def __init__( self, stepid ):
self.initialize( stepid )
self.setName( '5. Place Screws' )
self.setDescription( 'Load screw models and change orientation using sliders' )
self.screwPath = None
self.screwName = None
self.coords = [0,0,0]
self.matrix1 = vtk.vtkMatrix3x3()
self.matrix2 = vtk.vtkMatrix3x3()
self.matrix3 = vtk.vtkMatrix3x3()
self.matrixScrew = vtk.vtkMatrix4x4()
self.fiduciallist = []
self.screwSummary = []
self.screwList = []
self.currentFidIndex = 0
self.currentFidLabel = None
self.fidNode = slicer.vtkMRMLMarkupsFiducialNode()
self.valueTemp1 = 0
self.valueTemp2 = 0
self.driveTemp = 0
self.__loadScrewButton = None
self.__parent = super( ScrewStep, self )
self.timer = qt.QTimer()
self.timer.setInterval(2)
self.timer.connect('timeout()', self.driveScrew)
self.timer2 = qt.QTimer()
self.timer2.setInterval(2)
self.timer2.connect('timeout()', self.reverseScrew)
self.screwInsert = 0.0
def transformScrewComposite(self, inputMatrix):
transformFid = slicer.mrmlScene.GetFirstNodeByName(
'Transform-%s' % self.currentFidLabel)
matrixScrew = transformFid.GetMatrixTransformToParent()
newMatrix = vtk.vtkMatrix3x3()
outputMatrix = vtk.vtkMatrix3x3()
newMatrix.SetElement(0, 0, matrixScrew.GetElement(0, 0))
newMatrix.SetElement(0, 1, matrixScrew.GetElement(0, 1))
newMatrix.SetElement(0, 2, matrixScrew.GetElement(0, 2))
newMatrix.SetElement(1, 0, matrixScrew.GetElement(1, 0))
newMatrix.SetElement(1, 1, matrixScrew.GetElement(1, 1))
newMatrix.SetElement(1, 2, matrixScrew.GetElement(1, 2))
newMatrix.SetElement(2, 0, matrixScrew.GetElement(2, 0))
newMatrix.SetElement(2, 1, matrixScrew.GetElement(2, 1))
newMatrix.SetElement(2, 2, matrixScrew.GetElement(2, 2))
vtk.vtkMatrix3x3.Multiply3x3(newMatrix, inputMatrix, outputMatrix)
#coords = [0,0,0]
#self.fid.GetFiducialCoordinates(coords)
matrixScrew.SetElement(0, 0, outputMatrix.GetElement(0, 0))
matrixScrew.SetElement(0, 1, outputMatrix.GetElement(0, 1))
matrixScrew.SetElement(0, 2, outputMatrix.GetElement(0, 2))
#matrixScrew.SetElement(0,3,self.coords[0])
matrixScrew.SetElement(1, 0, outputMatrix.GetElement(1, 0))
matrixScrew.SetElement(1, 1, outputMatrix.GetElement(1, 1))
matrixScrew.SetElement(1, 2, outputMatrix.GetElement(1, 2))
#matrixScrew.SetElement(1,3,self.coords[1])
matrixScrew.SetElement(2, 0, outputMatrix.GetElement(2, 0))
matrixScrew.SetElement(2, 1, outputMatrix.GetElement(2, 1))
matrixScrew.SetElement(2, 2, outputMatrix.GetElement(2, 2))
#matrixScrew.SetElement(2,3,self.coords[2])
matrixScrew.SetElement(3, 0, 0)
matrixScrew.SetElement(3, 1, 0)
matrixScrew.SetElement(3, 2, 0)
matrixScrew.SetElement(3, 3, 1)
transformFid.SetMatrixTransformToParent(matrixScrew)
transformFid.UpdateScene(slicer.mrmlScene)
def transformScrewComposite(self, inputMatrix):
transformFid = slicer.util.getNode('Transform-%s' % self.currentFidLabel)
matrixScrew = transformFid.GetMatrixTransformToParent()
newMatrix = vtk.vtkMatrix3x3()
outputMatrix = vtk.vtkMatrix3x3()
newMatrix.SetElement(0,0,matrixScrew.GetElement(0,0))
newMatrix.SetElement(0,1,matrixScrew.GetElement(0,1))
newMatrix.SetElement(0,2,matrixScrew.GetElement(0,2))
newMatrix.SetElement(1,0,matrixScrew.GetElement(1,0))
newMatrix.SetElement(1,1,matrixScrew.GetElement(1,1))
newMatrix.SetElement(1,2,matrixScrew.GetElement(1,2))
newMatrix.SetElement(2,0,matrixScrew.GetElement(2,0))
newMatrix.SetElement(2,1,matrixScrew.GetElement(2,1))
newMatrix.SetElement(2,2,matrixScrew.GetElement(2,2))
vtk.vtkMatrix3x3.Multiply3x3(newMatrix, inputMatrix, outputMatrix)
#coords = [0,0,0]
#self.fid.GetFiducialCoordinates(coords)
matrixScrew.SetElement(0,0,outputMatrix.GetElement(0,0))
matrixScrew.SetElement(0,1,outputMatrix.GetElement(0,1))
matrixScrew.SetElement(0,2,outputMatrix.GetElement(0,2))
#matrixScrew.SetElement(0,3,self.coords[0])
matrixScrew.SetElement(1,0,outputMatrix.GetElement(1,0))
matrixScrew.SetElement(1,1,outputMatrix.GetElement(1,1))
matrixScrew.SetElement(1,2,outputMatrix.GetElement(1,2))
#matrixScrew.SetElement(1,3,self.coords[1])
matrixScrew.SetElement(2,0,outputMatrix.GetElement(2,0))
matrixScrew.SetElement(2,1,outputMatrix.GetElement(2,1))
matrixScrew.SetElement(2,2,outputMatrix.GetElement(2,2))
#matrixScrew.SetElement(2,3,self.coords[2])
matrixScrew.SetElement(3,0,0)
matrixScrew.SetElement(3,1,0)
matrixScrew.SetElement(3,2,0)
matrixScrew.SetElement(3,3,1)
transformFid.SetMatrixTransformToParent(matrixScrew)
transformFid.UpdateScene(slicer.mrmlScene)
def getVTKMatrixFromNumpyMatrix(self, numpyMatrix):
dimensions = len(numpyMatrix) - 1
if dimensions == 2:
vtkMatrix = vtk.vtkMatrix3x3()
elif dimensions == 3:
vtkMatrix = vtk.vtkMatrix4x4()
else:
raise ValueError('Unknown matrix dimensions.')
for row in range(dimensions + 1):
for col in range(dimensions + 1):
vtkMatrix.SetElement(row, col, numpyMatrix[row, col])
return vtkMatrix
def driveScrew(self):
if self.screwInsert < int(self.__diameter):
value = self.screwInsert
# attempt to rotate with driving
angle3 = math.pi / 180.0 * 72 #((360/2.5)*self.screwInsert)
matrix3 = vtk.vtkMatrix3x3()
matrix3.DeepCopy([
math.cos(angle3), 0, -math.sin(angle3), 0, 1, 0,
math.sin(angle3), 0,
math.cos(angle3)
])
self.transformScrewComposite(matrix3)
value = value * -1
transformFid = slicer.mrmlScene.GetFirstNodeByName(
'Transform-%s' % self.currentFidLabel)
matrixScrew = transformFid.GetMatrixTransformToParent()
newVal = value - self.driveTemp
drive1 = matrixScrew.GetElement(0, 1)
drive2 = matrixScrew.GetElement(1, 1)
drive3 = matrixScrew.GetElement(2, 1)
coord1 = drive1 * newVal + matrixScrew.GetElement(0, 3)
coord2 = drive2 * newVal + matrixScrew.GetElement(1, 3)
coord3 = drive3 * newVal + matrixScrew.GetElement(2, 3)
matrixScrew.SetElement(0, 3, coord1)
matrixScrew.SetElement(1, 3, coord2)
matrixScrew.SetElement(2, 3, coord3)
transformFid.SetMatrixTransformToParent(matrixScrew)
#transformFid.UpdateScene(slicer.mrmlScene)
#self.delayDisplay(transformFid.UpdateScene(slicer.mrmlScene), 2000)
self.driveTemp = value
self.screwInsert += 1
else:
self.timer.stop()
self.screwInsert = 0.0
self.driveTemp = 0
'''
def driveScrew(self):
if self.screwInsert < int(self.__diameter):
value = self.screwInsert
#print(value)
# attempt to rotate with driving
angle3 = math.pi / 180.0 * 72 #((360/2.5)*self.screwInsert)
matrix3 = vtk.vtkMatrix3x3()
matrix3.DeepCopy([ math.cos(angle3), 0, -math.sin(angle3),
0, 1, 0,
math.sin(angle3), 0, math.cos(angle3)])
self.transformScrewComposite(matrix3)
value = value*-1
transformFid = slicer.util.getNode('Transform-%s' % self.currentFidLabel)
matrixScrew = transformFid.GetMatrixTransformToParent()
newVal = value - self.driveTemp
print(newVal)
drive1 = matrixScrew.GetElement(0,1)
drive2 = matrixScrew.GetElement(1,1)
drive3 = matrixScrew.GetElement(2,1)
coord1 = drive1 * newVal + matrixScrew.GetElement(0,3)
coord2 = drive2 * newVal + matrixScrew.GetElement(1,3)
coord3 = drive3 * newVal + matrixScrew.GetElement(2,3)
matrixScrew.SetElement(0,3,coord1)
matrixScrew.SetElement(1,3,coord2)
matrixScrew.SetElement(2,3,coord3)
transformFid.SetMatrixTransformToParent(matrixScrew)
#transformFid.UpdateScene(slicer.mrmlScene)
#self.delayDisplay(transformFid.UpdateScene(slicer.mrmlScene), 2000)
self.driveTemp = value
self.screwInsert += 1
else:
self.timer.stop()
self.screwInsert = 0.0
self.driveTemp = 0
'''
def transformSlider2ValueChanged(self, value):
print(value)
newValue = value - self.valueTemp2
angle2 = math.pi / 180.0 * newValue * -1 # Match screw direction
matrix2 = vtk.vtkMatrix3x3()
matrix2.DeepCopy([ math.cos(angle2), -math.sin(angle2), 0,
math.sin(angle2), math.cos(angle2), 0,
0, 0, 1])
self.transformScrewComposite(matrix2)
self.valueTemp2 = value
temp = self.screwList[self.currentFidIndex]
temp[5] = str(value)
self.screwList[self.currentFidIndex] = temp
print self.screwList
def transformSlider2ValueChanged(self, value):
logging.debug("Transform slider 2 changed: {0}".format(value))
newValue = value - self.valueTemp2
angle2 = math.pi / 180.0 * newValue * -1 # Match screw direction
matrix2 = vtk.vtkMatrix3x3()
matrix2.DeepCopy([ math.cos(angle2), -math.sin(angle2), 0,
math.sin(angle2), math.cos(angle2), 0,
0, 0, 1])
self.transformScrewComposite(matrix2)
self.valueTemp2 = value
temp = self.screwList[self.currentFidIndex]
temp[5] = str(value)
self.screwList[self.currentFidIndex] = temp
logging.debug("Screw list: {0}".format(self.screwList))
def sampleVolumeParameters(self):
"""Calculate the dictionary of substitutions for the
current state of the volume node in a form for
substitution into the sampleVolume shader function
TODO: this would probably be better as uniforms, but that
requires doing a lot of parsing and data management in C++
"""
rasToIJK = vtk.vtkMatrix4x4()
self.node.GetRASToIJKMatrix(rasToIJK)
transformNode = self.node.GetParentTransformNode()
if transformNode:
if transformNode.IsTransformToWorldLinear():
rasToRAS = vtk.vtkMatrix4x4()
transformNode.GetMatrixTransformToWorld(rasToRAS)
rasToRAS.Invert()
rasToRAS.Multiply4x4(rasToIJK, rasToRAS, rasToIJK)
else:
error.warn('Cannot handle nonlinear transforms')
# dimensions are number of pixels in (row, column, slice)
# which maps to 0-1 space of S, T, P
dimensions = self.node.GetImageData().GetDimensions()
ijkToSTP = vtk.vtkMatrix4x4()
ijkToSTP.Identity()
for diagonal in range(3):
ijkToSTP.SetElement(diagonal,diagonal, 1./dimensions[diagonal])
rasToSTP = vtk.vtkMatrix4x4()
ijkToSTP.Multiply4x4(ijkToSTP, rasToIJK, rasToSTP)
parameters = {}
rows = ('rasToS', 'rasToT', 'rasToP')
for row in range(3):
rowKey = rows[row]
parameters[rowKey] = ""
for col in range(4):
element = rasToSTP.GetElement(row,col)
parameters[rowKey] += "%f," % element
parameters[rowKey] = parameters[rowKey][:-1] # clear trailing comma
# since texture is 0-1, take into account both pixel spacing
# and dimension as layed out in memory so that the normals
# is calculated in a uniform space
spacings = self.node.GetSpacing()
parameters['mmToS'] = spacings[0] / dimensions[0]
parameters['mmToT'] = spacings[1] / dimensions[1]
parameters['mmToP'] = spacings[2] / dimensions[2]
# the inverse transpose of the upper 3x3 of the stpToRAS matrix,
# which is the transpose of the upper 3x3 of the rasTSTP matrix
normalSTPToRAS = vtk.vtkMatrix3x3();
for row in range(3):
for column in range(3):
normalSTPToRAS.SetElement(row,column, rasToSTP.GetElement(row,column));
normalSTPToRAS.Transpose()
parameters['normalSTPToRAS'] = ''
for column in range(3):
for row in range(3):
# write in column-major order for glsl mat3 constructor
parameters['normalSTPToRAS'] += "%f," % normalSTPToRAS.GetElement(row,column)
parameters['normalSTPToRAS'] = parameters['normalSTPToRAS'][:-1] # clear trailing comma
return parameters
def getPlaneIntersectionPoint(self, axialNode, ortho1Node, ortho2Node):
# Compute the center of rotation (common intersection point of the three planes)
# http://mathworld.wolfram.com/Plane-PlaneIntersection.html
#axialNode = slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeRed')
#ortho1Node = slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeYellow')
#ortho2Node = slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeGreen')
axialSliceToRas = axialNode.GetSliceToRAS()
n1 = [axialSliceToRas.GetElement(0,2),axialSliceToRas.GetElement(1,2),axialSliceToRas.GetElement(2,2)]
x1 = [axialSliceToRas.GetElement(0,3),axialSliceToRas.GetElement(1,3),axialSliceToRas.GetElement(2,3)]
ortho1SliceToRas = ortho1Node.GetSliceToRAS()
n2 = [ortho1SliceToRas.GetElement(0,2),ortho1SliceToRas.GetElement(1,2),ortho1SliceToRas.GetElement(2,2)]
x2 = [ortho1SliceToRas.GetElement(0,3),ortho1SliceToRas.GetElement(1,3),ortho1SliceToRas.GetElement(2,3)]
ortho2SliceToRas = ortho2Node.GetSliceToRAS()
n3 = [ortho2SliceToRas.GetElement(0,2),ortho2SliceToRas.GetElement(1,2),ortho2SliceToRas.GetElement(2,2)]
x3 = [ortho2SliceToRas.GetElement(0,3),ortho2SliceToRas.GetElement(1,3),ortho2SliceToRas.GetElement(2,3)]
# Computed intersection point of all planes
x = [0,0,0]
n2_xp_n3 = [0,0,0]
x1_dp_n1 = vtk.vtkMath.Dot(x1,n1)
vtk.vtkMath.Cross(n2,n3,n2_xp_n3)
vtk.vtkMath.MultiplyScalar(n2_xp_n3, x1_dp_n1)
vtk.vtkMath.Add(x,n2_xp_n3,x)
n3_xp_n1 = [0,0,0]
x2_dp_n2 = vtk.vtkMath.Dot(x2,n2)
vtk.vtkMath.Cross(n3,n1,n3_xp_n1)
vtk.vtkMath.MultiplyScalar(n3_xp_n1, x2_dp_n2)
vtk.vtkMath.Add(x,n3_xp_n1,x)
n1_xp_n2 = [0,0,0]
x3_dp_n3 = vtk.vtkMath.Dot(x3,n3)
vtk.vtkMath.Cross(n1,n2,n1_xp_n2)
vtk.vtkMath.MultiplyScalar(n1_xp_n2, x3_dp_n3)
vtk.vtkMath.Add(x,n1_xp_n2,x)
normalMatrix = vtk.vtkMatrix3x3()
normalMatrix.SetElement(0,0,n1[0])
normalMatrix.SetElement(1,0,n1[1])
normalMatrix.SetElement(2,0,n1[2])
normalMatrix.SetElement(0,1,n2[0])
normalMatrix.SetElement(1,1,n2[1])
normalMatrix.SetElement(2,1,n2[2])
normalMatrix.SetElement(0,2,n3[0])
normalMatrix.SetElement(1,2,n3[1])
normalMatrix.SetElement(2,2,n3[2])
normalMatrixDeterminant = normalMatrix.Determinant()
if abs(normalMatrixDeterminant)>0.01:
# there is an intersection point
vtk.vtkMath.MultiplyScalar(x, 1/normalMatrixDeterminant)
else:
# no intersection point can be determined, use just the position of the axial slice
x = x1
return x
def getPlaneIntersectionPoint(axialNode, ortho1Node, ortho2Node):
"""
Compute the center of rotation (common intersection point of the three planes)
http://mathworld.wolfram.com/Plane-PlaneIntersection.html
Copied from ValveViewLogic to remove dependency on SlicerHeart extension.
"""
axialSliceToRas = axialNode.GetSliceToRAS()
n1 = [
axialSliceToRas.GetElement(0, 2),
axialSliceToRas.GetElement(1, 2),
axialSliceToRas.GetElement(2, 2)
]
x1 = [
axialSliceToRas.GetElement(0, 3),
axialSliceToRas.GetElement(1, 3),
axialSliceToRas.GetElement(2, 3)
]
ortho1SliceToRas = ortho1Node.GetSliceToRAS()
n2 = [
ortho1SliceToRas.GetElement(0, 2),
ortho1SliceToRas.GetElement(1, 2),
ortho1SliceToRas.GetElement(2, 2)
]
x2 = [
ortho1SliceToRas.GetElement(0, 3),
ortho1SliceToRas.GetElement(1, 3),
ortho1SliceToRas.GetElement(2, 3)
]
ortho2SliceToRas = ortho2Node.GetSliceToRAS()
n3 = [
ortho2SliceToRas.GetElement(0, 2),
ortho2SliceToRas.GetElement(1, 2),
ortho2SliceToRas.GetElement(2, 2)
]
x3 = [
ortho2SliceToRas.GetElement(0, 3),
ortho2SliceToRas.GetElement(1, 3),
ortho2SliceToRas.GetElement(2, 3)
]
# Computed intersection point of all planes
x = [0, 0, 0]
n2_xp_n3 = [0, 0, 0]
x1_dp_n1 = vtk.vtkMath.Dot(x1, n1)
vtk.vtkMath.Cross(n2, n3, n2_xp_n3)
vtk.vtkMath.MultiplyScalar(n2_xp_n3, x1_dp_n1)
vtk.vtkMath.Add(x, n2_xp_n3, x)
n3_xp_n1 = [0, 0, 0]
x2_dp_n2 = vtk.vtkMath.Dot(x2, n2)
vtk.vtkMath.Cross(n3, n1, n3_xp_n1)
vtk.vtkMath.MultiplyScalar(n3_xp_n1, x2_dp_n2)
vtk.vtkMath.Add(x, n3_xp_n1, x)
n1_xp_n2 = [0, 0, 0]
x3_dp_n3 = vtk.vtkMath.Dot(x3, n3)
vtk.vtkMath.Cross(n1, n2, n1_xp_n2)
vtk.vtkMath.MultiplyScalar(n1_xp_n2, x3_dp_n3)
vtk.vtkMath.Add(x, n1_xp_n2, x)
normalMatrix = vtk.vtkMatrix3x3()
normalMatrix.SetElement(0, 0, n1[0])
normalMatrix.SetElement(1, 0, n1[1])
normalMatrix.SetElement(2, 0, n1[2])
normalMatrix.SetElement(0, 1, n2[0])
normalMatrix.SetElement(1, 1, n2[1])
normalMatrix.SetElement(2, 1, n2[2])
normalMatrix.SetElement(0, 2, n3[0])
normalMatrix.SetElement(1, 2, n3[1])
normalMatrix.SetElement(2, 2, n3[2])
normalMatrixDeterminant = normalMatrix.Determinant()
if abs(normalMatrixDeterminant) > 0.01:
# there is an intersection point
vtk.vtkMath.MultiplyScalar(x, 1 / normalMatrixDeterminant)
else:
# no intersection point can be determined, use just the position of the axial slice
x = x1
return x
def getPlaneIntersectionPoint(self, axialNode, ortho1Node, ortho2Node):
# Compute the center of rotation (common intersection point of the three planes)
# http://mathworld.wolfram.com/Plane-PlaneIntersection.html
#axialNode = slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeRed')
#ortho1Node = slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeYellow')
#ortho2Node = slicer.mrmlScene.GetNodeByID('vtkMRMLSliceNodeGreen')
axialSliceToRas = axialNode.GetSliceToRAS()
n1 = [
axialSliceToRas.GetElement(0, 2),
axialSliceToRas.GetElement(1, 2),
axialSliceToRas.GetElement(2, 2)
]
x1 = [
axialSliceToRas.GetElement(0, 3),
axialSliceToRas.GetElement(1, 3),
axialSliceToRas.GetElement(2, 3)
]
ortho1SliceToRas = ortho1Node.GetSliceToRAS()
n2 = [
ortho1SliceToRas.GetElement(0, 2),
ortho1SliceToRas.GetElement(1, 2),
ortho1SliceToRas.GetElement(2, 2)
]
x2 = [
ortho1SliceToRas.GetElement(0, 3),
ortho1SliceToRas.GetElement(1, 3),
ortho1SliceToRas.GetElement(2, 3)
]
ortho2SliceToRas = ortho2Node.GetSliceToRAS()
n3 = [
ortho2SliceToRas.GetElement(0, 2),
ortho2SliceToRas.GetElement(1, 2),
ortho2SliceToRas.GetElement(2, 2)
]
x3 = [
ortho2SliceToRas.GetElement(0, 3),
ortho2SliceToRas.GetElement(1, 3),
ortho2SliceToRas.GetElement(2, 3)
]
# Computed intersection point of all planes
x = [0, 0, 0]
n2_xp_n3 = [0, 0, 0]
x1_dp_n1 = vtk.vtkMath.Dot(x1, n1)
vtk.vtkMath.Cross(n2, n3, n2_xp_n3)
vtk.vtkMath.MultiplyScalar(n2_xp_n3, x1_dp_n1)
vtk.vtkMath.Add(x, n2_xp_n3, x)
n3_xp_n1 = [0, 0, 0]
x2_dp_n2 = vtk.vtkMath.Dot(x2, n2)
vtk.vtkMath.Cross(n3, n1, n3_xp_n1)
vtk.vtkMath.MultiplyScalar(n3_xp_n1, x2_dp_n2)
vtk.vtkMath.Add(x, n3_xp_n1, x)
n1_xp_n2 = [0, 0, 0]
x3_dp_n3 = vtk.vtkMath.Dot(x3, n3)
vtk.vtkMath.Cross(n1, n2, n1_xp_n2)
vtk.vtkMath.MultiplyScalar(n1_xp_n2, x3_dp_n3)
vtk.vtkMath.Add(x, n1_xp_n2, x)
normalMatrix = vtk.vtkMatrix3x3()
normalMatrix.SetElement(0, 0, n1[0])
normalMatrix.SetElement(1, 0, n1[1])
normalMatrix.SetElement(2, 0, n1[2])
normalMatrix.SetElement(0, 1, n2[0])
normalMatrix.SetElement(1, 1, n2[1])
normalMatrix.SetElement(2, 1, n2[2])
normalMatrix.SetElement(0, 2, n3[0])
normalMatrix.SetElement(1, 2, n3[1])
normalMatrix.SetElement(2, 2, n3[2])
normalMatrixDeterminant = normalMatrix.Determinant()
if abs(normalMatrixDeterminant) > 0.01:
# there is an intersection point
vtk.vtkMath.MultiplyScalar(x, 1 / normalMatrixDeterminant)
else:
# no intersection point can be determined, use just the position of the axial slice
x = x1
return x
def sampleVolumeParameters(self):
"""Calculate the dictionary of substitutions for the
current state of the volume node in a form for
substitution into the sampleVolume shader function
TODO: this would probably be better as uniforms, but that
requires doing a lot of parsing and data management in C++
"""
rasToIJK = vtk.vtkMatrix4x4()
self.node.GetRASToIJKMatrix(rasToIJK)
transformNode = self.node.GetParentTransformNode()
if transformNode:
if transformNode.IsTransformToWorldLinear():
rasToRAS = vtk.vtkMatrix4x4()
transformNode.GetMatrixTransformToWorld(rasToRAS)
rasToRAS.Invert()
rasToRAS.Multiply4x4(rasToIJK, rasToRAS, rasToIJK)
else:
error.warn('Cannot handle nonlinear transforms')
# dimensions are number of pixels in (row, column, slice)
# which maps to 0-1 space of S, T, P
dimensions = self.node.GetImageData().GetDimensions()
ijkToSTP = vtk.vtkMatrix4x4()
ijkToSTP.Identity()
for diagonal in range(3):
ijkToSTP.SetElement(diagonal, diagonal, 1. / dimensions[diagonal])
rasToSTP = vtk.vtkMatrix4x4()
ijkToSTP.Multiply4x4(ijkToSTP, rasToIJK, rasToSTP)
parameters = {}
rows = ('rasToS', 'rasToT', 'rasToP')
for row in range(3):
rowKey = rows[row]
parameters[rowKey] = ""
for col in range(4):
element = rasToSTP.GetElement(row, col)
parameters[rowKey] += "%f," % element
parameters[rowKey] = parameters[rowKey][:
-1] # clear trailing comma
# since texture is 0-1, take into account both pixel spacing
# and dimension as layed out in memory so that the normals
# is calculated in a uniform space
spacings = self.node.GetSpacing()
parameters['mmToS'] = spacings[0] / dimensions[0]
parameters['mmToT'] = spacings[1] / dimensions[1]
parameters['mmToP'] = spacings[2] / dimensions[2]
# the inverse transpose of the upper 3x3 of the stpToRAS matrix,
# which is the transpose of the upper 3x3 of the rasTSTP matrix
normalSTPToRAS = vtk.vtkMatrix3x3()
for row in range(3):
for column in range(3):
normalSTPToRAS.SetElement(row, column,
rasToSTP.GetElement(row, column))
normalSTPToRAS.Transpose()
parameters['normalSTPToRAS'] = ''
for column in range(3):
for row in range(3):
# write in column-major order for glsl mat3 constructor
parameters[
'normalSTPToRAS'] += "%f," % normalSTPToRAS.GetElement(
row, column)
parameters['normalSTPToRAS'] = parameters[
'normalSTPToRAS'][:-1] # clear trailing comma
return parameters