def onPointCollectionButtonClicked(self):
"""Connected to 'create path' button. It allows to:
- compute the path
- create the associated model"""
listExitence = False
hierarchyNodes = slicer.util.getNodes('vtkMRMLAnnotationHierarchyNode*')
for hierarchyNode in hierarchyNodes.keys():
if hierarchyNode=='Template Fiducials':
listExitence = True
if listExitence == False:
templateFiducialAnnotationList = slicer.vtkMRMLAnnotationHierarchyNode()
templateFiducialAnnotationList.SetName('Template Fiducials')
templateFiducialAnnotationList.SetHideFromEditors(0)
templateFiducialAnnotationList.SetScene(self.scene)
self.scene.AddNode(templateFiducialAnnotationList)
self.templateFiducialAnnotationList = templateFiducialAnnotationList
self.logic.SetActiveHierarchyNodeID(self.templateFiducialAnnotationList.GetID())
if self.iterationNo < self.numberOfFiducialPoints:
self.templateFiducialList[self.iterationNo] = self.collect()
if self.iterationNo == self.numberOfFiducialPoints-1:
print "Point collection Finished Succesfullly, the Fiducial Coordinates are:"
print self.templateFiducialList
self.registrationCollapsibleButton.enabled = True
self.pointCollectionButton.enabled = False
self.pointResetButton.enabled = True
self.iterationNo += 1
def __init__(self, slicerVersion):
self.volume = slicer.vtkMRMLScalarVolumeNode()
self.display = slicer.vtkMRMLScalarVolumeDisplayNode()
if slicerVersion == 4:
self.fiducialList = slicer.vtkMRMLAnnotationHierarchyNode()
self.newFiducial = slicer.vtkMRMLAnnotationFiducialNode()
else:
self.fiducialList = slicer.vtkMRMLFiducialListNode()
self.newFiducial = slicer.vtkMRMLFiducial()
def _setFiducialLists(self, sceneFixedList=None, sceneMovingList=None):
self.fixed = sceneFixedList
self.moving = sceneMovingList
if self.fixed.GetClassName() == 'vtkMRMLAnnotationHierarchyNode':
# slicer4 style
self.fiducialStyle = 4
self.fixedCount = self.fixed.GetNumberOfChildren()
self.movingCount = self.moving.GetNumberOfChildren()
self.newFixed = slicer.vtkMRMLAnnotationHierarchyNode()
self.newMoving = slicer.vtkMRMLAnnotationHierarchyNode()
else:
# slicer3 style
self.fiducialStyle = 3
self.fixedCount = self.fixed.GetNumberOfFiducials()
self.movingCount = self.moving.GetNumberOfFiducials()
self.newFixed = slicer.vtkMRMLFiducialListNode()
self.newMoving = slicer.vtkMRMLFiducialListNode()
return self.run()
def _setFiducialLists(self, sceneFixedList=None, sceneMovingList=None):
self.fixed = sceneFixedList
self.moving = sceneMovingList
if self.fixed.GetClassName() == 'vtkMRMLAnnotationHierarchyNode':
# slicer4 style
self.fiducialStyle = 4
self.fixedCount = self.fixed.GetNumberOfChildren()
self.movingCount = self.moving.GetNumberOfChildren()
self.newFixed = slicer.vtkMRMLAnnotationHierarchyNode()
self.newMoving = slicer.vtkMRMLAnnotationHierarchyNode()
else:
# slicer3 style
self.fiducialStyle = 3
self.fixedCount = self.fixed.GetNumberOfFiducials()
self.movingCount = self.moving.GetNumberOfFiducials()
self.newFixed = slicer.vtkMRMLFiducialListNode()
self.newMoving = slicer.vtkMRMLFiducialListNode()
return self.run()
def __init__(self, slicerVersion):
self.volume = slicer.vtkMRMLScalarVolumeNode()
self.display = slicer.vtkMRMLScalarVolumeDisplayNode()
if slicerVersion == 4:
self.fiducialList = slicer.vtkMRMLAnnotationHierarchyNode()
self.newFiducial = slicer.vtkMRMLAnnotationFiducialNode()
else:
self.fiducialList = slicer.vtkMRMLFiducialListNode()
self.newFiducial = slicer.vtkMRMLFiducial()
def create_fiducials_list(seedList):
saml = slicer.modules.annotations.logic()
saml.SetActiveHierarchyNodeID(saml.GetTopLevelHierarchyNodeID())
saml.AddHierarchy()
currentList = saml.GetActiveHierarchyNode()
for seed in seedList:
seedFN = slicer.vtkMRMLAnnotationFiducialNode()
seedFN.SetFiducialWorldCoordinates(seed)
seedFN.Initialize(slicer.mrmlScene)
seedHN = slicer.vtkMRMLAnnotationHierarchyNode()
seedHN.SetParentNodeID(currentList.GetID())
seedHN.SetAssociatedNodeID(seedFN.GetID())
return currentList
def addFiducial(self,name,position=(0,0,0),associatedNode=None):
"""Add an instance of a fiducial to the scene for a given
volume node"""
annoLogic = slicer.modules.annotations.logic()
originalActiveHierarchy = annoLogic.GetActiveHierarchyNodeID()
slicer.mrmlScene.StartState(slicer.mrmlScene.BatchProcessState)
# make the fiducial list if required
listName = associatedNode.GetName() + "-landmarks"
fidListHierarchyNode = slicer.util.getNode(listName)
if not fidListHierarchyNode:
fidListHierarchyNode = slicer.vtkMRMLAnnotationHierarchyNode()
fidListHierarchyNode.HideFromEditorsOff()
fidListHierarchyNode.SetName(listName)
slicer.mrmlScene.AddNode(fidListHierarchyNode)
# make it a child of the top level node
fidListHierarchyNode.SetParentNodeID(annoLogic.GetTopLevelHierarchyNodeID())
# make this active so that the fids will be added to it
annoLogic.SetActiveHierarchyNodeID(fidListHierarchyNode.GetID())
fiducialNode = slicer.vtkMRMLAnnotationFiducialNode()
if associatedNode:
fiducialNode.SetAttribute("AssociatedNodeID", associatedNode.GetID())
fiducialNode.SetName(name)
fiducialNode.AddControlPoint(position, True, True)
fiducialNode.SetSelected(False)
fiducialNode.SetLocked(False)
slicer.mrmlScene.AddNode(fiducialNode)
fiducialNode.CreateAnnotationTextDisplayNode()
fiducialNode.CreateAnnotationPointDisplayNode()
# TODO: pick appropriate defaults
# 135,135,84
fiducialNode.SetTextScale(3.)
fiducialNode.GetAnnotationPointDisplayNode().SetGlyphScale(3.)
fiducialNode.GetAnnotationPointDisplayNode().SetGlyphTypeFromString('StarBurst2D')
fiducialNode.GetAnnotationPointDisplayNode().SetColor((1,1,0))
fiducialNode.GetAnnotationTextDisplayNode().SetColor((1,1,0))
fiducialNode.SetDisplayVisibility(True)
annoLogic.SetActiveHierarchyNodeID(originalActiveHierarchy)
slicer.mrmlScene.EndState(slicer.mrmlScene.BatchProcessState)
def onRegistrationButtonClicked(self):
print "Hello Registration :) "
self.referenceAttachmentCollapsibleButton.enabled = True
linearTransformExistence = False
linearTransformNodes = slicer.util.getNodes('vtkMRMLlinearTransformNode*')
for linearTransformNode in linearTransformNodes.keys():
if linearTransformNode=='ModelToTemplateTransform':
linearTransformExistence = True
if linearTransformExistence == False:
followupTransform = slicer.vtkMRMLLinearTransformNode()
followupTransform.SetName('ModelToTemplateTransform')
followupTransform.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(followupTransform)
self.followupTransform = followupTransform
self.fiducialListNode = slicer.util.getNode('Template Fiducials')
movingLandmarksListID = self.fiducialListNode.GetID()
modelFiducials = self.modelFiducialSelector.currentNode()
# extracting the effects of transform parameters
transformNode1 = self.templateSelector.currentNode().GetParentTransformNode()
#print transformNode1
shiftTransform1 = [0 , 0, 0]
rotationTransform1 = [[1, 0,0],[0,1,0],[0,0,1]]
#shiftTransform2 = [0, 0, 0]
#rotationTransform2 = [1, 0,0],[0,1,0],[0,0,1]]
if transformNode1 != None:
m = vtk.vtkMatrix4x4()
transformNode1.GetMatrixTransformToWorld(m)
shiftTransform1 = [ m.GetElement(0,3), m.GetElement(1,3), m.GetElement(2,3) ]
rotationTransform1 = [[m.GetElement(0,0), m.GetElement(0,1),m.GetElement(0,2)],[m.GetElement(1,0), m.GetElement(1,1),m.GetElement(1,2)],[m.GetElement(2,0), m.GetElement(2,1),m.GetElement(2,2)]]
#transformNode2 = transformNode1.GetParentTransformNode()
#if transformNode2 != None:
#transformNode2.GetMatrixTransformToWorld(m)
#shiftTransform2 = [ m.GetElement(0,3), m.GetElement(1,3), m.GetElement(2,3) ]
#rotationTransform2 = [[m.GetElement(0,0), m.GetElement(0,1),m.GetElement(0,2)],[m.GetElement(1,0), m.GetElement(1,1),m.GetElement(1,2)],[m.GetElement(2,0), m.GetElement(2,1),m.GetElement(2,2)]
#shiftTransform = numpy.add(shiftTransform1,shiftTransform2)
# Changing the fiducial coordinates according to the transform
if modelFiducials.GetClassName() == "vtkMRMLAnnotationHierarchyNode":
# slicer4 style hierarchy nodes
collection = vtk.vtkCollection()
modelFiducials.GetChildrenDisplayableNodes(collection)
n = collection.GetNumberOfItems()
if n != 6:
return
# output an error and ask user to select a fiducial with 6 points
listExitence = False
hierarchyNodes = slicer.util.getNodes('vtkMRMLAnnotationHierarchyNode*')
for hierarchyNode in hierarchyNodes.keys():
if hierarchyNode=='New Model Fiducials':
listExitence = True
self.newModelFiducialAnnotationList.RemoveAllChildrenNodes()
if listExitence == False:
newModelFiducialAnnotationList = slicer.vtkMRMLAnnotationHierarchyNode()
newModelFiducialAnnotationList.SetName('New Model Fiducials')
# hide the fiducial list from the scene
newModelFiducialAnnotationList.SetHideFromEditors(1)
newModelFiducialAnnotationList.SetScene(self.scene)
self.scene.AddNode(newModelFiducialAnnotationList)
self.newModelFiducialAnnotationList = newModelFiducialAnnotationList
self.logic.SetActiveHierarchyNodeID(self.newModelFiducialAnnotationList.GetID())
#self.logic.AddHierarchy
#a=self.logic.GetActiveHierarchyNode()
#a.SetName('New Model Fiducials')
p = numpy.zeros((n,3))
for i in xrange(n):
f = collection.GetItemAsObject(i)
coords = [0,0,0]
# Need to change to consider the transform that is applied to the points
f.GetFiducialCoordinates(coords)
newCoords = numpy.add(numpy.dot(rotationTransform1,coords),shiftTransform1)
newfid = slicer.vtkMRMLAnnotationFiducialNode()
newfid.SetFiducialCoordinates(newCoords)
newfid.SetHideFromEditors(0)
newfid.SetName(str(i))
self.scene.AddNode(newfid)
fixedLandmarksListID = self.newModelFiducialAnnotationList.GetID()
self.OutputMessage = ""
parameters = {}
parameters["fixedLandmarks"] = fixedLandmarksListID
parameters["movingLandmarks"] = movingLandmarksListID
parameters["saveTransform"] = self.followupTransform
parameters["transformType"] = "Rigid"
parameters["rms"] = self.RMS
parameters["outputMessage"] = self.OutputMessage
fidreg = slicer.modules.fiducialregistration
self.__cliNode = None
self.__cliNode = slicer.cli.run(fidreg, self.__cliNode, parameters)
print "RMS is", self.RMS
#self.__cliObserverTag = self.__cliNode.AddObserver('ModifiedEvent', self.processRegistrationCompletion)
#self.__registrationStatus.setText('Wait ...')
#self.firstRegButton.setEnabled(0)
stylusNode = self.stylusTrackerSelector.currentNode()
stylusNode.SetAndObserveTransformNodeID(self.followupTransform.GetID())
