def onCalibrate2Button(self):
self.inverseTransform = slicer.vtkMRMLLinearTransformNode()
self.inverseTransform.SetName("InverseTransform")
orientationTransform = self.IMUTransformNode
self.inverseTransform.SetMatrixTransformFromParent(orientationTransform.GetMatrixTransformFromParent())
self.inverseTransform.Inverse()
slicer.mrmlScene.AddNode(self.inverseTransform)
self.translateTransform = slicer.vtkMRMLLinearTransformNode()
self.translateTransform.SetName("TranslateTransform")
matrix = self.translateTransform.GetMatrixTransformFromParent()
matrix.SetElement(1,3,-80)
self.translateTransform.SetMatrixTransformToParent(matrix)
slicer.mrmlScene.AddNode(self.translateTransform)
self.probeTransform = slicer.vtkMRMLLinearTransformNode()
self.probeTransform.SetName("ProbeTransform")
matrix.SetElement(1,3,-60)
self.probeTransform.SetMatrixTransformToParent(matrix)
slicer.mrmlScene.AddNode(self.probeTransform)
slicer.util.loadVolume("H:/src/S4Mods/UltrasoundSimulator/Data/Linear_probe.mha")
self.maskVolumeNode = slicer.util.getNode("Linear_probe")
self.maskVolumeNode.SetAndObserveTransformNodeID(self.probeTransform.GetID())
slicer.util.loadVolume("H:/Data/CT/CT_abdominal_phantom.mha")
self.volumeCurrentlyLoaded = slicer.util.getNode("CT_abdominal_phantom")
self.volumeCurrentlyLoaded.SetAndObserveTransformNodeID(self.translateTransform.GetID())
self.IMUTransformNode.SetAndObserveTransformNodeID(self.inverseTransform.GetID())
self.translateTransform.SetAndObserveTransformNodeID(self.IMUTransformNode.GetID())
self.volumeCurrentlyLoaded.GetScalarVolumeDisplayNode().SetAutoWindowLevel(False)
self.volumeCurrentlyLoaded.GetScalarVolumeDisplayNode().SetWindowLevel(350, 40)
#xyzOrigSampleVol = self.volumeCurrentlyLoaded.GetOrigin()
#self.volumeCurrentlyLoaded.SetOrigin(xyzOrigSampleVol[0], xyzOrigSampleVol[1] - xyzOrigSampleVol[1] / 2, xyzOrigSampleVol[2])
self.redSliceNode.SetSliceOrigin(0, -80, 0)
self.redSliceNode.SetFieldOfView(180, 180,0)
self.lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUpRedSliceView)
self.redSliceCompositeNode.SetForegroundVolumeID(self.volumeCurrentlyLoaded.GetID())
#self.redSliceFGLayer.SetVolumeNode(self.volumeCurrentlyLoaded)
self.redSliceCompositeNode.SetForegroundOpacity(1.0)
self.applicationLogic.PropagateForegroundVolumeSelection() # Not working
self.redSliceCompositeNode.SetBackgroundVolumeID(self.maskVolumeNode.GetID())
#self.redSliceBGLayer.SetVolumeNode(self.maskVolumeNode)
self.applicationLogic.PropagateBackgroundVolumeSelection() # Not working
maskVolumeDisplayNode = self.maskVolumeNode.GetVolumeDisplayNode()
maskVolumeDisplayNode.SetLowerThreshold(10)
maskVolumeDisplayNode.ApplyThresholdOn ()
'''
def connectWithTracker(self):
self.connectorNode.SetTypeClient("localhost",18944)
print("Status before start(): " + str(self.connectorNode.GetState()))
self.startTracking()
print("Connected with Plus Server in Slicelet Class ")
print("Status after start(): " + str(self.connectorNode.GetState()))
## The nodes StylusTipToReference and ProbeToReference are added
stylusTipToReference=slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(stylusTipToReference)
stylusTipToReference.SetName("StylusTipToReference")
probeToReference=slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(probeToReference)
probeToReference.SetName("ProbeToReference")
def cameraTransform(self):
"""Create the transform and the observer for the camera
"""
transformName = 'Camera-To-RAS'
transformNode = slicer.util.getNode(transformName)
if not transformNode:
# Create transform node
transformNode = slicer.vtkMRMLLinearTransformNode()
transformNode.SetName(transformName)
slicer.mrmlScene.AddNode(transformNode)
camera = self.cameraNode().GetCamera()
import numpy
position = numpy.array(camera.GetPosition())
focalPoint = numpy.array(camera.GetFocalPoint())
viewUp = numpy.array(camera.GetViewUp())
viewPlaneNormal = numpy.array(camera.GetViewPlaneNormal())
viewAngle = camera.GetViewAngle()
viewRight = numpy.cross(viewUp,viewPlaneNormal)
viewDistance = numpy.linalg.norm(focalPoint - position)
cameraToRAS = vtk.vtkMatrix4x4()
for row in xrange(3):
cameraToRAS.SetElement(row, 0, viewRight[row])
cameraToRAS.SetElement(row, 1, viewUp[row])
cameraToRAS.SetElement(row, 2, viewPlaneNormal[row])
cameraToRAS.SetElement(row, 3, position[row])
transformNode.GetMatrixTransformToParent().DeepCopy(cameraToRAS)
return transformNode,viewDistance
def putInfo(self, caller, event): # caller: vtkMRMLIGTLConnectorNode
self.times1 = self.times1+1
#print "********************"
#print ("into caller", self.times1)
if caller.IsA('vtkMRMLIGTLConnectorNode'):
nInNode = caller.GetNumberOfIncomingMRMLNodes()
for i in range(nInNode): # start from 0
node = caller.GetIncomingMRMLNode(i)
if node.IsA("vtkMRMLLinearTransformNode"): # lineartransform node
if node.GetName() == "CURRENT": # node name the same robot controller part
if self.receiveCurrentNode == None:
self.receiveCurrentNode = slicer.vtkMRMLLinearTransformNode()
self.receiveCurrentNode.SetName("receiveCurrent")
slicer.mrmlScene.AddNode(self.receiveCurrentNode)
else:
mat4x4 = self.receiveCurrentNode.GetMatrixTransformToParent()
self.matR = mat4x4.GetElement(0, 3)
self.matA = mat4x4.GetElement(1, 3)
self.matS = mat4x4.GetElement(2, 3)
strCurrent = "(%.3f, %.3f, %.3f)" %(self.matR, self.matA, self.matS)
self.lineEditCurrent.setText(strCurrent)
self.connectNode.UnregisterIncomingMRMLNode(node)
elif node.IsA("vtkMRMLTextNode"): # text node
if node.GetName() == "feedStatus":
self.lineEditStatus.setText(node.GetText())
self.lineEditStatus.setStyleSheet("background-color: green")
self.connectNode.UnregisterIncomingMRMLNode(node)
elif node.GetName() == "feedInfoRegistTime":
self.lineEditRegistTime.setText(node.GetText())
qt.QMessageBox.information(
slicer.util.mainWindow(),
"Slicer Python", "Registration Accepted!")
self.connectNode.UnregisterIncomingMRMLNode(node)
self.buttonSendTarget.setEnabled(True)
elif node.GetName() == "feedTarget":
print node.GetText()
qt.QMessageBox.information(
slicer.util.mainWindow(),
"Slicer Python", "Target Accepted!")
self.connectNode.UnregisterIncomingMRMLNode(node)
self.buttonCurrent.setEnabled(True)
elif node.GetName() == "feedTargetCell":
print node.GetText()
qt.QMessageBox.information(
slicer.util.mainWindow(),
"Slicer Python", "Cell Accepted!")
self.connectNode.UnregisterIncomingMRMLNode(node)
else: # else to node.IsA
print "no feedBack!!!!!"
def onSendButtonClicked(self):
"""Send the data to the Extral Devices which support the OpenIGTLink protocal"""
# Get the number of the 'vtkMRMLIGTLConnectorNode'
n = slicer.mrmlScene.GetNumberOfNodesByClass('vtkMRMLIGTLConnectorNode')
# Set the 'vtkMRMLIGTLConnectorNode' node
if n > 0:
for i in range(n):
if slicer.mrmlScene.GetNthNodeByClass(i, 'vtkMRMLIGTLConnectorNode').GetName() == 'Send-Data':
connectorNode = slicer.mrmlScene.GetNthNodeByClass(i, 'vtkMRMLIGTLConnectorNode')
else:
connectorNode = slicer.vtkMRMLIGTLConnectorNode()
slicer.mrmlScene.AddNode(connectorNode)
connectorNode.SetName('Send-Data')
else:
connectorNode = slicer.vtkMRMLIGTLConnectorNode()
slicer.mrmlScene.AddNode(connectorNode)
connectorNode.SetName('Send-Data')
hostname = self.hostnameLineEdit.text
port = int(self.portLineEdit.text)
connectorNode.SetTypeClient(hostname, port)
checker = connectorNode.Start()
#Get the number of the 'vtkMRMLLinearTransformNode'
n = slicer.mrmlScene.GetNumberOfNodesByClass('vtkMRMLLinearTransformNode')
#Set the 'vtkMRMLLinearTransformNode' node
nodes = []
for i in range(n):
nodes.append(slicer.mrmlScene.GetNthNodeByClass(i, 'vtkMRMLLinearTransformNode'))
for i in range(n):
if nodes[i].GetName() == 'Result-Data':
slicer.mrmlScene.RemoveNode(nodes[i])
transformNode = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(transformNode)
transformNode.SetName('Result-Data')
connectorNode.RegisterOutgoingMRMLNode(transformNode)
matrix = transformNode.GetMatrixTransformToParent()
theta = self.result.angleRed
omega = self.result.angleGreen
phi = self.result.angleBlue
e1 = numpy.cos(phi)*numpy.cos(omega)
e2 = numpy.sin(phi)*numpy.cos(theta) + numpy.cos(phi)*numpy.sin(omega)*numpy.sin(theta)
e3 = numpy.sin(phi)*numpy.sin(theta) - numpy.cos(phi)*numpy.sin(omega)*numpy.cos(theta)
e4 = self.result.distance
e5 = numpy.sin(phi)*numpy.cos(omega)*(-1)
e6 = numpy.cos(phi)*numpy.cos(theta) - numpy.sin(phi)*numpy.sin(omega)*numpy.sin(theta)
e7 = numpy.cos(phi)*numpy.sin(theta) + numpy.sin(phi)*numpy.sin(omega)*numpy.cos(theta)
e8 = 0
e9 = numpy.sin(omega)
e10 = numpy.cos(omega)*numpy.sin(theta)*(-1)
e11 = numpy.cos(omega)*numpy.cos(theta)
e12 = 0
time.sleep(1)
matrix.DeepCopy((e1,e2,e3,e4,e5,e6,e7,e8,e9,e10,e11,e12,0,0,0,1))
time.sleep(1)
connectorNode.Stop()
def registerVolumes(self, fixedVolumeName, fixedTransformName, movingVolumeName, movingTransformName, registrationTransformName):
# self.Registered = False
# get the nodes
fixedTransformNode = slicer.util.getNode(fixedTransformName)
movingTransformNode = slicer.util.getNode(movingTransformName)
fixedVolumeNode = slicer.util.getNode(fixedVolumeName)
movingVolumeNode = slicer.util.getNode(movingVolumeName)
# check volumes
if not fixedVolumeNode or not movingVolumeNode:
print('Registration failed: the volume nodes are not set correctly')
return False
# setup the brainsfit CLI module
parameters = {}
parameters["fixedVolume"] = fixedVolumeNode.GetID()
parameters["movingVolume"] = movingVolumeNode.GetID()
parameters["useRigid"] = True
transformNode = slicer.util.getNode(registrationTransformName);
if not transformNode == None:
slicer.mrmlScene.RemoveNode(transformNode)
registrationTransformNode = slicer.vtkMRMLLinearTransformNode()
registrationTransformNode.SetName(registrationTransformName)
slicer.mrmlScene.AddNode(registrationTransformNode)
parameters["linearTransform"] = registrationTransformNode.GetID()
parameters["initializeTransformMode"] = "useCenterOfHeadAlign"
outputVolumeName = movingVolumeNode.GetName() + "_" + fixedVolumeNode.GetName();
outputVolumeNode = slicer.util.getNode(outputVolumeName)
if outputVolumeNode is None:
outputVolumeNode = slicer.vtkMRMLScalarVolumeNode()
slicer.mrmlScene.AddNode(outputVolumeNode)
outputVolumeNode.SetName(outputVolumeName)
parameters["outputVolume"] = outputVolumeNode.GetID()
brainsfit = slicer.modules.brainsfit
# run the registration
cliBrainsFitRigidNode = slicer.cli.run(brainsfit, None, parameters)
# cliBrainsFitRigidNode = slicer.cli.run(brainsfit, None, parameters, True) # El ultimo true es para que espere hasta la finalizacion
waitCount = 0
while cliBrainsFitRigidNode.GetStatusString() != 'Completed' and waitCount < self.REGISTRATION_TIMEOUT:
self.delayDisplay("Register " + movingVolumeNode.GetName() + " to " + fixedVolumeNode.GetName() + "... %d" % waitCount)
waitCount += 1
self.delayDisplay("Register " + movingVolumeNode.GetName() + "to " + fixedVolumeNode.GetName() + " finished")
qt.QApplication.restoreOverrideCursor()
if not cliBrainsFitRigidNode:
slicer.mrmlScene.RemoveNode(registrationTransformNode.GetID())
print('Registration failed: Brainsfit module failed')
else:
# attach the transform to the moving volume
movingVolumeNode.SetAndObserveTransformNodeID(registrationTransformNode.GetID())
pass
return cliBrainsFitRigidNode
def testingData(self):
"""Load some default data for development
and set up a transform and viewing scenario for it.
"""
if not slicer.util.getNodes('MRHead*'):
import os
fileName = "C:/Work/data/MR-head.nrrd"
vl = slicer.modules.volumes.logic()
volumeNode = vl.AddArchetypeScalarVolume (fileName, "MRHead", 0)
if not slicer.util.getNodes('neutral*'):
import os
fileName = "C:/Work/data/neutral.nrrd"
vl = slicer.modules.volumes.logic()
volumeNode = vl.AddArchetypeScalarVolume (fileName, "neutral", 0)
if not slicer.util.getNodes('movingToFixed'):
# Create transform node
transform = slicer.vtkMRMLLinearTransformNode()
transform.SetName('movingToFixed')
slicer.mrmlScene.AddNode(transform)
head = slicer.util.getNode('MRHead')
self.neutral = slicer.util.getNode('neutral')
self.transformNode = slicer.util.getNode('movingToFixed')
self.neutral.SetAndObserveTransformNodeID(self.transformNode.GetID())
compositeNodes = slicer.util.getNodes('vtkMRMLSliceCompositeNode*')
for compositeNode in compositeNodes.values():
compositeNode.SetBackgroundVolumeID(head.GetID())
compositeNode.SetForegroundVolumeID(self.neutral.GetID())
compositeNode.SetForegroundOpacity(0.5)
applicationLogic = slicer.app.applicationLogic()
applicationLogic.FitSliceToAll()
def createMovingLRSToFixedLRS(self, movingLRS = None):
if movingLRS.GetNumberOfFiducials() < 3:
logging.warning('Moving LRS fiducials list needs to contain at least three fiducials!')
return False
fixedLRS = slicer.util.getNode('FixedLRS')
if not fixedLRS:
# Create FixedLRS markups node
fixedLRS = slicer.vtkMRMLMarkupsFiducialNode()
fixedLRS.SetName('FixedLRS')
fixedLRS.AddFiducial(-100.0, 0.0, 0.0)
fixedLRS.SetNthFiducialLabel(0, 'FixedL')
fixedLRS.AddFiducial(100.0, 0.0, 0.0)
fixedLRS.SetNthFiducialLabel(1, 'FixedR')
fixedLRS.AddFiducial(0.0, 0.0, 100.0)
fixedLRS.SetNthFiducialLabel(2, 'FixedS')
slicer.mrmlScene.AddNode(fixedLRS)
fixedLRS.SetDisplayVisibility(False)
movingLRSToFixedLRS = slicer.util.getNode('MovingLRSToFixedLRS')
if not movingLRSToFixedLRS:
# Create MovingLRSToFixedLRS transform node
movingLRSToFixedLRS = slicer.vtkMRMLLinearTransformNode()
movingLRSToFixedLRS.SetName('MovingLRSToFixedLRS')
slicer.mrmlScene.AddNode(movingLRSToFixedLRS)
self.fiducialRegistration(movingLRSToFixedLRS, fixedLRS, movingLRS, "Rigid")
return True
def babyVolume(self,filePath=None,name='baby'):
"""Make a volume node as the target for the babys"""
babyVolume = slicer.util.getNode(name)
# create the volume for displaying the baby
if not babyVolume:
volumeLogic = slicer.modules.volumes.logic()
babyVolume = volumeLogic.AddArchetypeScalarVolume (filePath, "baby", 0, None)
displayNode = babyVolume.GetDisplayNode()
displayNode.SetAutoWindowLevel(False)
displayNode.SetWindow(470)
displayNode.SetLevel(250)
# automatically select the volume to display
mrmlLogic = slicer.app.applicationLogic()
selNode = mrmlLogic.GetSelectionNode()
selNode.SetReferenceActiveVolumeID(babyVolume.GetID())
mrmlLogic.PropagateVolumeSelection()
# Create transform node
transform = slicer.vtkMRMLLinearTransformNode()
transform.SetName('Baby to Template' )
slicer.mrmlScene.AddNode(transform)
babyVolume.SetAndObserveTransformNodeID(transform.GetID())
return babyVolume
def setupMRMLTracking(self):
if not hasattr(self, "trackingDevice"):
""" set up the mrml parts or use existing """
nodes = slicer.mrmlScene.GetNodesByName('trackingDevice')
if nodes.GetNumberOfItems() > 0:
self.trackingDevice = nodes.GetItemAsObject(0)
nodes = slicer.mrmlScene.GetNodesByName('tracker')
self.tracker = nodes.GetItemAsObject(0)
else:
# trackingDevice cursor
self.cube = vtk.vtkCubeSource()
self.cube.SetXLength(30)
self.cube.SetYLength(70)
self.cube.SetZLength(5)
self.cube.Update()
# display node
self.modelDisplay = slicer.vtkMRMLModelDisplayNode()
self.modelDisplay.SetColor(1,1,0) # yellow
slicer.mrmlScene.AddNode(self.modelDisplay)
# self.modelDisplay.SetPolyData(self.cube.GetOutputPort())
# Create model node
self.trackingDevice = slicer.vtkMRMLModelNode()
self.trackingDevice.SetScene(slicer.mrmlScene)
self.trackingDevice.SetName("trackingDevice")
self.trackingDevice.SetAndObservePolyData(self.cube.GetOutputDataObject(0))
self.trackingDevice.SetAndObserveDisplayNodeID(self.modelDisplay.GetID())
slicer.mrmlScene.AddNode(self.trackingDevice)
# tracker
self.tracker = slicer.vtkMRMLLinearTransformNode()
self.tracker.SetName('tracker')
slicer.mrmlScene.AddNode(self.tracker)
self.trackingDevice.SetAndObserveTransformNodeID(self.tracker.GetID())
def ROIPrep(self):
""" vtk, the image analysis library, and Slicer use different coordinate
systems: IJK and RAS, respectively. This prep calculates a simple matrix
transformation on a ROI transform node to be used in the next step.
"""
pNode = self.parameterNode()
subtractVolume = Helper.getNodeByID(pNode.GetParameter('subtractVolumeID'))
roiTransformID = pNode.GetParameter('roiTransformID')
roiTransformNode = None
if roiTransformID != '':
roiTransformNode = Helper.getNodeByID(roiTransformID)
else:
roiTransformNode = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(roiTransformNode)
pNode.SetParameter('roiTransformID', roiTransformNode.GetID())
# TO-DO: Understand the precise math behind this section of code..
dm = vtk.vtkMatrix4x4()
subtractVolume.GetIJKToRASDirectionMatrix(dm)
dm.SetElement(0,3,0)
dm.SetElement(1,3,0)
dm.SetElement(2,3,0)
dm.SetElement(0,0,abs(dm.GetElement(0,0)))
dm.SetElement(1,1,abs(dm.GetElement(1,1)))
dm.SetElement(2,2,abs(dm.GetElement(2,2)))
roiTransformNode.SetAndObserveMatrixTransformToParent(dm)
def setupScene(self):
logging.info("UltraSound.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().
'''
if self.referenceToRas is None or (self.referenceToRas and slicer.mrmlScene.GetNodeByID(self.referenceToRas.GetID()) is None):
self.referenceToRas = slicer.mrmlScene.GetFirstNodeByName('ReferenceToRas')
if self.referenceToRas is None:
self.referenceToRas = slicer.vtkMRMLLinearTransformNode()
self.referenceToRas.SetName("ReferenceToRas")
m = self.guideletParent.logic.readTransformFromSettings('ReferenceToRas', self.guideletParent.configurationName)
if m is None:
m = self.guideletParent.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)
# live ultrasound
liveUltrasoundNodeName = self.guideletParent.parameterNode.GetParameter('LiveUltrasoundNodeName')
self.liveUltrasoundNode_Reference = slicer.mrmlScene.GetFirstNodeByName(liveUltrasoundNodeName)
if not self.liveUltrasoundNode_Reference:
imageSpacing=[0.2, 0.2, 0.2]
# Create an empty image volume
imageData=vtk.vtkImageData()
imageData.SetDimensions(self.DEFAULT_IMAGE_SIZE)
imageData.AllocateScalars(vtk.VTK_UNSIGNED_CHAR, 1)
thresholder=vtk.vtkImageThreshold()
thresholder.SetInputData(imageData)
thresholder.SetInValue(0)
thresholder.SetOutValue(0)
# Create volume node
self.liveUltrasoundNode_Reference=slicer.vtkMRMLScalarVolumeNode()
self.liveUltrasoundNode_Reference.SetName(liveUltrasoundNodeName)
self.liveUltrasoundNode_Reference.SetSpacing(imageSpacing)
self.liveUltrasoundNode_Reference.SetImageDataConnection(thresholder.GetOutputPort())
# Add volume to scene
slicer.mrmlScene.AddNode(self.liveUltrasoundNode_Reference)
displayNode=slicer.vtkMRMLScalarVolumeDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
colorNode = slicer.mrmlScene.GetFirstNodeByName('Grey')
displayNode.SetAndObserveColorNodeID(colorNode.GetID())
self.liveUltrasoundNode_Reference.SetAndObserveDisplayNodeID(displayNode.GetID())
self.plusRemoteNode = slicer.mrmlScene.GetFirstNodeByClass('vtkMRMLPlusRemoteNode')
if self.plusRemoteNode is None:
self.plusRemoteNode = slicer.vtkMRMLPlusRemoteNode()
self.plusRemoteNode.SetName("PlusRemoteNode")
slicer.mrmlScene.AddNode(self.plusRemoteNode)
self.plusRemoteNode.AddObserver(slicer.vtkMRMLPlusRemoteNode.RecordingStartedEvent, self.recordingCommandCompleted)
self.plusRemoteNode.AddObserver(slicer.vtkMRMLPlusRemoteNode.RecordingCompletedEvent, self.recordingCommandCompleted)
self.plusRemoteNode.SetAndObserveOpenIGTLinkConnectorNode(self.guideletParent.connectorNode)
self.setupResliceDriver()
def __init__(self, targetFiducialListNode, radius):
target = targetFiducialListNode
scene = slicer.mrmlScene
sphere = vtk.vtkSphereSource()
sphere.SetRadius(radius)
sphere.SetThetaResolution(20)
sphere.SetPhiResolution(20)
sphere.Update()
# Create model node
insertionRadiusModel = slicer.vtkMRMLModelNode()
insertionRadiusModel.SetScene(scene)
insertionRadiusModel.SetName("InsertionSphere-%s" % target.GetName())
insertionRadiusModel.SetAndObservePolyData(sphere.GetOutput())
# Create display node
insertionRadiusModelDisplay = slicer.vtkMRMLModelDisplayNode()
insertionRadiusModelDisplay.SetColor(0.8,0.8,0.8)
insertionRadiusModelDisplay.SetOpacity(0.3)
insertionRadiusModelDisplay.SliceIntersectionVisibilityOn()
insertionRadiusModelDisplay.SetScene(scene)
scene.AddNode(insertionRadiusModelDisplay)
insertionRadiusModel.SetAndObserveDisplayNodeID(insertionRadiusModelDisplay.GetID())
# Add to scene
insertionRadiusModelDisplay.SetPolyData(sphere.GetOutput())
scene.AddNode(insertionRadiusModel)
# Create insertionRadiusTransform node
insertionRadiusTransform = slicer.vtkMRMLLinearTransformNode()
insertionRadiusTransform.SetName('InsertionRadiusTransform-%s' % target.GetName())
scene.AddNode(insertionRadiusTransform)
# Translation
transformMatrix = vtk.vtkMatrix4x4()
# get coordinates from current fiducial
currentFiducialCoordinatesRAS = [0, 0, 0]
target.GetFiducialCoordinates(currentFiducialCoordinatesRAS)
transformMatrix.SetElement(0, 3, currentFiducialCoordinatesRAS[0])
transformMatrix.SetElement(1, 3, currentFiducialCoordinatesRAS[1])
transformMatrix.SetElement(2, 3, currentFiducialCoordinatesRAS[2])
insertionRadiusTransform.ApplyTransformMatrix(transformMatrix)
insertionRadiusModel.SetAndObserveTransformNodeID(insertionRadiusTransform.GetID())
self.sphere = sphere
self.insertionRadiusModel = insertionRadiusModel
self.insertionRadiusModelDisplay = insertionRadiusModelDisplay
self.insertionRadiusTransform = insertionRadiusTransform
def doStepProcessing(self):
#transforms center of imported volume to world origin
coords = [0,0,0]
coords = self.__baseline.GetOrigin()
transformVolmat = vtk.vtkMatrix4x4()
transformVolmat.SetElement(0,3,coords[0]*-1)
transformVolmat.SetElement(1,3,coords[1]*-1)
transformVolmat.SetElement(2,3,coords[2]*-1)
transformVol = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(transformVol)
transformVol.ApplyTransformMatrix(transformVolmat)
#harden transform
self.__baseline.SetAndObserveTransformNodeID(transformVol.GetID())
slicer.vtkSlicerTransformLogic.hardenTransform(self.__baseline)
#offsets volume so its center is registered to world origin
newCoords = [0,0,0,0,0,0]
self.__baseline.GetRASBounds(newCoords)
print newCoords
shift = [0,0,0]
shift[0] = 0.5*(newCoords[1] - newCoords[0])
shift[1] = 0.5*(newCoords[3] - newCoords[2])
shift[2] = 0.5*(newCoords[4] - newCoords[5])
transformVolmat2 = vtk.vtkMatrix4x4()
transformVolmat2.SetElement(0,3,shift[0])
transformVolmat2.SetElement(1,3,shift[1])
transformVolmat2.SetElement(2,3,shift[2])
transformVol2 = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(transformVol2)
transformVol2.ApplyTransformMatrix(transformVolmat2)
#harden transform
self.__baseline.SetAndObserveTransformNodeID(transformVol2.GetID())
slicer.vtkSlicerTransformLogic.hardenTransform(self.__baseline)
#remove transformations from scene
slicer.mrmlScene.RemoveNode(transformVol)
slicer.mrmlScene.RemoveNode(transformVol2)
print('Done')
def test_Regimatic1(self):
"""Set up two copies of the same data and try to recover identity"""
self.delayDisplay("Starting the test",50)
#
# first, get some data
#
import urllib
downloads = (
('http://www.slicer.org/slicerWiki/images/4/43/MR-head.nrrd', 'Head_moving.nrrd', slicer.util.loadVolume),
('http://www.slicer.org/slicerWiki/images/4/43/MR-head.nrrd', 'Head_fixed.nrrd', slicer.util.loadVolume),
)
for url,name,loader in downloads:
filePath = slicer.app.temporaryPath + '/' + name
if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
print('Requesting download %s from %s...\n' % (name, url))
urllib.urlretrieve(url, filePath)
if loader:
print('Loading %s...\n' % (name,))
loader(filePath)
self.delayDisplay('Finished with download and loading\n',50)
volumeNode = slicer.util.getNode(pattern="Head")
# Create transform node
movingToFixed = slicer.vtkMRMLLinearTransformNode()
movingToFixed.SetName('movingToFixed')
slicer.mrmlScene.AddNode(movingToFixed)
# set up the nodes for viewing
fixed = slicer.util.getNode('Head_fixed')
moving = slicer.util.getNode('Head_moving')
moving.SetAndObserveTransformNodeID(movingToFixed.GetID())
compositeNodes = slicer.util.getNodes('vtkMRMLSliceCompositeNode*')
for compositeNode in compositeNodes.values():
compositeNode.SetBackgroundVolumeID(fixed.GetID())
compositeNode.SetForegroundVolumeID(moving.GetID())
compositeNode.SetForegroundOpacity(0.5)
applicationLogic = slicer.app.applicationLogic()
applicationLogic.FitSliceToAll()
# apply an initial transform
transform = vtk.vtkTransform()
# transform.RotateWXYZ(.1, 1,1,1) # TODO: fix quaternion
transform.Translate(50, 33, -32)
movingToFixed.SetMatrixTransformToParent(transform.GetMatrix())
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('Regimatic')
regimaticWidget = slicer.modules.RegimaticWidget
regimaticWidget.fixedSelector.setCurrentNode(fixed)
regimaticWidget.movingSelector.setCurrentNode(moving)
self.delayDisplay('Test passed!',50)
def onCalculateTransformButton(self):
self.calibrationInstructionsLabel42.setStyleSheet("QLabel {color: #000000; text-decoration: line-through;}")
self.calculateTransformButton.setEnabled(False)
self.saveTransform = slicer.vtkMRMLLinearTransformNode()
self.saveTransform.SetName("EndToStartTransform")
slicer.mrmlScene.AddNode(self.saveTransform)
logic = UltrasoundSimulatorLogic()
logic.calculateStartToEnd(self.saveTransform, self.startFiducialNode, self.endFiducialNode)
self.currentCalibrationState = "APPLY_AND_FINALIZE_CALIBRATION"
def clipping(self):
planeCollection = vtk.vtkPlaneCollection()
harden = slicer.vtkSlicerTransformLogic()
tempTransform = slicer.vtkMRMLLinearTransformNode()
tempTransform.HideFromEditorsOn()
slicer.mrmlScene.AddNode(tempTransform)
numNodes = slicer.mrmlScene.GetNumberOfNodesByClass("vtkMRMLModelNode")
dictionnaryModel = dict()
hardenModelIDdict = dict()
landmarkDescriptionDict = dict()
modelIDdict = dict()
for i in range(3, numNodes):
planeCollection.RemoveAllItems()
mh = slicer.mrmlScene.GetNthNodeByClass(i, "vtkMRMLModelNode")
if mh.GetDisplayVisibility() == 0:
continue
model = slicer.util.getNode(mh.GetName())
transform = model.GetParentTransformNode()
if transform:
tempTransform.Copy(transform)
harden.hardenTransform(tempTransform)
m = vtk.vtkMatrix4x4()
tempTransform.GetMatrixTransformToParent(m)
m.Invert(m, m)
else:
m = vtk.vtkMatrix4x4()
for key, planeDef in self.planeDict.iteritems():
hardenP = m.MultiplyPoint(planeDef.P)
hardenN = m.MultiplyPoint(planeDef.n)
if planeDef.boxState:
planeDef.vtkPlane.SetOrigin(hardenP[0], hardenP[1], hardenP[2])
if planeDef.negState:
planeDef.vtkPlane.SetNormal(-hardenN[0], -hardenN[1], -hardenN[2])
if planeDef.posState:
planeDef.vtkPlane.SetNormal(hardenN[0], hardenN[1], hardenN[2])
planeCollection.AddItem(planeDef.vtkPlane)
dictionnaryModel[model.GetID()]= model.GetPolyData()
polyData = model.GetPolyData()
clipper = vtk.vtkClipClosedSurface()
clipper.SetClippingPlanes(planeCollection)
clipper.SetInputData(polyData)
clipper.SetGenerateFaces(1)
clipper.SetScalarModeToLabels()
clipper.Update()
polyDataNew = clipper.GetOutput()
model.SetAndObservePolyData(polyDataNew)
# Checking if one ore more fiducial list are connected to this model
list = slicer.mrmlScene.GetNodesByClass("vtkMRMLMarkupsFiducialNode")
end = list.GetNumberOfItems()
for i in range(0,end):
fidList = list.GetItemAsObject(i)
if fidList.GetAttribute("connectedModelID"):
if fidList.GetAttribute("connectedModelID") == model.GetID():
modelIDdict[fidList.GetID()], hardenModelIDdict[fidList.GetID()], landmarkDescriptionDict[fidList.GetID()] = \
self.unprojectLandmarks(fidList)
return dictionnaryModel, modelIDdict, hardenModelIDdict, landmarkDescriptionDict
def TestNeedleDetection(self):
parameters = {}
scene = slicer.mrmlScene
collection = scene.GetNodesByClass('vtkMRMLScalarVolumeNode');
nimages = collection.GetNumberOfItems()
collection.InitTraversal()
n = 0
cliList = []
while n < nimages:
inImage = collection.GetNextItemAsObject()
if inImage == None:
break
id = inImage.GetID()
print('Processing image node = %s...' % id)
# Create a new image node
outImage = slicer.vtkMRMLScalarVolumeNode()
name = inImage.GetName() + '_Needle'
outImage.SetName(name)
scene.AddNode(outImage)
outImage.SetLabelMap(1)
# Create a new linear transform node (for needle position/orientation)
needleTransform = slicer.vtkMRMLLinearTransformNode()
name = inImage.GetName() + '_Transform'
needleTransform.SetName(name)
scene.AddNode(needleTransform)
parameters = {}
parameters['inputVolume'] = inImage.GetID()
parameters['outputVolume'] = outImage.GetID()
parameters['needleTransform'] = needleTransform.GetID()
parameters['sigma1'] = 0.5
parameters['minsigma'] = 0.5
parameters['maxsigma'] = 1.3
parameters['stepsigma'] = 5
parameters['minlinemeasure'] = 40
parameters['alpha1'] = 0.5
parameters['alpha2'] = 2
parameters['anglethreshold'] = 25
parameters['normal'] = [0.0, 0.0, 1.0]
parameters['numberOfBins'] = 128
parameters['minimumObjectSize'] = 50
parameters['minPrincipalAxisLength'] = 50
parameters['closestPoint'] = [0.0, 0.0, 0.0]
nd = slicer.modules.needledetection
c = slicer.cli.run(nd, None, parameters)
c.AddObserver('ModifiedEvent', self.printStatus)
self.cliList.append(c)
n = n + 1
def loadScrew(self):
print "load screw button"
self.fidChanged
fid = self.fidNode
collectionS = slicer.mrmlScene.GetNodesByName('Screw at point %s' % self.currentFidLabel)
screwCheck = collectionS.GetItemAsObject(0)
if screwCheck == None:
screwDescrip = ["0","0","0","0","0","0"]
screwModel = slicer.modules.models.logic().AddModel(self.screwPath)
if screwModel != None:
fid.AddObserver('ModifiedEvent', self.fidMove)
matrix = vtk.vtkMatrix4x4()
matrix.DeepCopy((1, 0, 0, self.coords[0],
0, -1, 0, self.coords[1],
0, 0, -1, self.coords[2],
0, 0, 0, 1))
transformScrewTemp = slicer.vtkMRMLLinearTransformNode()
transformScrewTemp.SetName("Transform-%s" % self.currentFidLabel)
slicer.mrmlScene.AddNode(transformScrewTemp)
transformScrewTemp.ApplyTransformMatrix(matrix)
screwModel.SetName('Screw at point %s' % self.currentFidLabel)
screwModel.SetAndObserveTransformNodeID(transformScrewTemp.GetID())
modelDisplay = screwModel.GetDisplayNode()
modelDisplay.SetColor(0.12,0.73,0.91)
modelDisplay.SetDiffuse(0.90)
modelDisplay.SetAmbient(0.10)
modelDisplay.SetSpecular(0.20)
modelDisplay.SetPower(10.0)
modelDisplay.SetSliceIntersectionVisibility(True)
screwModel.SetAndObserveDisplayNodeID(modelDisplay.GetID())
screwDescrip[0] = self.currentFidLabel
screwDescrip[1] = self.__length
screwDescrip[2] = self.__diameter
self.screwList.append(screwDescrip)
else:
return
else:
return
def ZFrameRegistrationTransform(self):
self.dataNodeZFrame = slicer.vtkMRMLLinearTransformNode()
self.dataNodeZFrame.SetName('ZFrameTransform')
slicer.mrmlScene.AddNode(self.dataNodeZFrame)
self.connectNode.RegisterOutgoingMRMLNode(self.dataNodeZFrame)
self.connectNode.PushNode(self.dataNodeZFrame)
print self.connectNode.PushNode(self.dataNodeZFrame)
'''query the status of server, if registration -> stop node and delete the node'''
def onButtonRegistrationClicked(self):
if self.registTag: # check already has a registration data node
self.connectNode.PushNode(self.dataNodeZFrame)
else: # fist time to creat the registration data node
self.dataNodeZFrame = slicer.vtkMRMLLinearTransformNode()
self.dataNodeZFrame.SetName("ZFrameTransform")
slicer.mrmlScene.AddNode(self.dataNodeZFrame)
self.connectNode.RegisterOutgoingMRMLNode(self.dataNodeZFrame)
self.connectNode.PushNode(self.dataNodeZFrame) # send the ZFrameTransform data to controller
self.registTag = True
def TargetTransform(self):
## change -> up func
self.dataNodeZFrame.Stop()
self.connectNode.UnregisterOutgoingMRMLNode(self.dataNodeZFrame)
##
self.dataNodeTarget = slicer.vtkMRMLLinearTransformNode()
self.dataNodeTarget.SetName('TARGET')
slicer.mrmlScene.AddNode(self.dataNodeTarget)
self.connectNode.RegisterOutgoingMRMLNode(self.dataNodeTarget)
'''check node status'''
def register(self,fixedVolume,movingVolume,parameters={}):
"""
Run BRAINSFit to register movingVolume in the space of fixedVolume.
Parameters is and optional dictionary.
Returns parameters with any defaults filled in.
"""
self.delayDisplay('Running the BRAINSFit')
# required parameters
parameters["fixedVolume"] = fixedVolume.GetID()
parameters["movingVolume"] = movingVolume.GetID()
# type of transform is optional, default to linear
keys = parameters.keys()
if "useBSpline" in keys:
if not 'bsplineTransform' in keys:
transform = slicer.vtkMRMLBSplineTransformNode()
slicer.mrmlScene.AddNode(transform)
parameters['bsplineTransform'] = transform.GetID()
else:
if not 'linearTransform' in keys:
transform = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(transform)
parameters['linearTransform'] = transform.GetID()
# if no phase picked, default to rigid
if not self.availablePhases.intersection(parameters):
parameters['useRigid'] = True
# if no output volume specified, clone the moving
if not "outputVolume" in parameters.keys():
outputName = movingVolume.GetName() + "-transformed"
volumesLogic = slicer.modules.volumes.logic()
outputVolume = volumesLogic.CloneVolume(slicer.mrmlScene, movingVolume, outputName)
parameters['outputVolume'] = outputVolume.GetID()
self.delayDisplay(parameters)
cliNode = slicer.cli.run(slicer.modules.brainsfit, None, parameters, delete_temporary_files=False)
waitCount = 0
maxWait = 10000
while cliNode.GetStatusString() != 'Completed' and waitCount < maxWait:
self.delayDisplay( "Running BRAINSFit... %d seconds" % waitCount )
waitCount += 1
if waitCount == maxWait:
raise Exception("Registration took too long to run!")
self.delayDisplay( "Finished after %d seconds" % waitCount )
return parameters
def activeEvent(self):
print "into activeEvent"
self.tempLinearNode = slicer.vtkMRMLLinearTransformNode()
self.tempLinearNode.SetName('temp')
#self.tagTemp = self.tempLinearNode.AddObserver('ModifiedEvent', self.putInfo)
#self.tagTemp = self.connectNode.AddObserver('ModifiedEvent', self.putInfo)
#self.tagTemp = self.connectNode.AddObserver(slicer.vtkMRMLIGTLConnectorNode.ReceiveEvent, self.putInfo)
#self.tagTemp = self.tempLinearNode.AddObserver(vtk.vtkCommand.ModifiedEvent, self.putInfo)
#self.tagTemp = self.tempLinearNode.AddObserver(self.connectNode.ReceiveEvent, self.putInfo)
self.tagTemp = self.connectNode.AddObserver(self.connectNode.ReceiveEvent, self.putInfo)
#test
self.times1 = 0
def loadScrew(self):
print "load screw button"
#self.fidChanged
screwCheck = slicer.util.getNode('Screw at point %s' % self.currentFidLabel)
if screwCheck != None:
# screw already loaded
return
screwDescrip = ["0","0","0","0","0","0"]
screwModel = slicer.modules.models.logic().AddModel(self.screwPath)
if screwModel is None:
logging.error("Failed to load screw model: "+self.screwPath)
return
matrix = vtk.vtkMatrix4x4()
matrix.DeepCopy((1, 0, 0, self.coords[0],
0, -1, 0, self.coords[1],
0, 0, -1, self.coords[2],
0, 0, 0, 1))
transformScrewTemp = slicer.vtkMRMLLinearTransformNode()
transformScrewTemp.SetName("Transform-%s" % self.currentFidLabel)
slicer.mrmlScene.AddNode(transformScrewTemp)
transformScrewTemp.ApplyTransformMatrix(matrix)
screwModel.SetName('Screw at point %s' % self.currentFidLabel)
screwModel.SetAndObserveTransformNodeID(transformScrewTemp.GetID())
modelDisplay = screwModel.GetDisplayNode()
modelDisplay.SetColor(0.12,0.73,0.91)
modelDisplay.SetDiffuse(0.90)
modelDisplay.SetAmbient(0.10)
modelDisplay.SetSpecular(0.20)
modelDisplay.SetPower(10.0)
modelDisplay.SetSliceIntersectionVisibility(True)
screwModel.SetAndObserveDisplayNodeID(modelDisplay.GetID())
screwDescrip[0] = self.currentFidLabel
screwDescrip[1] = self.__length
screwDescrip[2] = self.__diameter
self.screwList.append(screwDescrip)
self.insertScrewButton.enabled = True
self.backoutScrewButton.enabled = False
self.b.enabled = True
self.transformSlider1.enabled = True
self.transformSlider2.enabled = True
def RegisterImageSequence(self, fixedVolumeNode, movingVolumeSequenceNode, linearTransformSequenceNode, outputVolumeSequenceNode, initializeTransformMode='useGeometryAlign', initialTransformNode=None, maskVolumeNode=None):
if linearTransformSequenceNode:
linearTransformSequenceNode.RemoveAllDataNodes()
if outputVolumeSequenceNode:
outputVolumeSequenceNode.RemoveAllDataNodes()
numOfImageNodes = movingVolumeSequenceNode.GetNumberOfDataNodes()
lastTransformNode = None
for i in range(numOfImageNodes):
movingVolumeNode = movingVolumeSequenceNode.GetNthDataNode(i)
movingVolumeIndexValue = movingVolumeSequenceNode.GetNthIndexValue(i)
slicer.mrmlScene.AddNode(movingVolumeNode)
outputTransformNode = slicer.vtkMRMLLinearTransformNode()
#outputTransformNode = slicer.vtkMRMLBSplineTransformNode()
slicer.mrmlScene.AddNode(outputTransformNode)
outputVolumeNode = None
if outputVolumeSequenceNode:
outputVolumeNode = slicer.vtkMRMLScalarVolumeNode()
slicer.mrmlScene.AddNode(outputVolumeNode)
initialTransformNode = linearTransformSequenceNode.GetNthDataNode(i-1)
if initialTransformNode:
slicer.mrmlScene.AddNode(initialTransformNode)
else:
initialTransformNode = None
self.RegisterImage(fixedVolumeNode, movingVolumeNode, outputTransformNode, outputVolumeNode, initializeTransformMode, initialTransformNode, maskVolumeNode)
if linearTransformSequenceNode:
linearTransformSequenceNode.SetDataNodeAtValue(outputTransformNode, movingVolumeIndexValue)
if outputVolumeSequenceNode:
outputVolumeSequenceNode.SetDataNodeAtValue(outputVolumeNode, movingVolumeIndexValue)
if initialTransformNode:
slicer.mrmlScene.RemoveNode(initialTransformNode)
slicer.mrmlScene.RemoveNode(movingVolumeNode)
if outputVolumeNode:
slicer.mrmlScene.RemoveNode(outputVolumeNode)
# Initialize the lastTransform so the next registration can start with this transform
lastTransform = outputTransformNode
slicer.mrmlScene.RemoveNode(outputTransformNode)
# This is required as a temp workaround to use the transform sequence to map baseline ROI to sequence ROI
if linearTransformSequenceNode:
for i in range(numOfImageNodes):
transformNode = linearTransformSequenceNode.GetNthDataNode(i)
transformNode.Inverse()
def ZFrameRegistrationTransform(self):
self.dataNodeZFrame = slicer.vtkMRMLLinearTransformNode()
self.dataNodeZFrame.SetName('ZFrameTransform')
slicer.mrmlScene.AddNode(self.dataNodeZFrame)
self.connectNode.RegisterOutgoingMRMLNode(self.dataNodeZFrame)
self.connectNode.PushNode(self.dataNodeZFrame)
print self.connectNode.PushNode(self.dataNodeZFrame)
'''query the status of server, if registration -> stop node and delete the node'''
# def TargetTransform(self):
# ## change -> up func
# self.dataNodeZFrame.Stop()
# self.connectNode.UnregisterOutgoingMRMLNode(self.dataNodeZFrame)
# ##
#
# self.dataNodeTarget = slicer.vtkMRMLLinearTransformNode()
# self.dataNodeTarget.SetName('TARGET')
# slicer.mrmlScene.AddNode(self.dataNodeTarget)
#
# self.connectNode.RegisterOutgoingMRMLNode(self.dataNodeTarget)
#
# '''check node status'''
#
#
# def SendTargetTransform(self):
# '''check whether dataNodeTarget exist'''
# self.connectNode.PushNode(self.dataNodeTarget)
#
#
# def CurrentTransform(self):
# self.dataNodeCurrent = slicer.vtkMRMLLinearTransformNode
# self.dataNodeCurrent.SetName('CURRENT')
# slicer.mrmlScene.AddNode(self.dataNodeCurrent)
# self.connectNode.RegisterIncomingMRMLNode(self.dataNodeCurrent)
#
'''queryNode = slicer.vtkMRMLIGTQueryNode()
'''
# self.connectNode.PushQuery
'''check node status'''
def __init__(self):
self.scene = slicer.mrmlScene
self.scene.SetUndoOn()
self.scene.SaveStateForUndo(self.scene.GetNodes())
self.currentSlice = Slice('/luscinia/ProstateStudy/invivo/Patient59/loupas/RadialImagesCC_imwrite/arfi_ts3_26.57.png')
# yay, adding images to slicer
planeSource = vtk.vtkPlaneSource()
planeSource.SetCenter(self.currentSlice.x, self.currentSlice.y, self.currentSlice.z)
reader = vtk.vtkPNGReader()
reader.SetFileName(self.currentSlice.name)
# model node
self.model = slicer.vtkMRMLModelNode()
self.model.SetScene(self.scene)
self.model.SetName(self.currentSlice.name)
self.model.SetAndObservePolyData(planeSource.GetOutput())
# model display node
self.modelDisplay = slicer.vtkMRMLModelDisplayNode()
self.modelDisplay.BackfaceCullingOff() # so plane can be seen from both front and back face
self.modelDisplay.SetScene(self.scene)
self.scene.AddNode(self.modelDisplay)
# connecting model node w/ its model display node
self.model.SetAndObserveDisplayNodeID(self.modelDisplay.GetID())
# adding tiff file as texture to modelDisplay
self.modelDisplay.SetAndObserveTextureImageData(reader.GetOutput())
self.scene.AddNode(self.model)
# now doing a linear transform to set coordinates and orientation of plane
self.transform = slicer.vtkMRMLLinearTransformNode()
self.scene.AddNode(self.transform)
self.model.SetAndObserveTransformNodeID(self.transform.GetID())
vTransform = vtk.vtkTransform()
vTransform.Scale(150, 150, 150)
vTransform.RotateX(0)
vTransform.RotateY(0)
vTransform.RotateZ(0)
self.transform.SetAndObserveMatrixTransformToParent(vTransform.GetMatrix())
def setupScene(self):
# create transforms
self.ReferenceToRas = slicer.util.getNode("ReferenceToRas")
if not self.ReferenceToRas:
self.ReferenceToRas = slicer.vtkMRMLLinearTransformNode()
self.ReferenceToRas.SetName("ReferenceToRas")
m = vtk.vtkMatrix4x4()
m.SetElement(0, 0, 0)
m.SetElement(0, 2, -1)
m.SetElement(1, 1, 0)
m.SetElement(1, 1, -1)
m.SetElement(2, 2, 0)
m.SetElement(2, 0, -1)
self.ReferenceToRas.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.ReferenceToRas)
# setup feature scene
self.ultrasound.setupScene()
def selectSlice(self, index):
self.scene.Undo()
self.scene.SaveStateForUndo(self.scene.GetNodes())
imgFilePrefix = './data/test'
imgFileSuffix = '.tiff'
# yay, adding images to slicer
planeSource = vtk.vtkPlaneSource()
reader = vtk.vtkTIFFReader()
reader.SetFileName(imgFilePrefix + str(self.imageList[index]) + imgFileSuffix)
#reader.CanReadFile('imgFilePrefix + str(self.imageList[0]) + imgFileSuffix')
# model node
model = slicer.vtkMRMLModelNode()
model.SetScene(self.scene)
model.SetName("test " + str(self.imageList[index]) + "cow")
model.SetAndObservePolyData(planeSource.GetOutput())
# model display node
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.BackfaceCullingOff() # so plane can be seen from both front and back face
modelDisplay.SetScene(self.scene)
self.scene.AddNode(modelDisplay)
# connecting model node w/ its model display node
model.SetAndObserveDisplayNodeID(modelDisplay.GetID())
# adding tiff file as texture to modelDisplay
modelDisplay.SetAndObserveTextureImageData(reader.GetOutput())
self.scene.AddNode(model)
# now doing a linear transform to set coordinates and orientation of plane
transform = slicer.vtkMRMLLinearTransformNode()
self.scene.AddNode(transform)
model.SetAndObserveTransformNodeID(transform.GetID())
vTransform = vtk.vtkTransform()
vTransform.Scale(150, 150, 150)
vTransform.RotateX(self.rotateXList[index])
vTransform.RotateY(self.rotateYList[index])
vTransform.RotateZ(self.rotateZList[index])
transform.SetAndObserveMatrixTransformToParent(vTransform.GetMatrix())
def test_BreachWarningSelfTest1(self):
"""Ideally you should have several levels of tests. At the lowest level
tests sould exercise the functionality of the logic with different inputs
(both valid and invalid). At higher levels your tests should emulate the
way the user would interact with your code and confirm that it still works
the way you intended.
One of the most important features of the tests is that it should alert other
developers when their changes will have an impact on the behavior of your
module. For example, if a developer removes a feature that you depend on,
your test should break so they know that the feature is needed.
"""
self.delayDisplay("Starting the test")
self.delayDisplay("Create models")
modelNodes = []
createModelsLogic = slicer.modules.createmodels.logic()
sphereRadius = 10.0
sphereModel = createModelsLogic.CreateSphere(
sphereRadius) # watched model
toolModel = createModelsLogic.CreateNeedle(50.0, 1.5, 0.0, False)
self.delayDisplay("Set up module GUI")
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('BreachWarning')
bwWidget = slicer.modules.breachwarning.widgetRepresentation()
bwColorPickerButton = slicer.util.findChildren(
widget=bwWidget,
className='ctkColorPickerButton',
name='ColorPickerButton')[0]
bwModelNodeCombobox = slicer.util.findChildren(
widget=bwWidget, name='ModelNodeComboBox')[0]
bwToolNodeCombobox = slicer.util.findChildren(widget=bwWidget,
name='ToolComboBox')[0]
bwModelNodeCombobox.setCurrentNodeID(sphereModel.GetID())
warningColor = (1.0, 0.0, 0.0)
color = qt.QColor(warningColor[0] * 255, warningColor[1] * 255,
warningColor[2] * 255, 1)
bwColorPickerButton.setColor(color)
# Transform the sphere somewhere
sphereTransform = slicer.vtkMRMLLinearTransformNode()
sphereTransformMatrix = vtk.vtkMatrix4x4()
sphereTransformMatrix.SetElement(0, 3, 80)
sphereTransformMatrix.SetElement(1, 3, 40)
sphereTransformMatrix.SetElement(2, 3, 30)
sphereTransform.SetMatrixTransformToParent(sphereTransformMatrix)
slicer.mrmlScene.AddNode(sphereTransform)
sphereModel.SetAndObserveTransformNodeID(sphereTransform.GetID())
# Create transforms node hierarchy for the tool
transforms = []
numberOfTransforms = 3
for i in range(numberOfTransforms):
transforms.append(slicer.vtkMRMLLinearTransformNode())
transformName = "Tool_" + str(i)
transforms[i].SetName(
slicer.mrmlScene.GenerateUniqueName(transformName))
slicer.mrmlScene.AddNode(transforms[i])
if i > 0:
transforms[i].SetAndObserveTransformNodeID(
transforms[i - 1].GetID())
# Tool transform is the one at the bottom of the transform hierarchy
# (to make sure transform changes in the middle of the transform hierarchy are used correctly)
toolModel.SetAndObserveTransformNodeID(transforms[-1].GetID())
bwToolNodeCombobox.setCurrentNodeID(transforms[-1].GetID())
# Pick a transform in the middle of the transform hierarchy that we change to simulate tool motion,
# leave the rest of the transforms unchanged
toolToWorldTransform = transforms[1]
transformMatrixOutside = vtk.vtkMatrix4x4()
transformMatrixOutside.DeepCopy(sphereTransformMatrix)
transformMatrixOutside.SetElement(
0, 3,
transformMatrixOutside.GetElement(0, 3) + sphereRadius * 2.1)
transformMatrixOutside.SetElement(
1, 3,
transformMatrixOutside.GetElement(1, 3) + sphereRadius * 1.3)
transformMatrixOutside.SetElement(
2, 3,
transformMatrixOutside.GetElement(2, 3) + sphereRadius * 3.2)
transformMatrixInside = vtk.vtkMatrix4x4()
transformMatrixInside.DeepCopy(sphereTransformMatrix)
transformMatrixInside.SetElement(
0, 3,
transformMatrixInside.GetElement(0, 3) + sphereRadius * 0.1)
transformMatrixInside.SetElement(
1, 3,
transformMatrixInside.GetElement(1, 3) + sphereRadius * 0.3)
transformMatrixInside.SetElement(
2, 3,
transformMatrixInside.GetElement(2, 3) + sphereRadius * 0.2)
# Start breach warning checks
self.delayDisplay('Tool is outside the sphere')
toolToWorldTransform.SetMatrixTransformToParent(transformMatrixOutside)
sphereColor = sphereModel.GetDisplayNode().GetColor()
self.assertNotEqual(sphereColor, warningColor)
self.delayDisplay('Tool is inside the sphere')
toolToWorldTransform.SetMatrixTransformToParent(transformMatrixInside)
sphereColor = sphereModel.GetDisplayNode().GetColor()
self.assertEqual(sphereColor, warningColor)
self.delayDisplay('Tool is outside the sphere')
toolToWorldTransform.SetMatrixTransformToParent(transformMatrixOutside)
sphereColor = sphereModel.GetDisplayNode().GetColor()
self.assertNotEqual(sphereColor, warningColor)
self.delayDisplay('Test passed!')
def rigido(self):
escena = slicer.mrmlScene
#Se recupera la escena cargada
volumen4D = self.inputSelector.currentNode()
imagenvtk4D = volumen4D.GetImageData()
extract1 = vtk.vtkImageExtractComponents()
extract1.SetInputData(imagenvtk4D)
imagen_fija = extract1.SetComponents(0)
extract1.Update()
#Matriz de transformacion
ras2ijk = vtk.vtkMatrix4x4()
ijk2ras = vtk.vtkMatrix4x4()
#Se solicita al volumen original que devuelva las matrices
volumen4D.GetRASToIJKMatrix(ras2ijk)
volumen4D.GetIJKToRASMatrix(ijk2ras)
#Se crea un volumen nuevo
volumenFijo = slicer.vtkMRMLScalarVolumeNode()
#Se asignan las transformaciones
volumenFijo.SetRASToIJKMatrix(ras2ijk)
volumenFijo.SetIJKToRASMatrix(ijk2ras)
#Se asigna el volumen 3D
volumenFijo.SetAndObserveImageData(extract1.GetOutput())
escena.AddNode(volumenFijo)
numero_imagenes = volumen4D.GetNumberOfFrames()
valor1 = []
# vector donde se guarda los valores de LR despues aplicar la transformada rigida
valor2 = []
# vector donde se guarda los valores de PA despues aplicar la transformada rigida
valor3 = []
# vector donde se guarda los valores de IS despues aplicar la transformada rigida
vecvolmay = []
# vector que muestra el frame, los volumenes que tienen un movimiento mayor a 4 mm
valor1.append(0)
valor2.append(0)
valor3.append(0)
#En esta parte se evaluan todos los volumenes moviles
for i in range(0, numero_imagenes, 1):
#extraer la imagen movil
extract2 = vtk.vtkImageExtractComponents()
extract2.SetInputData(imagenvtk4D)
imagen_movil = extract2.SetComponents(i)
extract2.Update()
#Se crea un volumen movil, y se realiza el mismo procedimiento que con el fijo
volumenMovil = slicer.vtkMRMLScalarVolumeNode()
volumenSalida = slicer.vtkMRMLScalarVolumeNode()
escena.AddNode(volumenSalida)
volumenMovil.SetRASToIJKMatrix(ras2ijk)
volumenMovil.SetIJKToRASMatrix(ijk2ras)
volumenMovil.SetAndObserveImageData(extract2.GetOutput())
escena.AddNode(volumenMovil)
#Se crea la transformada para alinear los volumenes
transformadaSalida = slicer.vtkMRMLLinearTransformNode()
transformadaSalida.SetName(
'Transformada de registro rigido' +
str(i)) #se le da un nombre especifico a la transformada
slicer.mrmlScene.AddNode(transformadaSalida)
parameters = {}
parameters['fixedVolume'] = volumenFijo.GetID()
parameters['movingVolume'] = volumenMovil.GetID()
parameters[
'transformType'] = 'Rigid' #Se coloca segun lo que se quiera hacer si rigido, afin o bspline
parameters['outputTransform'] = transformadaSalida.GetID()
parameters['outputVolume'] = volumenSalida.GetID()
cliNode = slicer.cli.run(slicer.modules.brainsfit,
None,
parameters,
wait_for_completion=True)
slicer.util.saveNode(
volumenSalida, 'volumenrigido' + str(i + 1) + '.nrrd'
) #se guarda el volumen registrado en la carpeta de documentos
# Este for se hace con el fin de ver los volumenes que tienen un desplazamiento mayor a 4 mm con respecto al fijo
for i in range(0, numero_imagenes):
nodo = escena.GetNodesByName('Transformada de registro rigido' +
str(i))
nodo = nodo.GetItemAsObject(0)
matriztransformada = nodo.GetMatrixTransformToParent(
) # Se obtiene la matriz de transformacion
# se obtiene para cada frame la ubicacion en las 3 direcciones
valor1inicial = matriztransformada.GetElement(
0, 3
) #se agrega el valor en la posicion 0 3 de la transformada valor que corresponde a LR
valor2inicial = matriztransformada.GetElement(
1, 3
) #se agrega el valor en la posicion 0 3 de la transformada valor que corresponde a PA
valor3inicial = matriztransformada.GetElement(
2, 3
) #se agrega el valor en la posicion 0 3 de la transformada valor que corresponde a IS
valor1.append(valor1inicial)
valor2.append(valor2inicial)
valor3.append(valor3inicial)
# Si la posicion en cualquier direccion de un volumen es mayor a 4mm respecto al del primer frame se obtiene un vector con su posicion
if ((abs(valor1[i]) > 4) or (abs(valor2[i]) > 4)
or (abs(valor3[i]) > 4)):
vecvolmay.append(i)
print("Los volumenes con los que se mueve mas de 4mm son")
print("Volumen")
print(vecvolmay)
if (len(vecvolmay) == 0): # Si no hay alguni no se muestra nada
print("Ningun volumen se movio mas de 4mm")
def setupScene(self): #applet specific
logging.debug('setupScene')
Guidelet.setupScene(self)
logging.debug('Create transforms')
self.cauteryTipToCautery = slicer.util.getNode('CauteryTipToCautery')
if not self.cauteryTipToCautery:
self.cauteryTipToCautery = slicer.vtkMRMLLinearTransformNode()
self.cauteryTipToCautery.SetName("CauteryTipToCautery")
m = self.readTransformFromSettings('CauteryTipToCautery')
if m:
self.cauteryTipToCautery.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.cauteryTipToCautery)
self.cauteryModelToCauteryTip = slicer.util.getNode(
'CauteryModelToCauteryTip')
if not self.cauteryModelToCauteryTip:
self.cauteryModelToCauteryTip = slicer.vtkMRMLLinearTransformNode()
self.cauteryModelToCauteryTip.SetName("CauteryModelToCauteryTip")
m = self.readTransformFromSettings('CauteryModelToCauteryTip')
if m:
self.cauteryModelToCauteryTip.SetMatrixTransformToParent(m)
self.cauteryModelToCauteryTip.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.cauteryModelToCauteryTip)
self.needleTipToNeedle = slicer.util.getNode('NeedleTipToNeedle')
if not self.needleTipToNeedle:
self.needleTipToNeedle = slicer.vtkMRMLLinearTransformNode()
self.needleTipToNeedle.SetName("NeedleTipToNeedle")
m = self.readTransformFromSettings('NeedleTipToNeedle')
if m:
self.needleTipToNeedle.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.needleTipToNeedle)
self.needleModelToNeedleTip = slicer.util.getNode(
'NeedleModelToNeedleTip')
if not self.needleModelToNeedleTip:
self.needleModelToNeedleTip = slicer.vtkMRMLLinearTransformNode()
self.needleModelToNeedleTip.SetName("NeedleModelToNeedleTip")
m = self.readTransformFromSettings('NeedleModelToNeedleTip')
if m:
self.needleModelToNeedleTip.SetMatrixTransformToParent(m)
self.needleModelToNeedleTip.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.needleModelToNeedleTip)
self.cauteryCameraToCautery = slicer.util.getNode(
'CauteryCameraToCautery')
if not self.cauteryCameraToCautery:
self.cauteryCameraToCautery = slicer.vtkMRMLLinearTransformNode()
self.cauteryCameraToCautery.SetName("CauteryCameraToCautery")
m = vtk.vtkMatrix4x4()
m.SetElement(0, 0, 0)
m.SetElement(0, 2, -1)
m.SetElement(1, 1, 0)
m.SetElement(1, 0, 1)
m.SetElement(2, 2, 0)
m.SetElement(2, 1, -1)
self.cauteryCameraToCautery.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.cauteryCameraToCautery)
self.CauteryToNeedle = slicer.util.getNode('CauteryToNeedle')
if not self.CauteryToNeedle:
self.CauteryToNeedle = slicer.vtkMRMLLinearTransformNode()
self.CauteryToNeedle.SetName("CauteryToNeedle")
slicer.mrmlScene.AddNode(self.CauteryToNeedle)
# Create transforms that will be updated through OpenIGTLink
self.cauteryToReference = slicer.util.getNode('CauteryToReference')
if not self.cauteryToReference:
self.cauteryToReference = slicer.vtkMRMLLinearTransformNode()
self.cauteryToReference.SetName("CauteryToReference")
slicer.mrmlScene.AddNode(self.cauteryToReference)
self.needleToReference = slicer.util.getNode('NeedleToReference')
if not self.needleToReference:
self.needleToReference = slicer.vtkMRMLLinearTransformNode()
self.needleToReference.SetName("NeedleToReference")
slicer.mrmlScene.AddNode(self.needleToReference)
# 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')
self.cauteryModel_CauteryTip = slicer.util.getNode('CauteryModel')
if not self.cauteryModel_CauteryTip:
if (self.parameterNode.GetParameter('TestMode') == 'True'):
moduleDirectoryPath = slicer.modules.lumpnav.path.replace(
'LumpNav.py', '')
slicer.util.loadModel(
qt.QDir.toNativeSeparators(
moduleDirectoryPath +
'../../../models/temporary/cautery.stl'))
self.cauteryModel_CauteryTip = slicer.util.getNode(
pattern="cautery")
else:
slicer.modules.createmodels.logic().CreateNeedle(
100, 1.0, 2.5, 0)
self.cauteryModel_CauteryTip = slicer.util.getNode(
pattern="NeedleModel")
self.cauteryModel_CauteryTip.GetDisplayNode().SetColor(
1.0, 1.0, 0)
self.cauteryModel_CauteryTip.SetName("CauteryModel")
self.needleModel_NeedleTip = slicer.util.getNode('NeedleModel')
if not self.needleModel_NeedleTip:
slicer.modules.createmodels.logic().CreateNeedle(80, 1.0, 2.5, 0)
self.needleModel_NeedleTip = slicer.util.getNode(
pattern="NeedleModel")
self.needleModel_NeedleTip.GetDisplayNode().SetColor(
0.333333, 1.0, 1.0)
self.needleModel_NeedleTip.SetName("NeedleModel")
self.needleModel_NeedleTip.GetDisplayNode(
).SliceIntersectionVisibilityOn()
# Create surface from point set
logging.debug('Create surface from point set')
self.tumorModel_Needle = slicer.util.getNode('TumorModel')
if not self.tumorModel_Needle:
self.tumorModel_Needle = slicer.vtkMRMLModelNode()
self.tumorModel_Needle.SetName("TumorModel")
sphereSource = vtk.vtkSphereSource()
sphereSource.SetRadius(0.001)
self.tumorModel_Needle.SetPolyDataConnection(
sphereSource.GetOutputPort())
slicer.mrmlScene.AddNode(self.tumorModel_Needle)
# Add display node
modelDisplayNode = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode.SetColor(0, 1, 0) # Green
modelDisplayNode.BackfaceCullingOff()
modelDisplayNode.SliceIntersectionVisibilityOn()
modelDisplayNode.SetSliceIntersectionThickness(4)
modelDisplayNode.SetOpacity(0.3) # Between 0-1, 1 being opaque
slicer.mrmlScene.AddNode(modelDisplayNode)
self.tumorModel_Needle.SetAndObserveDisplayNodeID(
modelDisplayNode.GetID())
tumorMarkups_Needle = slicer.util.getNode('T')
if not tumorMarkups_Needle:
tumorMarkups_Needle = slicer.vtkMRMLMarkupsFiducialNode()
tumorMarkups_Needle.SetName("T")
slicer.mrmlScene.AddNode(tumorMarkups_Needle)
tumorMarkups_Needle.CreateDefaultDisplayNodes()
tumorMarkups_Needle.GetDisplayNode().SetTextScale(0)
self.setAndObserveTumorMarkupsNode(tumorMarkups_Needle)
# Set up breach warning node
logging.debug('Set up breach warning')
self.breachWarningNode = slicer.util.getNode('LumpNavBreachWarning')
if not self.breachWarningNode:
self.breachWarningNode = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLBreachWarningNode')
self.breachWarningNode.SetName("LumpNavBreachWarning")
slicer.mrmlScene.AddNode(self.breachWarningNode)
self.breachWarningNode.SetPlayWarningSound(True)
self.breachWarningNode.SetWarningColor(1, 0, 0)
self.breachWarningNode.SetOriginalColor(
self.tumorModel_Needle.GetDisplayNode().GetColor())
self.breachWarningNode.SetAndObserveToolTransformNodeId(
self.cauteryTipToCautery.GetID())
self.breachWarningNode.SetAndObserveWatchedModelNodeID(
self.tumorModel_Needle.GetID())
# Set up breach warning light
import BreachWarningLight
logging.debug('Set up breach warning light')
self.breachWarningLightLogic = BreachWarningLight.BreachWarningLightLogic(
)
self.breachWarningLightLogic.setMarginSizeMm(
float(
self.parameterNode.GetParameter(
'BreachWarningLightMarginSizeMm')))
if (self.parameterNode.GetParameter('EnableBreachWarningLight') ==
'True'):
logging.debug("BreachWarningLight: active")
self.breachWarningLightLogic.startLightFeedback(
self.breachWarningNode, self.connectorNode)
else:
logging.debug("BreachWarningLight: shutdown")
self.breachWarningLightLogic.shutdownLight(self.connectorNode)
# Build transform tree
logging.debug('Set up transform tree')
self.cauteryToReference.SetAndObserveTransformNodeID(
self.ReferenceToRas.GetID())
self.cauteryCameraToCautery.SetAndObserveTransformNodeID(
self.cauteryToReference.GetID())
self.cauteryTipToCautery.SetAndObserveTransformNodeID(
self.cauteryToReference.GetID())
self.cauteryModelToCauteryTip.SetAndObserveTransformNodeID(
self.cauteryTipToCautery.GetID())
self.needleToReference.SetAndObserveTransformNodeID(
self.ReferenceToRas.GetID())
self.needleTipToNeedle.SetAndObserveTransformNodeID(
self.needleToReference.GetID())
self.needleModelToNeedleTip.SetAndObserveTransformNodeID(
self.needleTipToNeedle.GetID())
self.cauteryModel_CauteryTip.SetAndObserveTransformNodeID(
self.cauteryModelToCauteryTip.GetID())
self.needleModel_NeedleTip.SetAndObserveTransformNodeID(
self.needleModelToNeedleTip.GetID())
self.tumorModel_Needle.SetAndObserveTransformNodeID(
self.needleToReference.GetID())
self.tumorMarkups_Needle.SetAndObserveTransformNodeID(
self.needleToReference.GetID())
# self.liveUltrasoundNode_Reference.SetAndObserveTransformNodeID(self.ReferenceToRas.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 transform(self, cmd):
if not hasattr(self, 'p'):
self.p = numpy.zeros(3)
self.dpdt = numpy.zeros(3)
self.d2pdt2 = numpy.zeros(3)
self.o = numpy.zeros(3)
self.dodt = numpy.zeros(3)
self.d2odt2 = numpy.zeros(3)
p = urlparse.urlparse(cmd)
q = urlparse.parse_qs(p.query)
self.logMessage(q)
dt = float(q['interval'][0])
self.d2pdt2 = 1000 * numpy.array(
[float(q['x'][0]),
float(q['y'][0]),
float(q['z'][0])])
if not hasattr(self, 'g0'):
self.g0 = self.d2pdt2
self.d2pdt2 = self.d2pdt2 - self.g0
self.dpdt = self.dpdt + dt * self.d2pdt2
self.p = self.p + dt * self.dpdt
# TODO: integrate rotations
if not hasattr(self, "idevice"):
""" set up the mrml parts or use existing """
nodes = slicer.mrmlScene.GetNodesByName('idevice')
if nodes.GetNumberOfItems() > 0:
self.idevice = nodes.GetItemAsObject(0)
nodes = slicer.mrmlScene.GetNodesByName('tracker')
self.tracker = nodes.GetItemAsObject(0)
else:
# idevice cursor
self.cube = vtk.vtkCubeSource()
self.cube.SetXLength(30)
self.cube.SetYLength(70)
self.cube.SetZLength(5)
self.cube.Update()
# display node
self.modelDisplay = slicer.vtkMRMLModelDisplayNode()
self.modelDisplay.SetColor(1, 1, 0) # yellow
slicer.mrmlScene.AddNode(self.modelDisplay)
self.modelDisplay.SetPolyData(self.cube.GetOutput())
# Create model node
self.idevice = slicer.vtkMRMLModelNode()
self.idevice.SetScene(slicer.mrmlScene)
self.idevice.SetName("idevice")
self.idevice.SetAndObservePolyData(self.cube.GetOutput())
self.idevice.SetAndObserveDisplayNodeID(
self.modelDisplay.GetID())
slicer.mrmlScene.AddNode(self.idevice)
# tracker
self.tracker = slicer.vtkMRMLLinearTransformNode()
self.tracker.SetName('tracker')
slicer.mrmlScene.AddNode(self.tracker)
self.idevice.SetAndObserveTransformNodeID(self.tracker.GetID())
m = self.tracker.GetMatrixTransformToParent()
m.Identity()
up = numpy.zeros(3)
up[2] = 1
d = self.d2pdt2
dd = d / numpy.sqrt(numpy.dot(d, d))
xx = numpy.cross(dd, up)
yy = numpy.cross(dd, xx)
for row in xrange(3):
m.SetElement(row, 0, dd[row])
m.SetElement(row, 1, xx[row])
m.SetElement(row, 2, yy[row])
#m.SetElement(row,3, self.p[row])
return ("got it")
def associateTransformations(self):
# # The nodes StylusTipToReference and ProbeToReference are added
stylusTipToTrackerNode = slicer.util.getNode("StylusTipToTracker")
if stylusTipToTrackerNode == None:
stylusTipToTrackerNode = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(stylusTipToTrackerNode)
stylusTipToTrackerNode.SetName("StylusTipToTracker")
# probeToTrackerNode = slicer.util.getNode("ProbeToTracker")
# if probeToTrackerNode == None:
# probeToTrackerNode = slicer.vtkMRMLLinearTransformNode()
# slicer.mrmlScene.AddNode(probeToTrackerNode)
# probeToTrackerNode.SetName("ProbeToTracker")
trackerToProbeNode = slicer.util.getNode("TrackerToProbe")
if trackerToProbeNode == None:
trackerToProbeNode = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(trackerToProbeNode)
trackerToProbeNode.SetName("TrackerToProbe")
stylusTipToProbeNode = slicer.util.getNode("StylusTipToProbe")
if stylusTipToProbeNode == None:
stylusTipToProbeNode = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(stylusTipToProbeNode)
stylusTipToProbeNode.SetName("StylusTipToProbe")
imageToProbeNode = slicer.util.getNode("ImageToProbe")
if imageToProbeNode == None:
imageToProbeNode = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(imageToProbeNode)
imageToProbeNode.SetName("ImageToProbe")
#imageNode = slicer.util.getNode("Image_Image")
# referenceToRASNode=slicer.util.getNode("ReferenceToRAS")
# imageReferenceNode=slicer.util.getNode("Image_Reference")
#imageNode.SetAndObserveTransformNodeID(imageToProbeNode.GetID())
# stylusTipToProbeNode.SetAndObserveTransformNodeID(probeToTrackerNode.GetID())
stylusTipToTrackerNode.SetAndObserveTransformNodeID(trackerToProbeNode.GetID())
self.stylusModelNode = slicer.util.getNode("Stylus_Example")
if self.stylusModelNode == None:
# Add the stylus model
modelsModule = slicer.modules.models
modelsModuleLogic = modelsModule.logic()
modelsModuleLogic.SetMRMLScene(slicer.mrmlScene)
path = slicer.modules.stylusbasedusprobecalibration.path
modulePath = os.path.dirname(path)
stylusModelFile = os.path.join(modulePath, "models/Stylus_Example.stl")
modelsModuleLogic.AddModel(stylusModelFile)
self.stylusModelNode = slicer.util.getNode("Stylus_Example")
self.stylusModelNode.RemoveAllNodeReferenceIDs("transform")
# # Associate the model of the stylus with the stylus tip transforms
stylusTipModelToStylusTipTransform = slicer.util.getNode("StylusTipModelToStylusTip")
if stylusTipModelToStylusTipTransform == None:
stylusTipModelToStylusTipTransform = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(stylusTipModelToStylusTipTransform)
stylusTipModelToStylusTipTransform.SetName("StylusTipModelToStylusTip")
matrix = vtk.vtkMatrix4x4()
matrix.SetElement(0, 3, -210)
stylusTipModelToStylusTipTransform.SetAndObserveMatrixTransformToParent(matrix)
stylusTipModelToStylusTipTransform.SetAndObserveTransformNodeID(stylusTipToTrackerNode.GetID())
self.stylusModelNode.SetAndObserveTransformNodeID(stylusTipModelToStylusTipTransform.GetID())
def setupScene(self): # applet specific
logging.debug('setupScene')
# Add a Qt timer, that fires every X ms (16.7ms = 60 FPS, 33ms = 30FPS)
# Connect the timeout() signal of the qt timer to a function in this class that you will write
self.timer.connect('timeout()', self.onTimerTimeout)
self.timer.start(16.7)
# ReferenceToRas is needed for ultrasound initialization, so we need to
# set it up before calling Guidelet.setupScene().
self.referenceToRasTransform = slicer.util.getNode('ReferenceToRas')
if not self.referenceToRasTransform:
self.referenceToRasTransform = slicer.vtkMRMLLinearTransformNode()
self.referenceToRasTransform.SetName("ReferenceToRas")
m = self.logic.readTransformFromSettings('ReferenceToRas',
self.configurationName)
if m is None:
# Create identity matrix
m = self.logic.createMatrixFromString(
'1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 0.0 0 0 0 1')
self.referenceToRasTransform.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.referenceToRasTransform)
Guidelet.setupScene(self)
logging.debug('Create transforms')
# Coordinate system definitions: https://app.assembla.com/spaces/slicerigt/wiki/Coordinate_Systems
self.needleTipToNeedleTransform = slicer.util.getNode(
'NeedleTipToNeedle')
if not self.needleTipToNeedleTransform:
self.needleTipToNeedleTransform = slicer.vtkMRMLLinearTransformNode(
)
self.needleTipToNeedleTransform.SetName("NeedleTipToNeedle")
m = self.logic.readTransformFromSettings('NeedleTipToNeedle',
self.configurationName)
if m:
self.needleTipToNeedleTransform.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.needleTipToNeedleTransform)
self.needleModelToNeedleTipTransform = slicer.util.getNode(
'NeedleModelToNeedleTip')
if not self.needleModelToNeedleTipTransform:
self.needleModelToNeedleTipTransform = slicer.vtkMRMLLinearTransformNode(
)
self.needleModelToNeedleTipTransform.SetName(
"NeedleModelToNeedleTip")
m = self.logic.readTransformFromSettings('NeedleModelToNeedleTip',
self.configurationName)
if m:
self.needleModelToNeedleTipTransform.SetMatrixTransformToParent(
m)
slicer.mrmlScene.AddNode(self.needleModelToNeedleTipTransform)
self.trajModelToNeedleTipTransform = slicer.util.getNode(
'TrajModelToNeedleTip')
if not self.trajModelToNeedleTipTransform:
self.trajModelToNeedleTipTransform = slicer.vtkMRMLLinearTransformNode(
)
self.trajModelToNeedleTipTransform.SetName("TrajModelToNeedleTip")
m = self.logic.readTransformFromSettings('TrajModelToNeedleTip',
self.configurationName)
if m:
self.trajModelToNeedleTipTransform.SetMatrixTransformToParent(
m)
slicer.mrmlScene.AddNode(self.trajModelToNeedleTipTransform)
# Create transforms that will be updated through OpenIGTLink
self.needleToReferenceTransform = slicer.util.getNode(
'NeedleToReference')
if not self.needleToReferenceTransform:
self.needleToReferenceTransform = slicer.vtkMRMLLinearTransformNode(
)
self.needleToReferenceTransform.SetName("NeedleToReference")
slicer.mrmlScene.AddNode(self.needleToReferenceTransform)
# Models
logging.debug('Create models')
self.needleWithTipModel = slicer.util.getNode('NeedleModel')
if not self.needleWithTipModel:
# length, radius, tipradius, bool markers, vtkMRMLModelNode(1 or 0: creates a ring close to tip)
# length, radius, tipradius, bool markers, vtkMRMLModelNode(1 or 0: creates a ring close to tip)
slicer.modules.createmodels.logic().CreateNeedle(
65, 1.0, self.needleModelTipRadius, 0)
self.needleWithTipModel = slicer.util.getNode(
pattern="NeedleModel")
self.needleWithTipModel.GetDisplayNode().SetColor(0.08, 0.84,
0.1) # (1,0,1)#
self.needleWithTipModel.SetName("NeedleModel")
self.needleWithTipModel.GetDisplayNode(
).SliceIntersectionVisibilityOn()
self.trajectoryModel_needleModel = slicer.util.getNode(
'TrajectoryModel')
cylinderLength = 100
if not self.trajectoryModel_needleModel:
self.trajectoryModel_needleModel = slicer.modules.createmodels.logic(
).CreateCylinder(cylinderLength, 0.1) # 0.5mm tall, 4mm radius
self.trajectoryModel_needleModel.SetName('TrajectoryModel')
self.trajectoryModel_needleModel.GetDisplayNode().SetColor(
0.69, 0.93, 0.93) # (1, 1, 0.5)
# here, we want to bake in a transform to move the origin of the cylinder to one of the ends (instead
# of being in the middle)
transformFilter = vtk.vtkTransformPolyDataFilter()
transformFilter.SetInputConnection(
self.trajectoryModel_needleModel.GetPolyDataConnection())
trans = vtk.vtkTransform()
trans.Translate(0, 0, cylinderLength / 2)
transformFilter.SetTransform(trans)
transformFilter.Update()
self.trajectoryModel_needleModel.SetPolyDataConnection(
transformFilter.GetOutputPort())
# number of balls = cylinderLength / distance between markers (may be -1, depending on ball at tip (giggggity))
number_spheres = cylinderLength / 10
for i in range(0, number_spheres):
# create sphere model if non-existent
model = slicer.util.getNode('DistanceMarkerModel_' + str(i))
if model is None:
model = slicer.modules.createmodels.logic().CreateSphere(0.7)
model.SetName('DistanceMarkerModel_' + str(i))
R = 1.0
G = 1.0
B = 0.1 + i * (0.7 / (number_spheres - 1.0)
) # yellow spectrum ranging from 0.1-0.7
model.GetDisplayNode().SetColor(R, G, B)
# create transform node, apply z translation i*distanceBetweenMarkers
node = slicer.util.getNode('DistanceMarkerTransform_' + str(i))
if node is None:
node = slicer.vtkMRMLLinearTransformNode()
node.SetName('DistanceMarkerTransform_' + str(i))
slicer.mrmlScene.AddNode(node)
m = self.logic.createMatrixFromString('1.0 0.0 0.0 0.0 '
'0.0 1.0 0.0 0.0 '
'0.0 0.0 1.0 ' +
str((i + 1) * 10.0) + ' '
'0.0 0.0 0.0 1.0')
node.SetMatrixTransformToParent(m)
model.SetAndObserveTransformNodeID(node.GetID())
node.SetAndObserveTransformNodeID(
self.needleTipToNeedleTransform.GetID())
# Setup the needle tip hierarchy
self.needleToReferenceTransform.SetAndObserveTransformNodeID(
self.referenceToRasTransform.GetID())
self.needleTipToNeedleTransform.SetAndObserveTransformNodeID(
self.needleToReferenceTransform.GetID())
self.needleWithTipModel.SetAndObserveTransformNodeID(
self.needleTipToNeedleTransform.GetID())
# Build transform tree
logging.debug('Set up transform tree')
self.needleModelToNeedleTipTransform.SetAndObserveTransformNodeID(
self.needleTipToNeedleTransform.GetID())
self.needleWithTipModel.SetAndObserveTransformNodeID(
self.needleModelToNeedleTipTransform.GetID())
# self.liveUltrasoundNode_Reference.SetAndObserveTransformNodeID(self.referenceToRasTransform.GetID()) # always commented out
# self.needleToReferenceTransform.SetAndObserveTransformNodeID(self.referenceToRasTransform.GetID())
# self.needleTipToNeedleTransform.SetAndObserveTransformNodeID(self.needleToReferenceTransform.GetID())
# self.needleModelToNeedleTipTransform.SetAndObserveTransformNodeID(self.needleTipToNeedleTransform.GetID())
self.trajModelToNeedleTipTransform.SetAndObserveTransformNodeID(
self.needleTipToNeedleTransform.GetID())
self.trajectoryModel_needleModel.SetAndObserveTransformNodeID(
self.trajModelToNeedleTipTransform.GetID())
def onEntry(self, comingFrom, transitionType):
super(DefineROIStep, self).onEntry(comingFrom, transitionType)
# setup the interface
lm = slicer.app.layoutManager()
lm.setLayout(3)
#create progress bar dialog
self.progress = qt.QProgressDialog(slicer.util.mainWindow())
self.progress.minimumDuration = 0
self.progress.show()
self.progress.setValue(0)
self.progress.setMaximum(0)
self.progress.setCancelButton(0)
self.progress.setMinimumWidth(500)
self.progress.setWindowModality(2)
self.progress.setLabelText('Generating Volume Rendering...')
slicer.app.processEvents(qt.QEventLoop.ExcludeUserInputEvents)
self.progress.repaint()
#read scalar volume node ID from previous step
pNode = self.parameterNode()
baselineVolume = Helper.getNodeByID(
pNode.GetParameter('baselineVolumeID'))
self.__baselineVolume = baselineVolume
#if ROI was created previously, get its transformation matrix and update current ROI
roiTransformID = pNode.GetParameter('roiTransformID')
roiTransformNode = None
if roiTransformID != '':
roiTransformNode = Helper.getNodeByID(roiTransformID)
else:
roiTransformNode = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(roiTransformNode)
pNode.SetParameter('roiTransformID', roiTransformNode.GetID())
dm = vtk.vtkMatrix4x4()
baselineVolume.GetIJKToRASDirectionMatrix(dm)
dm.SetElement(0, 3, 0)
dm.SetElement(1, 3, 0)
dm.SetElement(2, 3, 0)
dm.SetElement(0, 0, abs(dm.GetElement(0, 0)))
dm.SetElement(1, 1, abs(dm.GetElement(1, 1)))
dm.SetElement(2, 2, abs(dm.GetElement(2, 2)))
roiTransformNode.SetAndObserveMatrixTransformToParent(dm)
Helper.SetBgFgVolumes(pNode.GetParameter('baselineVolumeID'))
Helper.SetLabelVolume(None)
# use this transform node to align ROI with the axes of the baseline
# volume
roiTfmNodeID = pNode.GetParameter('roiTransformID')
if roiTfmNodeID != '':
self.__roiTransformNode = Helper.getNodeByID(roiTfmNodeID)
else:
Helper.Error(
'Internal error! Error code CT-S2-NRT, please report!')
# get the roiNode from parameters node, if it exists, and initialize the
# GUI
self.updateWidgetFromParameterNode(pNode)
# start VR
if self.__roi != None:
self.__roi.SetDisplayVisibility(1)
self.InitVRDisplayNode()
#close progress bar
self.progress.setValue(2)
self.progress.repaint()
slicer.app.processEvents(qt.QEventLoop.ExcludeUserInputEvents)
self.progress.close()
self.progress = None
#pNode.SetParameter('currentStep', self.stepid)
qt.QTimer.singleShot(0, self.killButton)
def onApplyCargar(self):
self.nombre = self.seleccionDeEstudianteComboBox.currentText
con = mysql.connector.connect(user="******",
password="******",
host="127.0.0.1",
database="basedatos_simulador_ttp")
cursor = con.cursor()
estudiantes = []
cursor.execute("SELECT * FROM estudiantes")
rows = cursor.fetchall()
for row in rows:
estudiantes.append(row)
for i in range(0, len(estudiantes)):
if (self.nombre == estudiantes[i][1]):
self.idEstudiante = estudiantes[i][0]
self.tornillo_1 = str(estudiantes[i][3])
self.tornillo_2 = str(estudiantes[i][4])
self.tranformadaTornillo1 = estudiantes[i][5]
self.tranformadaTornillo2 = estudiantes[i][6]
break
nombreTornillo1 = self.tornillo_1
nombreTornillo1 = nombreTornillo1.split('.')
nombreTornillo1 = nombreTornillo1[0]
nombreTornillo2 = self.tornillo_2
nombreTornillo2 = nombreTornillo2.split('.')
nombreTornillo2 = nombreTornillo2[0]
x = 0
c = []
for i in self.tranformadaTornillo1:
if (i == '[' or i == ']' or i == ',' or i == '' or i == "'"):
pass
else:
c.append(self.tranformadaTornillo1[x])
x = x + 1
d = ''.join(c)
d.split(' ')
self.tranformadaTornillo1 = [float(x) for x in d.split()]
mt1 = vtk.vtkMatrix4x4()
mt1.SetElement(0, 0, float(self.tranformadaTornillo1[0]))
mt1.SetElement(0, 1, float(self.tranformadaTornillo1[1]))
mt1.SetElement(0, 2, float(self.tranformadaTornillo1[2]))
mt1.SetElement(0, 3, float(self.tranformadaTornillo1[3]))
mt1.SetElement(1, 0, float(self.tranformadaTornillo1[4]))
mt1.SetElement(1, 1, float(self.tranformadaTornillo1[5]))
mt1.SetElement(1, 2, float(self.tranformadaTornillo1[6]))
mt1.SetElement(1, 3, float(self.tranformadaTornillo1[7]))
mt1.SetElement(2, 0, float(self.tranformadaTornillo1[8]))
mt1.SetElement(2, 1, float(self.tranformadaTornillo1[9]))
mt1.SetElement(2, 2, float(self.tranformadaTornillo1[10]))
mt1.SetElement(2, 3, float(self.tranformadaTornillo1[11]))
mt1.SetElement(3, 0, 0)
mt1.SetElement(3, 1, 0)
mt1.SetElement(3, 2, 0)
mt1.SetElement(3, 3, 1)
x = 0
c = []
for i in self.tranformadaTornillo2:
if (i == '[' or i == ']' or i == ',' or i == '' or i == "'"):
pass
else:
c.append(self.tranformadaTornillo2[x])
x = x + 1
d = ''.join(c)
d.split(' ')
self.tranformadaTornillo2 = [float(x) for x in d.split()]
mt2 = vtk.vtkMatrix4x4()
mt2.SetElement(0, 0, float(self.tranformadaTornillo2[0]))
mt2.SetElement(0, 1, float(self.tranformadaTornillo2[1]))
mt2.SetElement(0, 2, float(self.tranformadaTornillo2[2]))
mt2.SetElement(0, 3, float(self.tranformadaTornillo2[3]))
mt2.SetElement(1, 0, float(self.tranformadaTornillo2[4]))
mt2.SetElement(1, 1, float(self.tranformadaTornillo2[5]))
mt2.SetElement(1, 2, float(self.tranformadaTornillo2[6]))
mt2.SetElement(1, 3, float(self.tranformadaTornillo2[7]))
mt2.SetElement(2, 0, float(self.tranformadaTornillo2[8]))
mt2.SetElement(2, 1, float(self.tranformadaTornillo2[9]))
mt2.SetElement(2, 2, float(self.tranformadaTornillo2[10]))
mt2.SetElement(2, 3, float(self.tranformadaTornillo2[11]))
mt2.SetElement(3, 0, 0)
mt2.SetElement(3, 1, 0)
mt2.SetElement(3, 2, 0)
mt2.SetElement(3, 3, 1)
moduleName = 'simuladorTornillosPediculares'
scriptedModulesPath = eval(
'slicer.modules.%s.path' %
moduleName.lower()) # devuelve la ruta del .py
scriptedModulesPath = os.path.dirname(
scriptedModulesPath) # lleva a la carpeta del modulo
path2 = os.path.join(scriptedModulesPath,
'simuladorTornillosPedicularesWizard', 'Modelos',
'Lumbar 2.5 B31s - 4/4 Lumbar 2.5 B31s.nrrd')
path1 = os.path.join(scriptedModulesPath,
'simuladorTornillosPedicularesWizard', 'Modelos',
'nucleos.stl')
path3 = os.path.join(scriptedModulesPath,
'simuladorTornillosPedicularesWizard', 'Modelos',
'stlcolumna.stl')
#path1='C:\Users\Camilo_Q\Documents\GitHub\simuladorTornillosPediculares\simuladorTornillosPedicularesWizard\Modelos/stlcolumna.stl' #Se obtiene direccion de la unbicación del tornillo
#path2='C:\Users\Camilo_Q\Documents\GitHub\simuladorTornillosPediculares\simuladorTornillosPedicularesWizard\Modelos\Lumbar 2.5 B31s - 4/4 Lumbar 2.5 B31s.nrrd'
#path3='C:\Users\Camilo_Q\Documents\GitHub\simuladorTornillosPediculares\simuladorTornillosPedicularesWizard\Modelos/nucleos.stl'
columna = slicer.util.getNode(
'stlcolumna') # Se obtiene el nodo del objeto en escena
if (columna == None):
slicer.util.loadModel(path1)
slicer.util.loadModel(path3)
slicer.util.loadVolume(path2)
columna = slicer.util.getNode('stlcolumna')
nucleo = slicer.util.getNode('nucleos')
nucleoModelDisplayNode = nucleo.GetDisplayNode()
nucleoModelDisplayNode.SetColor(0.729411, 0.7529411, 0.8745098)
nucleoModelDisplayNode.SetAmbient(0.10)
nucleoModelDisplayNode.SetDiffuse(0.90)
nucleoModelDisplayNode.SetSpecular(0.20)
nucleoModelDisplayNode.SetPower(10)
nucleoModelDisplayNode.SetSliceIntersectionVisibility(1)
columnaModelDisplayNode = columna.GetDisplayNode()
columnaModelDisplayNode.SetColor(
0.9451, 0.8392, 0.5686) #Colores parametrizados sobre 255
columnaModelDisplayNode.SetSliceIntersectionVisibility(1)
columnaModelDisplayNode.SetAmbient(0.33)
columnaModelDisplayNode.SetDiffuse(0.78)
columnaModelDisplayNode.SetSpecular(0.13)
columnaModelDisplayNode.SetPower(15.5)
self.layoutManager = slicer.app.layoutManager()
threeDWidget = self.layoutManager.threeDWidget(0)
self.threeDView = threeDWidget.threeDView()
self.threeDView.resetFocalPoint()
try:
slicer.mrmlScene.RemoveNode(self.tornillo1)
except:
pass
try:
slicer.mrmlScene.RemoveNode(self.tornillo2)
except:
pass
a = slicer.util.getNode('Transformada Tornillo 1')
try:
slicer.mrmlScene.RemoveNode(a)
except:
pass
a = slicer.util.getNode('Transformada Tornillo 2')
try:
slicer.mrmlScene.RemoveNode(a)
except:
pass
self.pathTornillos = os.path.join(
scriptedModulesPath, 'simuladorTornillosPedicularesWizard',
'Modelos', 'Tornillos', '%s' % self.tornillo_1)
#self.pathTornillos = 'C:\Users\Camilo_Q\Documents\GitHub\simuladorTornillosPediculares\simuladorTornillosPedicularesWizard\Modelos\Tornillos/'+self.tornillo_1
slicer.util.loadModel(self.pathTornillos)
self.pathTornillos = os.path.join(
scriptedModulesPath, 'simuladorTornillosPedicularesWizard',
'Modelos', 'Tornillos', '%s' % self.tornillo_2)
#self.pathTornillos = 'C:\Users\Camilo_Q\Documents\GitHub\simuladorTornillosPediculares\simuladorTornillosPedicularesWizard\Modelos\Tornillos/'+self.tornillo_2
slicer.util.loadModel(self.pathTornillos)
for i in range(0, 20):
if self.contadorTornillos1 == 1:
self.tornillo1 = slicer.util.getNode(
str(nombreTornillo1) + "_" + str(i))
if self.contadorTornillos1 == 0:
self.tornillo1 = slicer.util.getNode(str(nombreTornillo1))
self.contadorTornillos1 = 1
if self.tornillo1 != None:
self.contadorTornillos1 = 0
self.tornillo1.SetName("Tornillo_1")
break
for i in range(0, 20):
if self.contadorTornillos2 == 1:
self.tornillo2 = slicer.util.getNode(
str(nombreTornillo2) + "_" + str(i))
if self.contadorTornillos2 == 0:
self.tornillo2 = slicer.util.getNode(str(nombreTornillo2))
self.contadorTornillos2 = 1
if self.tornillo2 != None:
self.contadorTornillos2 = 0
self.tornillo2.SetName("Tornillo_2")
break
tornilloModelDisplayNode = self.tornillo1.GetDisplayNode()
tornilloModelDisplayNode.SetColor(0.847059, 0.847059, 0.847059)
tornilloModelDisplayNode.SetAmbient(0.10)
tornilloModelDisplayNode.SetDiffuse(0.6)
tornilloModelDisplayNode.SetSpecular(1)
tornilloModelDisplayNode.SetPower(40)
tornilloModelDisplayNode.SetSliceIntersectionVisibility(1)
self.transformadaTornillo1 = slicer.vtkMRMLLinearTransformNode(
) #Se crea una transformada lineal
self.transformadaTornillo1.SetName(
'Transformada Tornillo 1') #Se asigna nombre a la transformada
slicer.mrmlScene.AddNode(self.transformadaTornillo1) #
self.tornillo1.SetAndObserveTransformNodeID(
self.transformadaTornillo1.GetID())
self.transformadaTornillo1.SetAndObserveMatrixTransformToParent(mt1)
tornilloModelDisplayNode = self.tornillo2.GetDisplayNode()
tornilloModelDisplayNode.SetColor(0.847059, 0.847059, 0.847059)
tornilloModelDisplayNode.SetAmbient(0.10)
tornilloModelDisplayNode.SetDiffuse(0.6)
tornilloModelDisplayNode.SetSpecular(1)
tornilloModelDisplayNode.SetPower(40)
tornilloModelDisplayNode.SetSliceIntersectionVisibility(1)
self.transformadaTornillo2 = slicer.vtkMRMLLinearTransformNode(
) #Se crea una transformada lineal
self.transformadaTornillo2.SetName(
'Transformada Tornillo 2') #Se asigna nombre a la transformada
slicer.mrmlScene.AddNode(self.transformadaTornillo2) #
self.tornillo2.SetAndObserveTransformNodeID(
self.transformadaTornillo2.GetID())
self.transformadaTornillo2.SetAndObserveMatrixTransformToParent(mt2)
def onHelloWorldButtonClicked(self):
scene = slicer.mrmlScene
inputModel = self.inputSelector.currentNode()
bounds = [0, 0, 0, 0, 0, 0]
inputModel.GetBounds(bounds)
print('Model Name is:')
print(inputModel.GetName())
X = bounds[1] - bounds[0]
Y = bounds[3] - bounds[2]
Z = bounds[5] - bounds[4]
mid = (bounds[0] + X / 2, bounds[2] + Y / 2, bounds[4] + Z / 2)
X_thick = .1 #TODO resolution input
Y_thick = .1 #TODO resolution input
Z_thick = .1 #TODO resolution input
z_slices = int(math.ceil(Z / Z_thick))
y_slices = int(math.ceil(Y / Y_thick))
x_slices = int(math.ceil(X / X_thick))
x_thick = X / x_slices
y_thick = Y / y_slices
z_thick = Z / z_slices
print('number of slices')
print((x_slices, y_slices, z_slices))
print('midpoint')
print(mid)
#TODO Bounding box calculation
imageSize = [x_slices, y_slices, z_slices]
imageSpacing = [x_thick, y_thick, z_thick]
voxelType = vtk.VTK_UNSIGNED_CHAR
imageData = vtk.vtkImageData()
imageData.SetDimensions(imageSize)
imageData.AllocateScalars(voxelType, 1)
thresholder = vtk.vtkImageThreshold()
thresholder.SetInputData(imageData)
thresholder.SetInValue(1)
thresholder.SetOutValue(1)
# Create volume node
volumeNode = slicer.vtkMRMLScalarVolumeNode()
volumeNode.SetSpacing(imageSpacing)
volumeNode.SetImageDataConnection(thresholder.GetOutputPort())
# Add volume to scene
slicer.mrmlScene.AddNode(volumeNode)
displayNode = slicer.vtkMRMLScalarVolumeDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
colorNode = slicer.util.getNode('Grey')
displayNode.SetAndObserveColorNodeID(colorNode.GetID())
volumeNode.SetAndObserveDisplayNodeID(displayNode.GetID())
volumeNode.CreateDefaultStorageNode()
#Transform the Volume to Fit Around the Model
transform = slicer.vtkMRMLLinearTransformNode()
scene.AddNode(transform)
volumeNode.SetAndObserveTransformNodeID(transform.GetID())
vTransform = vtk.vtkTransform()
vTransform.Translate(
(-X / 2 + mid[0], -Y / 2 + mid[1], -Z / 2 + mid[2]))
transform.SetAndObserveMatrixTransformToParent(vTransform.GetMatrix())
#Create a segmentation Node
segmentationNode = slicer.vtkMRMLSegmentationNode()
slicer.mrmlScene.AddNode(segmentationNode)
segmentationNode.CreateDefaultDisplayNodes()
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(
volumeNode)
#Add the model as a segmentation
#sphereSource = vtk.vtkSphereSource()
#sphereSource.SetRadius(10)
#sphereSource.SetCenter(6,30,28)
#sphereSource.Update()
#segmentationNode.AddSegmentFromClosedSurfaceRepresentation(sphereSource.GetOutput(), "Test")
segmentID = segmentationNode.GetSegmentation().GenerateUniqueSegmentID(
"Test")
segmentationNode.AddSegmentFromClosedSurfaceRepresentation(
inputModel.GetPolyData(), segmentID)
#TODO, Unique ID
segmentationNode.SetMasterRepresentationToBinaryLabelmap()
modelLabelMap = segmentationNode.GetBinaryLabelmapRepresentation(
segmentID) #TODO Unique ID
segmentationNode.SetMasterRepresentationToBinaryLabelmap()
shape = list(modelLabelMap.GetDimensions())
shape.reverse() #why reverse?
labelArray = vtk.util.numpy_support.vtk_to_numpy(
modelLabelMap.GetPointData().GetScalars()).reshape(shape)
for n in range(1, shape[0] - 1):
labelArray[n, :, :] = numpy.maximum(labelArray[n, :, :],
labelArray[n - 1, :, :])
outputPolyData = vtk.vtkPolyData()
slicer.vtkSlicerSegmentationsModuleLogic.GetSegmentClosedSurfaceRepresentation(
segmentationNode, segmentID, outputPolyData)
# Create model node
model = slicer.vtkMRMLModelNode()
model.SetScene(scene)
model.SetName(scene.GenerateUniqueName("Model_Undercuts_Removed"))
model.SetAndObservePolyData(outputPolyData)
# Create display node
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetColor(1, 1, 0) # yellow
modelDisplay.SetBackfaceCulling(0)
modelDisplay.SetScene(scene)
scene.AddNode(modelDisplay)
model.SetAndObserveDisplayNodeID(modelDisplay.GetID())
# Add to scene
scene.AddNode(model)
def __init__(self, path, fiducialListNode):
fids = fiducialListNode
scene = slicer.mrmlScene
points = vtk.vtkPoints()
polyData = vtk.vtkPolyData()
polyData.SetPoints(points)
lines = vtk.vtkCellArray()
polyData.SetLines(lines)
linesIDArray = lines.GetData()
linesIDArray.Reset()
linesIDArray.InsertNextTuple1(0)
polygons = vtk.vtkCellArray()
polyData.SetPolys(polygons)
idArray = polygons.GetData()
idArray.Reset()
idArray.InsertNextTuple1(0)
for point in path:
pointIndex = points.InsertNextPoint(*point)
linesIDArray.InsertNextTuple1(pointIndex)
linesIDArray.SetTuple1(0, linesIDArray.GetNumberOfTuples() - 1)
lines.SetNumberOfCells(1)
# Create model node
model = slicer.vtkMRMLModelNode()
model.SetScene(scene)
model.SetName("Path-%s" % fids.GetName())
model.SetAndObservePolyData(polyData)
# Create display node
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetColor(1, 1, 0) # yellow
modelDisplay.SetScene(scene)
scene.AddNode(modelDisplay)
model.SetAndObserveDisplayNodeID(modelDisplay.GetID())
# Add to scene
modelDisplay.SetInputPolyData(model.GetPolyData())
scene.AddNode(model)
# Camera cursor
sphere = vtk.vtkSphereSource()
sphere.Update()
# Create model node
cursor = slicer.vtkMRMLModelNode()
cursor.SetScene(scene)
cursor.SetName("Cursor-%s" % fids.GetName())
cursor.SetAndObservePolyData(sphere.GetOutput())
# Create display node
cursorModelDisplay = slicer.vtkMRMLModelDisplayNode()
cursorModelDisplay.SetColor(1, 0, 0) # red
cursorModelDisplay.SetScene(scene)
scene.AddNode(cursorModelDisplay)
cursor.SetAndObserveDisplayNodeID(cursorModelDisplay.GetID())
# Add to scene
cursorModelDisplay.SetInputPolyData(sphere.GetOutput())
scene.AddNode(cursor)
# Create transform node
transform = slicer.vtkMRMLLinearTransformNode()
transform.SetName('Transform-%s' % fids.GetName())
scene.AddNode(transform)
cursor.SetAndObserveTransformNodeID(transform.GetID())
self.transform = transform
def setupScene(self):
logging.info("UltraSound.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().
'''
if self.referenceToRas is None or (
self.referenceToRas and slicer.mrmlScene.GetNodeByID(
self.referenceToRas.GetID()) is None):
self.referenceToRas = slicer.mrmlScene.GetFirstNodeByName(
'ReferenceToRas')
if self.referenceToRas is None:
self.referenceToRas = slicer.vtkMRMLLinearTransformNode()
self.referenceToRas.SetName("ReferenceToRas")
m = self.guideletParent.logic.readTransformFromSettings(
'ReferenceToRas', self.guideletParent.configurationName)
if m is None:
m = self.guideletParent.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)
# live ultrasound
liveUltrasoundNodeName = self.guideletParent.parameterNode.GetParameter(
'LiveUltrasoundNodeName')
self.liveUltrasoundNode_Reference = slicer.mrmlScene.GetFirstNodeByName(
liveUltrasoundNodeName)
if not self.liveUltrasoundNode_Reference:
imageSpacing = [0.2, 0.2, 0.2]
# Create an empty image volume
imageData = vtk.vtkImageData()
imageData.SetDimensions(self.DEFAULT_IMAGE_SIZE)
imageData.AllocateScalars(vtk.VTK_UNSIGNED_CHAR, 1)
thresholder = vtk.vtkImageThreshold()
thresholder.SetInputData(imageData)
thresholder.SetInValue(0)
thresholder.SetOutValue(0)
# Create volume node
self.liveUltrasoundNode_Reference = slicer.vtkMRMLScalarVolumeNode(
)
self.liveUltrasoundNode_Reference.SetName(liveUltrasoundNodeName)
self.liveUltrasoundNode_Reference.SetSpacing(imageSpacing)
self.liveUltrasoundNode_Reference.SetImageDataConnection(
thresholder.GetOutputPort())
# Add volume to scene
slicer.mrmlScene.AddNode(self.liveUltrasoundNode_Reference)
displayNode = slicer.vtkMRMLScalarVolumeDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
colorNode = slicer.mrmlScene.GetFirstNodeByName('Grey')
displayNode.SetAndObserveColorNodeID(colorNode.GetID())
self.liveUltrasoundNode_Reference.SetAndObserveDisplayNodeID(
displayNode.GetID())
self.plusRemoteNode = slicer.mrmlScene.GetFirstNodeByClass(
'vtkMRMLPlusRemoteNode')
if self.plusRemoteNode is None:
self.plusRemoteNode = slicer.vtkMRMLPlusRemoteNode()
self.plusRemoteNode.SetName("PlusRemoteNode")
slicer.mrmlScene.AddNode(self.plusRemoteNode)
self.plusRemoteNode.AddObserver(
slicer.vtkMRMLPlusRemoteNode.RecordingStartedEvent,
self.recordingCommandCompleted)
self.plusRemoteNode.AddObserver(
slicer.vtkMRMLPlusRemoteNode.RecordingCompletedEvent,
self.recordingCommandCompleted)
self.plusRemoteNode.SetAndObserveOpenIGTLinkConnectorNode(
self.guideletParent.connectorNode)
self.setupResliceDriver()
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 refineLandmark(self, state):
"""Refine the specified landmark"""
# Refine landmark, or if none, do nothing
# Crop images around the fiducial
# Affine registration of the cropped images
# Transform the fiducial using the transformation
#
# No need to take into account the current transformation because landmarks are in World RAS
timing = False
if self.VerboseMode == "Verbose":
timing = True
if state.fixed == None or state.moving == None or state.fixedFiducials == None or state.movingFiducials == None or state.currentLandmarkName == None:
print "Cannot refine landmarks. Images or landmarks not selected."
return
print("Refining landmark " +
state.currentLandmarkName) + " using " + self.name
start = time.time()
volumes = (state.fixed, state.moving)
(fixedVolume, movingVolume) = volumes
slicer.mrmlScene.StartState(slicer.mrmlScene.BatchProcessState)
landmarks = state.logic.landmarksForVolumes(volumes)
cvpn = slicer.vtkMRMLCropVolumeParametersNode()
cvpn.SetInterpolationMode(1)
cvpn.SetVoxelBased(1)
fixedPoint = [
0,
] * 3
movingPoint = [
0,
] * 3
(fixedFiducial, movingFiducial) = landmarks[state.currentLandmarkName]
(fixedList, fixedIndex) = fixedFiducial
(movingList, movingIndex) = movingFiducial
# define an roi for the fixed
if timing: roiStart = time.time()
roiFixed = slicer.vtkMRMLAnnotationROINode()
slicer.mrmlScene.AddNode(roiFixed)
fixedList.GetNthFiducialPosition(fixedIndex, fixedPoint)
roiFixed.SetDisplayVisibility(0)
roiFixed.SelectableOff()
roiFixed.SetXYZ(fixedPoint)
roiFixed.SetRadiusXYZ(30, 30, 30)
# crop the fixed. note we hide the display node temporarily to avoid the automated
# window level calculation on temporary nodes created by cloning
cvpn.SetROINodeID(roiFixed.GetID())
cvpn.SetInputVolumeNodeID(fixedVolume.GetID())
fixedDisplayNode = fixedVolume.GetDisplayNode()
fixedVolume.SetAndObserveDisplayNodeID(
'This is not a valid DisplayNode ID')
if timing: roiEnd = time.time()
if timing: cropStart = time.time()
state.logic.cropLogic.Apply(cvpn)
if timing: cropEnd = time.time()
croppedFixedVolume = slicer.mrmlScene.GetNodeByID(
cvpn.GetOutputVolumeNodeID())
fixedVolume.SetAndObserveDisplayNodeID(fixedDisplayNode.GetID())
# define an roi for the moving
if timing: roi2Start = time.time()
roiMoving = slicer.vtkMRMLAnnotationROINode()
slicer.mrmlScene.AddNode(roiMoving)
movingList.GetNthFiducialPosition(movingIndex, movingPoint)
roiMoving.SetDisplayVisibility(0)
roiMoving.SelectableOff()
roiMoving.SetXYZ(movingPoint)
if self.LocalBRAINSFitMode == "Small":
roiMoving.SetRadiusXYZ(45, 45, 45)
else:
roiMoving.SetRadiusXYZ(60, 60, 60)
# crop the moving. note we hide the display node temporarily to avoid the automated
# window level calculation on temporary nodes created by cloning
cvpn.SetROINodeID(roiMoving.GetID())
cvpn.SetInputVolumeNodeID(movingVolume.GetID())
movingDisplayNode = movingVolume.GetDisplayNode()
movingVolume.SetAndObserveDisplayNodeID(
'This is not a valid DisplayNode ID')
if timing: roi2End = time.time()
if timing: crop2Start = time.time()
state.logic.cropLogic.Apply(cvpn)
if timing: crop2End = time.time()
croppedMovingVolume = slicer.mrmlScene.GetNodeByID(
cvpn.GetOutputVolumeNodeID())
movingVolume.SetAndObserveDisplayNodeID(movingDisplayNode.GetID())
if timing:
print 'Time to set up fixed ROI was ' + str(roiEnd -
roiStart) + ' seconds'
if timing:
print 'Time to set up moving ROI was ' + str(
roi2End - roi2Start) + ' seconds'
if timing:
print 'Time to crop fixed volume ' + str(cropEnd -
cropStart) + ' seconds'
if timing:
print 'Time to crop moving volume ' + str(crop2End -
crop2Start) + ' seconds'
#
transform = slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(transform)
matrix = vtk.vtkMatrix4x4()
# define the registration parameters
minPixelSpacing = min(croppedFixedVolume.GetSpacing())
parameters = {}
parameters['fixedVolume'] = croppedFixedVolume.GetID()
parameters['movingVolume'] = croppedMovingVolume.GetID()
parameters['linearTransform'] = transform.GetID()
parameters['useRigid'] = True
parameters['initializeTransformMode'] = 'useGeometryAlign'
parameters['samplingPercentage'] = 0.2
parameters['minimumStepLength'] = 0.1 * minPixelSpacing
parameters['maximumStepLength'] = minPixelSpacing
# run the registration
if timing: regStart = time.time()
slicer.cli.run(slicer.modules.brainsfit,
None,
parameters,
wait_for_completion=True)
if timing: regEnd = time.time()
if timing:
print 'Time for local registration ' + str(regEnd -
regStart) + ' seconds'
# apply the local transform to the landmark
#print transform
if timing: resultStart = time.time()
transform.GetMatrixTransformToWorld(matrix)
matrix.Invert()
tp = [
0,
] * 4
tp = matrix.MultiplyPoint(fixedPoint + [
1,
])
#print fixedPoint, movingPoint, tp[:3]
movingList.SetNthFiducialPosition(movingIndex, tp[0], tp[1], tp[2])
if timing: resultEnd = time.time()
if timing:
print 'Time for transforming landmark was ' + str(
resultEnd - resultStart) + ' seconds'
# clean up cropped volmes, need to reset the foreground/background display before we delete it
if timing: cleanUpStart = time.time()
slicer.mrmlScene.RemoveNode(croppedFixedVolume)
slicer.mrmlScene.RemoveNode(croppedMovingVolume)
slicer.mrmlScene.RemoveNode(roiFixed)
slicer.mrmlScene.RemoveNode(roiMoving)
slicer.mrmlScene.RemoveNode(transform)
roiFixed = None
roiMoving = None
transform = None
matrix = None
if timing: cleanUpEnd = time.time()
if timing:
print 'Cleanup took ' + str(cleanUpEnd - cleanUpStart) + ' seconds'
end = time.time()
print 'Refined landmark ' + state.currentLandmarkName + ' in ' + str(
end - start) + ' seconds'
slicer.mrmlScene.EndState(slicer.mrmlScene.BatchProcessState)
def registrarButton(self):
mvNode = self.outputRegSelector.currentNode()
inputVolume = self.inputRegSelector.currentNode()
"""
Run the actual algorithm
"""
#se obtiene la escena y se obtiene el volumen 4D a partir del Volumen 4D de
#entrada de la ventana desplegable
escena = slicer.mrmlScene
imagenvtk4D = inputVolume.GetImageData()
#Se obtiene el número de volúmenes que tiene el volumen 4D
numero_imagenes = inputVolume.GetNumberOfFrames()
print('imagenes: ' + str(numero_imagenes))
#filtro vtk para descomponer un volumen 4D
extract1 = vtk.vtkImageExtractComponents()
extract1.SetInputData(imagenvtk4D)
#matriz de transformación
ras2ijk = vtk.vtkMatrix4x4()
ijk2ras = vtk.vtkMatrix4x4()
#le solicitamos al volumen original que nos devuelva sus matrices
inputVolume.GetRASToIJKMatrix(ras2ijk)
inputVolume.GetIJKToRASMatrix(ijk2ras)
#creo un volumen nuevo
volumenFijo = slicer.vtkMRMLScalarVolumeNode()
volumenSalida = slicer.vtkMRMLMultiVolumeNode()
#le asigno las transformaciones
volumenFijo.SetRASToIJKMatrix(ras2ijk)
volumenFijo.SetIJKToRASMatrix(ijk2ras)
#le asigno el volumen 3D fijo
imagen_fija = extract1.SetComponents(0)
extract1.Update()
volumenFijo.SetName('fijo')
volumenFijo.SetAndObserveImageData(extract1.GetOutput())
#anado el nuevo volumen a la escena
escena.AddNode(volumenFijo)
#se crea un vector para guardar el número del volumen que tenga un
#desplazamiento de mas de 4mm en cualquier dirección
v = []
#se hace un ciclo for para registrar todos los demás volúmenes del volumen 4D
#con el primer volumen que se definió como fijo
frameLabelsAttr = ''
frames = []
volumeLabels = vtk.vtkDoubleArray()
volumeLabels.SetNumberOfTuples(numero_imagenes)
volumeLabels.SetNumberOfComponents(1)
volumeLabels.Allocate(numero_imagenes)
for i in range(numero_imagenes):
# extraigo la imagen móvil en la posición i+1 ya que el primero es el fijo
imagen_movil = extract1.SetComponents(
i + 1) #Seleccionar un volumen i+1
extract1.Update()
#Creo el volumen móvil, y realizo el mismo procedimiento que con el fijo
volumenMovil = slicer.vtkMRMLScalarVolumeNode()
volumenMovil.SetRASToIJKMatrix(ras2ijk)
volumenMovil.SetIJKToRASMatrix(ijk2ras)
volumenMovil.SetAndObserveImageData(extract1.GetOutput())
volumenMovil.SetName('movil ' + str(i + 1))
escena.AddNode(volumenMovil)
#creamos la transformada para alinear los volúmenes
transformadaSalida = slicer.vtkMRMLLinearTransformNode()
transformadaSalida.SetName('Transformadaderegistro' + str(i + 1))
slicer.mrmlScene.AddNode(transformadaSalida)
#parámetros para la operación de registro
parameters = {}
#parameters['InitialTransform'] = transI.GetID()
parameters['fixedVolume'] = volumenFijo.GetID()
parameters['movingVolume'] = volumenMovil.GetID()
parameters['transformType'] = 'Rigid'
parameters['outputTransform'] = transformadaSalida.GetID()
frames.append(volumenMovil)
## parameters['outputVolume']=volumenSalida.GetID()
#Realizo el registro
cliNode = slicer.cli.run(slicer.modules.brainsfit,
None,
parameters,
wait_for_completion=True)
#obtengo la transformada lineal que se usó en el registro
transformada = escena.GetFirstNodeByName('Transformadaderegistro' +
str(i + 1))
#Obtengo la matriz de la transformada, esta matriz es de dimensiones 4x4
#en la cual estan todos los desplazamientos y rotaciones que se hicieron
#en la transformada, a partir de ella se obtienen los volumenes que se
#desplazaron mas de 4mm en cualquier direccion
hm = vtk.vtkMatrix4x4()
transformadaSalida.GetMatrixTransformToWorld(hm)
volumenMovil.ApplyTransformMatrix(hm)
volumenMovil.SetAndObserveTransformNodeID(None)
frameId = i
volumeLabels.SetComponent(i, 0, frameId)
frameLabelsAttr += str(frameId) + ','
## Matriz=transformada.GetMatrixTransformToParent()
## LR=Matriz.GetElement(0,3)#dirección izquierda o derecha en la fila 1, columna 4
## PA=Matriz.GetElement(1,3)#dirección anterior o posterior en la fila 2, columna 4
## IS=Matriz.GetElement(2,3)#dirección inferior o superior en la fila 3, columna 4
## #Se mira si el volumen "i" en alguna dirección tuvo un desplazamiento
## #mayor a 4mm, en caso de ser cierto se guarda en el vector "v"
## if abs(LR)>4:
## v.append(i+2)
## elif abs(PA)>4:
## v.append(i+2)
## elif abs(IS)>4:
## v.append(i+2)
## print("MovilExtent: "+str(volumenMovil.GetImageData().GetExtent()))
#### print("valor de f: "+ str(volumenMovil))
## frameLabelsAttr = frameLabelsAttr[:-1]
mvImage = vtk.vtkImageData()
mvImage.SetExtent(volumenMovil.GetImageData().GetExtent()
) ##Se le asigna la dimensión del miltuvolumen
mvImage.AllocateScalars(
volumenMovil.GetImageData().GetScalarType(), numero_imagenes
) ##Se le asigna el tipo y número de cortes al multivolumen
mvImageArray = vtk.util.numpy_support.vtk_to_numpy(
mvImage.GetPointData().GetScalars()
) ## Se crea la matriz de datos donde va a ir la imagen
mat = vtk.vtkMatrix4x4()
##Se hace la conversión y se obtiene la matriz de transformación del nodo
volumenMovil.GetRASToIJKMatrix(mat)
mvNode.SetRASToIJKMatrix(mat)
volumenMovil.GetIJKToRASMatrix(mat)
mvNode.SetIJKToRASMatrix(mat)
print("frameId: " + str(frameId))
print("# imag: " + str(numero_imagenes))
## print("Long frame1: "+str(len(frame)))
print("Long frames: " + str(len(frames)))
##
for frameId in range(numero_imagenes):
# TODO: check consistent size and orientation!
frame = frames[frameId]
frameImage = frame.GetImageData()
frameImageArray = vtk.util.numpy_support.vtk_to_numpy(
frameImage.GetPointData().GetScalars())
mvImageArray.T[frameId] = frameImageArray
##Se crea el nodo del multivolumen
mvDisplayNode = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLMultiVolumeDisplayNode')
mvDisplayNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(mvDisplayNode)
mvDisplayNode.SetReferenceCount(mvDisplayNode.GetReferenceCount() - 1)
mvDisplayNode.SetDefaultColorMap()
mvNode.SetAndObserveDisplayNodeID(mvDisplayNode.GetID())
mvNode.SetAndObserveImageData(mvImage)
mvNode.SetNumberOfFrames(numero_imagenes)
mvNode.SetLabelArray(volumeLabels)
mvNode.SetLabelName('na')
mvNode.SetAttribute('MultiVolume.FrameLabels', frameLabelsAttr)
mvNode.SetAttribute('MultiVolume.NumberOfFrames', str(numero_imagenes))
mvNode.SetAttribute('MultiVolume.FrameIdentifyingDICOMTagName', 'NA')
mvNode.SetAttribute('MultiVolume.FrameIdentifyingDICOMTagUnits', 'na')
mvNode.SetName('MultiVolume Registrado')
Helper.SetBgFgVolumes(mvNode.GetID(), None)
print('Registro completo')
#al terminar el ciclo for con todos los volúmenes registrados se genera una
#ventana emergente con un mensaje("Registro completo!") y mostrando los
#volúmenes que se desplazaron mas de 4mm
qt.QMessageBox.information(slicer.util.mainWindow(), 'Slicer Python',
'Registro completo')
return True
def computeSpline(self, spline, startVertexID, endVertexID, startPointPosition, endPointPosition, resolution):
print ("compute spline")
scene = slicer.mrmlScene
dijkstra = vtk.vtkDijkstraGraphGeodesicPath()
dijkstra.SetInputData(self.modelNode.GetPolyData())
dijkstra.SetStartVertex(startVertexID)
dijkstra.SetEndVertex(endVertexID)
dijkstra.Update()
#compute step size in according to resolution
vertices = dijkstra.GetOutput().GetPoints()
numVertices = vertices.GetNumberOfPoints()
resStepSize = float(numVertices) / (float(resolution) - 1.0)# -2 because of start and end point
print (numVertices)
print (resolution)
print (resStepSize)
equidistantIndices = []
curStep = 0
for i in range(0, int(resolution)):
curStep = (i * resStepSize) - 1
equidistantIndices.append(int(curStep + 0.5))
#create spline
splinePoints = []
points = vtk.vtkPoints()
for index in equidistantIndices:
print ("index")
print (index)
print ("position")
position = [0, 0, 0]
vertices.GetPoint(index, position)
print (position)
points.InsertNextPoint(position)
splinePoints.append(position)
spline.points = splinePoints
parametricSpline = vtk.vtkParametricSpline()
parametricSpline.SetPoints(points)
functionSource = vtk.vtkParametricFunctionSource()
functionSource.SetParametricFunction(parametricSpline)
functionSource.Update()
#create model node
splineModel = slicer.vtkMRMLModelNode()
splineModel.SetScene(scene)
splineModel.SetName("splineModel-%i" % 1) #todo
splineModel.SetAndObservePolyData(functionSource.GetOutput())
#create display node
splineModelDisplay = slicer.vtkMRMLModelDisplayNode()
splineModelDisplay.SetColor(1, 0, 0)
splineModelDisplay.SetOpacity(1)
splineModelDisplay.SetLineWidth(4)
splineModelDisplay.SliceIntersectionVisibilityOn()
splineModelDisplay.SetScene(scene)
scene.AddNode(splineModelDisplay)
splineModel.SetAndObserveDisplayNodeID(splineModelDisplay.GetID())
# add to scene
splineModelDisplay.GetPolyData = functionSource.GetOutput()
scene.AddNode(splineModel)
splineModelTransform = slicer.vtkMRMLLinearTransformNode()
splineModelTransform.SetName("SplineModelTransform-%i" % 1) # todo
scene.AddNode(splineModelTransform)
def clipping(self):
planeCollection = vtk.vtkPlaneCollection()
harden = slicer.vtkSlicerTransformLogic()
tempTransform = slicer.vtkMRMLLinearTransformNode()
tempTransform.HideFromEditorsOn()
slicer.mrmlScene.AddNode(tempTransform)
numNodes = slicer.mrmlScene.GetNumberOfNodesByClass("vtkMRMLModelNode")
dictionnaryModel = dict()
hardenModelIDdict = dict()
landmarkDescriptionDict = dict()
modelIDdict = dict()
for i in range(3, numNodes):
planeCollection.RemoveAllItems()
mh = slicer.mrmlScene.GetNthNodeByClass(i, "vtkMRMLModelNode")
if mh.GetDisplayVisibility() == 0:
continue
model = slicer.util.getNode(mh.GetName())
transform = model.GetParentTransformNode()
if transform:
tempTransform.Copy(transform)
harden.hardenTransform(tempTransform)
m = vtk.vtkMatrix4x4()
tempTransform.GetMatrixTransformToParent(m)
m.Invert(m, m)
else:
m = vtk.vtkMatrix4x4()
for key, planeDef in self.planeDict.items():
hardenP = m.MultiplyPoint(planeDef.P)
hardenN = m.MultiplyPoint(planeDef.n)
if planeDef.boxState:
planeDef.vtkPlane.SetOrigin(hardenP[0], hardenP[1],
hardenP[2])
if planeDef.negState:
planeDef.vtkPlane.SetNormal(-hardenN[0], -hardenN[1],
-hardenN[2])
if planeDef.posState:
planeDef.vtkPlane.SetNormal(hardenN[0], hardenN[1],
hardenN[2])
planeCollection.AddItem(planeDef.vtkPlane)
dictionnaryModel[model.GetID()] = model.GetPolyData()
polyData = model.GetPolyData()
clipper = vtk.vtkClipClosedSurface()
clipper.SetClippingPlanes(planeCollection)
clipper.SetInputData(polyData)
clipper.SetGenerateFaces(1)
clipper.SetScalarModeToLabels()
clipper.Update()
polyDataNew = clipper.GetOutput()
model.SetAndObservePolyData(polyDataNew)
# Checking if one ore more fiducial list are connected to this model
list = slicer.mrmlScene.GetNodesByClass(
"vtkMRMLMarkupsFiducialNode")
end = list.GetNumberOfItems()
for i in range(0, end):
fidList = list.GetItemAsObject(i)
if fidList.GetAttribute("connectedModelID"):
if fidList.GetAttribute(
"connectedModelID") == model.GetID():
modelIDdict[fidList.GetID()], hardenModelIDdict[fidList.GetID()], landmarkDescriptionDict[fidList.GetID()] = \
self.unprojectLandmarks(fidList)
return dictionnaryModel, modelIDdict, hardenModelIDdict, landmarkDescriptionDict
