Tracker Points List (for registration)")
