def registerCustomVrPresets(usPresetsScenePath):
"""
Set volume rendering presets from Resources/VrPresets/US-VrPresets.mrml
"""
import os
if not os.path.isfile(usPresetsScenePath):
logging.warning('Volume rendering presets are not found at {0}'.format(
usPresetsScenePath))
return
# Read scene
usPresetsScene = slicer.vtkMRMLScene()
vrPropNode = slicer.vtkMRMLVolumePropertyNode()
usPresetsScene.RegisterNodeClass(vrPropNode)
usPresetsScene.SetURL(usPresetsScenePath)
usPresetsScene.Connect()
# Add presets to volume rendering logic
vrLogic = slicer.modules.volumerendering.logic()
presetsScene = vrLogic.GetPresetsScene()
vrNodes = usPresetsScene.GetNodesByClass("vtkMRMLVolumePropertyNode")
vrNodes.UnRegister(None)
for itemNum in range(vrNodes.GetNumberOfItems()):
node = vrNodes.GetItemAsObject(itemNum)
vrLogic.AddPreset(node)
def InitVRDisplayNode(vrDisplayNode, volumeID, roiID):
vrLogic = slicer.modules.volumerendering.logic()
print('ChangeTracker VR: will observe ID '+volumeID)
propNode = vrDisplayNode.GetVolumePropertyNode()
if propNode == None:
propNode = slicer.vtkMRMLVolumePropertyNode()
slicer.mrmlScene.AddNode(propNode)
else:
print('Property node: '+propNode.GetID())
vrDisplayNode.SetAndObserveVolumePropertyNodeID(propNode.GetID())
vrDisplayNode.SetAndObserveROINodeID(roiID)
vrDisplayNode.SetAndObserveVolumeNodeID(volumeID)
vrLogic.CopyDisplayToVolumeRenderingDisplayNode(vrDisplayNode)
def InitVRDisplayNode(vrDisplayNode, volumeID, roiID):
vrLogic = slicer.modules.volumerendering.logic()
logging.debug('PedicleScrewSimulator VR: will observe ID ' + volumeID)
propNode = vrDisplayNode.GetVolumePropertyNode()
if propNode == None:
propNode = slicer.vtkMRMLVolumePropertyNode()
slicer.mrmlScene.AddNode(propNode)
else:
logging.debug('Property node: ' + propNode.GetID())
vrDisplayNode.SetAndObserveVolumePropertyNodeID(propNode.GetID())
vrDisplayNode.SetAndObserveROINodeID(roiID)
vrDisplayNode.SetAndObserveVolumeNodeID(volumeID)
vrLogic.CopyDisplayToVolumeRenderingDisplayNode(vrDisplayNode)
def InitVRDisplayNode(vrDisplayNode, volumeID, roiID):
# Takes most of the steps necessary to create a 3D Visualization of an image.
vrLogic = slicer.modules.volumerendering.logic()
propNode = vrDisplayNode.GetVolumePropertyNode()
if propNode == None:
propNode = slicer.vtkMRMLVolumePropertyNode()
slicer.mrmlScene.AddNode(propNode)
vrDisplayNode.SetAndObserveVolumePropertyNodeID(propNode.GetID())
if roiID != '':
vrDisplayNode.SetAndObserveROINodeID(roiID)
vrDisplayNode.SetAndObserveVolumeNodeID(volumeID)
vrLogic.CopyDisplayToVolumeRenderingDisplayNode(vrDisplayNode)
def InitVRDisplayNode(vrDisplayNode, volumeID, roiID): # Takes most of the steps necessary to create a 3D Visualization of an image. vrLogic = slicer.modules.volumerendering.logic() propNode = vrDisplayNode.GetVolumePropertyNode() if propNode == None: propNode = slicer.vtkMRMLVolumePropertyNode() slicer.mrmlScene.AddNode(propNode) vrDisplayNode.SetAndObserveVolumePropertyNodeID(propNode.GetID()) if roiID != '': vrDisplayNode.SetAndObserveROINodeID(roiID) vrDisplayNode.SetAndObserveVolumeNodeID(volumeID) vrLogic.CopyDisplayToVolumeRenderingDisplayNode(vrDisplayNode)
def InitVRDisplayNode(vrDisplayNode, volumeID, roiID):
# Uses the volume rendering module to initiate 3D visualizations.
# NOTE: This code seems to be duplicated several times within individual
# steps. It would be best to consolidate them in this code if possible..
vrLogic = slicer.modules.volumerendering.logic()
propNode = vrDisplayNode.GetVolumePropertyNode()
if propNode == None:
propNode = slicer.vtkMRMLVolumePropertyNode()
slicer.mrmlScene.AddNode(propNode)
vrDisplayNode.SetAndObserveVolumePropertyNodeID(propNode.GetID())
if roiID != '':
vrDisplayNode.SetAndObserveROINodeID(roiID)
vrDisplayNode.SetAndObserveVolumeNodeID(volumeID)
vrLogic.CopyDisplayToVolumeRenderingDisplayNode(vrDisplayNode)
def addDefaultVolumeProperty(self):
# create a volume property node in the scene if needed. This is used
# for the color transfer function and can be manipulated in the
# Slicer Volume Rendering module widget
volumePropertyNode = slicer.util.getNode('ShaderVolumeProperty')
if not volumePropertyNode:
volumePropertyNode = slicer.vtkMRMLVolumePropertyNode()
volumePropertyNode.SetName('ShaderVolumeProperty')
scalarOpacity = vtk.vtkPiecewiseFunction()
points = ( (-1024., 0.), (20., 0.), (300., 1.), (3532., 1.) )
for point in points:
scalarOpacity.AddPoint(*point)
volumePropertyNode.SetScalarOpacity(scalarOpacity)
colorTransfer = vtk.vtkColorTransferFunction()
colors = ( (-1024., (0., 0., 0.)), (3., (0., 0., 0.)), (131., (1., 1., 0.)) )
colors = ( (-1024., (0., 0., 0.)), (-984., (0., 0., 0.)), (469., (1., 1., 1.)) )
for intensity,rgb in colors:
colorTransfer.AddRGBPoint(intensity, *rgb)
volumePropertyNode.SetScalarOpacity(scalarOpacity)
volumePropertyNode.SetColor(colorTransfer, 0)
slicer.mrmlScene.AddNode(volumePropertyNode)
self.volumePropertyNode = volumePropertyNode
def addDefaultVolumeProperty(self):
# create a volume property node in the scene if needed. This is used
# for the color transfer function and can be manipulated in the
# Slicer Volume Rendering module widget
volumePropertyNode = slicer.util.getNode('ShaderVolumeProperty')
if not volumePropertyNode:
volumePropertyNode = slicer.vtkMRMLVolumePropertyNode()
volumePropertyNode.SetName('ShaderVolumeProperty')
scalarOpacity = vtk.vtkPiecewiseFunction()
points = ((-1024., 0.), (20., 0.), (300., 1.), (3532., 1.))
for point in points:
scalarOpacity.AddPoint(*point)
volumePropertyNode.SetScalarOpacity(scalarOpacity)
colorTransfer = vtk.vtkColorTransferFunction()
colors = ((-1024., (0., 0., 0.)), (3., (0., 0., 0.)),
(131., (1., 1., 0.)))
colors = ((-1024., (0., 0., 0.)), (-984., (0., 0., 0.)),
(469., (1., 1., 1.)))
for intensity, rgb in colors:
colorTransfer.AddRGBPoint(intensity, *rgb)
volumePropertyNode.SetScalarOpacity(scalarOpacity)
volumePropertyNode.SetColor(colorTransfer, 0)
slicer.mrmlScene.AddNode(volumePropertyNode)
self.volumePropertyNode = volumePropertyNode
def onVolumeAdded(self,volumeNode):
print("A volume was added!!")
volumeNode.AddObserver("ModifiedEvent",self.onVolumeModified)
'''
It is assumed that the volume was created with respect to the Reference
The matrix associated with the volume must have the following structure
sx 0 0 ox
0 sy 0 oy
0 0 sz oz
with sx, sy, and sz >0
This is checked and if it is not true is modified.
By default Slicer add a volume with a ijkToRas matrix of the form:
-1 0 0
0 -1 0
0 0 1
In this case we want a ijkToRAS matrix equal to identity because we want to place the
volume with respect to the Reference.
ReferenceToRAS matrix is calculated during registration
'''
matrix=vtk.vtkMatrix4x4()
volumeNode.GetIJKToRASMatrix(matrix)
print matrix
sx = matrix.GetElement(0,0)
if (sx<0):
ox=matrix.GetElement(0,3)
matrix.SetElement(0,0,-sx)
matrix.SetElement(0,3,-ox)
sy = matrix.GetElement(1,1)
if (sy<0):
oy=matrix.GetElement(1,3)
matrix.SetElement(1,1,-sy)
matrix.SetElement(1,3,-oy)
volumeNode.SetIJKToRASMatrix(matrix)
print matrix
# Volumes are placed under the Reference coordinate system
referenceToRASNode=slicer.util.getNode("ReferenceToRAS")
if referenceToRASNode==None:
referenceToRASNode=slicer.vtkMRMLLinearTransformNode()
slicer.mrmlScene.AddNode(referenceToRASNode)
referenceToRASNode.SetName("ReferenceToRAS")
volumeNode.SetAndObserveTransformNodeID(referenceToRASNode.GetID())
volumeNode.SetDisplayVisibility(True)
volumePropertyNode=slicer.vtkMRMLVolumePropertyNode()
slicer.mrmlScene.RegisterNodeClass(volumePropertyNode);
# the scalar opacity mapping function is configured
# it is a ramp with opacity of 0 equal to zero and opacity of 1 equal to 1.
scalarOpacity = vtk.vtkPiecewiseFunction()
scalarOpacity.AddPoint(self.scalarRange[0],0.)
scalarOpacity.AddPoint(self.windowLevelMinMax[0],0.)
scalarOpacity.AddPoint(self.windowLevelMinMax[1],1.)
scalarOpacity.AddPoint(self.scalarRange[1],1.)
volumePropertyNode.SetScalarOpacity(scalarOpacity);
# the color function is configured
# zero is associated to the scalar zero and 1 to the scalar 255
colorTransfer = vtk.vtkColorTransferFunction()
black=[0., 0., 0.]
white=[1.,1.,1.]
colorTransfer.AddRGBPoint(self.scalarRange[0],black[0],black[1],black[2])
colorTransfer.AddRGBPoint(self.windowLevelMinMax[0], black[0], black[1], black[2])
colorTransfer.AddRGBPoint(self.windowLevelMinMax[1], white[0], white[1], white[2]);
colorTransfer.AddRGBPoint(self.scalarRange[1], white[0], white[1], white[2]);
volumePropertyNode.SetColor(colorTransfer)
vtkVolumeProperty=volumePropertyNode.GetVolumeProperty()
vtkVolumeProperty.SetInterpolationTypeToNearest();
vtkVolumeProperty.ShadeOn();
vtkVolumeProperty.SetAmbient(0.30);
vtkVolumeProperty.SetDiffuse(0.60);
vtkVolumeProperty.SetSpecular(0.50);
vtkVolumeProperty.SetSpecularPower(40);
slicer.mrmlScene.AddNode(volumePropertyNode)
# The volume rendering display node is created
vrDisplayNode=slicer.vtkMRMLCPURayCastVolumeRenderingDisplayNode()
vrDisplayNode.SetAndObserveVolumeNodeID(volumeNode.GetID())
vrDisplayNode.SetAndObserveVolumePropertyNodeID(volumePropertyNode.GetID())
slicer.mrmlScene.AddNode(vrDisplayNode)
vrDisplayNode.SetVisibility(True)
vrDisplayNode.AddObserver("ModifiedEvent",self.onVolumeRenderingModified)
vrDisplayNode.Modified()
vrDisplayNode.UpdateScene(slicer.mrmlScene)
