def computeYaw(self, markupsNode1, landmark1Index, markupsNode2, landmark2Index, markupsNode3, landmark3Index, markupsNode4, landmark4Index):
# Yaw is computed by projection on the plan (x,y)
coord1 = [-1, -1, -1]
coord2 = [-1, -1, -1]
coord3 = [-1, -1, -1]
coord4 = [-1, -1, -1]
markupsNode1.GetNthFiducialPosition(landmark1Index, coord1)
markupsNode2.GetNthFiducialPosition(landmark2Index, coord2)
markupsNode3.GetNthFiducialPosition(landmark3Index, coord3)
markupsNode4.GetNthFiducialPosition(landmark4Index, coord4)
vectLine1 = [coord2[0]-coord1[0], coord2[1]-coord1[1], 0 ]
normVectLine1 = numpy.sqrt( vectLine1[0]*vectLine1[0] + vectLine1[1]*vectLine1[1] )
print "vecline1", vectLine1, normVectLine1
vectLine2 = [coord4[0]-coord3[0],coord4[1]-coord3[1], 0]
normVectLine2 = numpy.sqrt( vectLine2[0]*vectLine2[0] + vectLine2[1]*vectLine2[1] )
print "vecline2", vectLine2, normVectLine2
yawNotSigned = round(vtk.vtkMath().DegreesFromRadians(vtk.vtkMath().AngleBetweenVectors(vectLine1, vectLine2)), self.numberOfDecimals)
print"YAWCOMPUTED", yawNotSigned
if normVectLine1 != 0 and normVectLine2 != 0:
normalizedVectLine1 = [(1/normVectLine1)*vectLine1[0], (1/normVectLine1)*vectLine1[1], 0]
print "normalizedVectLine1" , normalizedVectLine1
normalizedVectLine2 = [(1/normVectLine2)*vectLine2[0], (1/normVectLine2)*vectLine2[1], 0]
print "normalizedVectLine2" , normalizedVectLine2
det2D = normalizedVectLine1[0]*normalizedVectLine2[1] - normalizedVectLine1[1]*normalizedVectLine2[0]
print det2D
print math.copysign(yawNotSigned, det2D)
return math.copysign(yawNotSigned, det2D)
else:
print " ERROR, norm of your vector is 0! DEFINE A VECTOR!"
return None
def __init__(self):
self._ROIVisibility = False
self._ROIStencil = None
self._IgnoreResetPoints = False
self._Objects3D = []
self.bIsConnected = False
self._Math = vtk.vtkMath()
self.__Cube = ROICubeFactory.ROICubeFactory()
self.__Cylinder = ROICylinderFactory.ROICylinderFactory()
self.__Sphere = ROISphereFactory.ROISphereFactory()
self.__Cube.SetVisibility(True)
self.__Cylinder.SetVisibility(False)
self.__Sphere.SetVisibility(False)
# two marks for visual cues for key 7 and 8
self._Mark = []
for i in range(2):
m = SphereMarkFactory.SphereMarkFactory()
m.SetColor(1.0, 1.0, 0.0)
m.SetSize(10.)
m.SetOpacity(0.)
self._Mark.append(m)
self._Objects3D.append(self.__Cylinder)
self._Objects3D.append(self.__Cube)
self._Objects3D.append(self.__Sphere)
self._Objects3D.append(self._Mark[0])
self._Objects3D.append(self._Mark[1])
# Bind some events
self.__Cube.AddObserver('StartAction', self.onStartAction)
def calc_seg_perp_vector(Xpts,Ypts,Zpts,direction): ## @brief Function to calculate the normal to three points. This is used for # the first and last segmentations to specify as an end derivative. # @param Xpts, x coordinate for three points # @param Ypts, y coordinate for three points # @param Zpts, z coordinate for three points # @param direction, direction in which the normal should face. The dot # product of this and the normal calculated will be > 0. # @return perp, the normal to the given three points math = vtk.vtkMath() #Initiate vecs for cross product vec1 = [Xpts[1]-Xpts[0],Ypts[1]-Ypts[0],Zpts[1]-Zpts[0]] vec2 = [Xpts[2]-Xpts[0],Ypts[2]-Ypts[2],Zpts[2]-Zpts[0]] perp = [0.0,0.0,0.0] dirl = [0.0,0.0,0.0] for i in range(3): dirl[i] = direction[i] math.Cross(vec1,vec2,perp) dotval = math.Dot(perp,dirl) if (dotval < 0): for i in range(3): perp[i] = -1.0*perp[i] return perp
def display(data, data2=None, data3=None):
# Generate some random points
math = vtk.vtkMath()
points = vtk.vtkPoints()
[data, scalefactor]=scaledata(data)
for i in range(len(data)):
points.InsertNextPoint( data[i,0],data[i,1], data[i,2]);
ballActor = vtksetup(points, color=red, radius=.001)
[ren,renWin,iren]=vtkwindow()
ren.AddActor(ballActor) # Add the actors to the renderer, set the background and size
if data2 != None:
data=data2*scalefactor
points = vtk.vtkPoints()
for i in range(len(data)):
points.InsertNextPoint( data[i,0],data[i,1], data[i,2]);
ballActor = vtksetup(points, color=blue)
ren.AddActor(ballActor)
if data3 != None:
data=data3*scalefactor
points = vtk.vtkPoints()
for i in range(len(data)):
points.InsertNextPoint( data[i,0],data[i,1], data[i,2]);
ballActor = vtksetup(points, color=green, radius=.007)
ren.AddActor(ballActor)
# Interact with the data.
iren.Initialize()
renWin.Render()
iren.Start()
def __init__(self):
self._ROIVisibility = False
self._ROIStencil = None
self._IgnoreResetPoints = False
self._Objects3D = []
self.bIsConnected = False
self._Math = vtk.vtkMath()
self.__Cube = ROICubeFactory.ROICubeFactory()
self.__Cylinder = ROICylinderFactory.ROICylinderFactory()
self.__Sphere = ROISphereFactory.ROISphereFactory()
self.__Cube.SetVisibility(True)
self.__Cylinder.SetVisibility(False)
self.__Sphere.SetVisibility(False)
# two marks for visual cues for key 7 and 8
self._Mark = []
for i in range(2):
m = SphereMarkFactory.SphereMarkFactory()
m.SetColor(1.0, 1.0, 0.0)
m.SetSize(10.)
m.SetOpacity(0.)
self._Mark.append(m)
self._Objects3D.append(self.__Cylinder)
self._Objects3D.append(self.__Cube)
self._Objects3D.append(self.__Sphere)
self._Objects3D.append(self._Mark[0])
self._Objects3D.append(self._Mark[1])
# Bind some events
self.__Cube.AddObserver('StartAction', self.onStartAction)
def get_arrow_orintation(endPoint, startPoint, norm=[0, 0, 1]):
""" Compute orientation matrix."""
normalizedX = zero3()
normalizedY = zero3()
normalizedZ = zero3()
math = vtk.vtkMath()
math.Subtract(endPoint, startPoint, normalizedX)
length = math.Norm(normalizedX)
math.Normalize(normalizedX)
# The Z axis is an arbitrary vector cross X
math.Cross(normalizedX, norm, normalizedZ)
math.Normalize(normalizedZ)
# The Y axis is Z cross X
math.Cross(normalizedZ, normalizedX, normalizedY)
# Create the direction cosine matrix
matrix = vtk.vtkMatrix4x4()
matrix.Identity()
for i in range(3):
matrix.SetElement(i, 0, normalizedX[i])
matrix.SetElement(i, 1, normalizedY[i])
matrix.SetElement(i, 2, normalizedZ[i])
return matrix, length
def __init__(self, startPoint, endPoint, zAxis, clr2plt):
super().__init__()
colors = vtk.vtkNamedColors()
USER_MATRIX = False
# Create an arrow.
arrowSource = vtk.vtkArrowSource()
# Compute a basis
normalizedX = [0 for i in range(3)]
normalizedY = [0 for i in range(3)]
normalizedZ = [0 for i in range(3)]
# The X axis is a vector from start to end
math = vtk.vtkMath()
math.Subtract(endPoint, startPoint, normalizedX)
length = math.Norm(normalizedX)
print(length)
math.Normalize(normalizedX)
# The Z axis is an arbitrary vector cross X
arbitrary = zAxis
math.Cross(normalizedX, arbitrary, normalizedZ)
math.Normalize(normalizedZ)
# The Y axis is Z cross X
math.Cross(normalizedZ, normalizedX, normalizedY)
matrix = vtk.vtkMatrix4x4()
# Create the direction cosine matrix
matrix.Identity()
for i in range(3):
matrix.SetElement(i, 0, normalizedX[i])
matrix.SetElement(i, 1, normalizedY[i])
matrix.SetElement(i, 2, normalizedZ[i])
# Apply the transforms
transform = vtk.vtkTransform()
transform.Translate(startPoint)
transform.Concatenate(matrix)
transform.Scale(length, length, length)
# Transform the polydata
transformPD = vtk.vtkTransformPolyDataFilter()
transformPD.SetTransform(transform)
transformPD.SetInputConnection(arrowSource.GetOutputPort())
# Create a mapper and actor for the arrow
mapper = vtk.vtkPolyDataMapper()
if USER_MATRIX:
mapper.SetInputConnection(arrowSource.GetOutputPort())
self.SetUserMatrix(transform.GetMatrix())
else:
mapper.SetInputConnection(transformPD.GetOutputPort())
self.SetMapper(mapper)
self.GetProperty().SetColor(colors.GetColor3d(clr2plt))
renderer.AddActor(self)
def get_actor_from_arrow_vector(start_point,
end_point,
color=(0, 0, 0),
line_width=20):
arrow_source = vtk.vtkArrowSource()
random.seed(8775070)
# Compute a basis
normalized_x = [0] * 3
normalized_y = [0] * 3
normalized_z = [0] * 3
# The X axis is a vector from start to end
math = vtk.vtkMath()
math.Subtract(end_point, start_point, normalized_x)
length = math.Norm(normalized_x)
math.Normalize(normalized_x)
# The Z axis is an arbitrary vector cross X
arbitrary = [0] * 3
arbitrary[0] = random.uniform(-10, 10)
arbitrary[1] = random.uniform(-10, 10)
arbitrary[2] = random.uniform(-10, 10)
math.Cross(normalized_x, arbitrary, normalized_z)
math.Normalize(normalized_z)
# The Y axis is Z cross X
math.Cross(normalized_z, normalized_x, normalized_y)
matrix = vtk.vtkMatrix4x4()
# Create the direction cosine matrix
matrix.Identity()
for i in range(3):
matrix.SetElement(i, 0, normalized_x[i])
matrix.SetElement(i, 1, normalized_y[i])
matrix.SetElement(i, 2, normalized_z[i])
# Apply the transforms
transform = vtk.vtkTransform()
transform.Translate(start_point)
transform.Concatenate(matrix)
transform.Scale(length, line_width, line_width)
# Transform the polydata
transform_pd = vtk.vtkTransformPolyDataFilter()
transform_pd.SetTransform(transform)
transform_pd.SetInputConnection(arrow_source.GetOutputPort())
# Create a mapper and actor for the arrow
mapper = vtk.vtkPolyDataMapper()
actor = vtk.vtkActor()
mapper.SetInputConnection(transform_pd.GetOutputPort())
actor.SetMapper(mapper)
actor.GetProperty().SetColor(color[0], color[1], color[2])
return actor
def hsv2rgb(hsv):
"""Convert HSV to RGB color.
:param hsv:
"""
ma = vtk.vtkMath()
return ma.HSVToRGB(hsv)
def SetQuatOrientation( self, quaternion, shift, i_actor ):
# if not self.iniOk :
# raise Exception("vtpDrawScene not initialized. Call initScene() first")
# Convert quat to the rotation matrix
# self.mtxRot = [[0,0,0],[0,0,0],[0,0,0]]
vtk.vtkMath().QuaternionToMatrix3x3(quaternion, self.mtxRot[i_actor])
# print(self.mtxRot[i_actor])
# norm matrix
self.mtxRot[i_actor] = np.array(self.mtxRot[i_actor]).dot(np.array(self.norm_mat[i_actor]))
# Rotation: convert 3x3 to 4x4 matrix
mtxTr2 = vtk.vtkMatrix4x4() # identity mtx
for i in range(3):
for j in range(3) :
mtxTr2.SetElement(i, j, self.mtxRot[i_actor][i][j])
# three transforms:
# 1. move the object so the rotation center is in the coord center
tr = vtk.vtkTransform()
origin = np.array(self.modelActor[i_actor].GetOrigin())
position = np.array(self.modelActor[i_actor].GetPosition())
#trans = origin + position
trans = position
#trans = origin
tr.Translate(-trans)
mtxTr1 = tr.GetMatrix()
# 2. rotate around coord center using mtxTr2
mtxTr12 = vtk.vtkMatrix4x4()
vtk.vtkMatrix4x4().Multiply4x4 (mtxTr2, mtxTr1, mtxTr12)
## 3. move the object back
tr = vtk.vtkTransform()
tr.Translate(trans + np.array(shift))
mtxTr3 = tr.GetMatrix()
mtxTr123 = vtk.vtkMatrix4x4()
vtk.vtkMatrix4x4().Multiply4x4 (mtxTr3, mtxTr12, mtxTr123)
tr = vtk.vtkTransform()
tr.PreMultiply()
# tr.PostMultiply()
tr.Concatenate(mtxTr123)
self.modelActor[i_actor].SetUserTransform(tr)
def get_distance(self, v0_id, v1_id):
# Get 3d vector from id
p0 = self.get_point(v0_id)
p1 = self.get_point(v1_id)
squaredDistance = vtk.vtkMath().Distance2BetweenPoints(p0, p1)
return np.sqrt(squaredDistance)
def SetQuatOrientation(self, quaternion):
if not self.iniOk:
raise Exception(
"vtpDrawScene not initialized. Call initScene() first")
# Convert quat to the rotation matrix
mtxRot = [[0, 0, 0], [0, 0, 0], [0, 0, 0]]
vtk.vtkMath().QuaternionToMatrix3x3(quaternion, mtxRot)
# Rotation: convert 3x3 to 4x4 matrix
mtxTr2 = vtk.vtkMatrix4x4() # identity mtx
for i in range(3):
for j in range(3):
mtxTr2.SetElement(i, j, mtxRot[i][j])
self.modelActor.SetUserMatrix(mtxTr2)
self.renWin.Render()
def rgb2hsv(rgb):
"""Convert RGB to HSV color.
:param rgb:
"""
ma = vtk.vtkMath()
return ma.RGBToHSV(getColor(rgb))
def wind_actor(x, y, speed, deg):
arrow_length = speed * 10
arrow_source = vtk.vtkArrowSource()
arrow_source.SetShaftResolution(50)
arrow_source.SetTipResolution(50)
start_point = [x, y, 25]
end_point = [x - arrow_length * sin(radians(deg)), y - arrow_length * cos(radians(deg)), 25]
normalizedX = [0 for i in range(3)]
normalizedY = [0 for i in range(3)]
normalizedZ = [0 for i in range(3)]
# The X axis is a vector from start to end
math = vtk.vtkMath()
math.Subtract(end_point, start_point, normalizedX)
length = math.Norm(normalizedX)
math.Normalize(normalizedX)
# The Z axis is an arbitrary vector cross X
arbitrary = [0 for i in range(3)]
arbitrary[0] = 1
arbitrary[1] = 1
arbitrary[2] = 1
math.Cross(normalizedX, arbitrary, normalizedZ)
math.Normalize(normalizedZ)
# The Y axis is Z cross X
math.Cross(normalizedZ, normalizedX, normalizedY)
matrix = vtk.vtkMatrix4x4()
# Create the direction cosine matrix
matrix.Identity()
for i in range(3):
matrix.SetElement(i, 0, normalizedX[i])
matrix.SetElement(i, 1, normalizedY[i])
matrix.SetElement(i, 2, normalizedZ[i])
transform = vtk.vtkTransform()
transform.Translate(start_point)
transform.Concatenate(matrix)
transform.Scale(length, length, length)
transform_filter = vtk.vtkTransformPolyDataFilter()
transform_filter.SetTransform(transform)
transform_filter.SetInputConnection(arrow_source.GetOutputPort())
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(transform_filter.GetOutputPort())
actor = vtk.vtkActor()
actor.SetMapper(mapper)
actor.GetProperty().SetColor(255, 0, 0)
actor.SetVisibility(True)
return actor
def ResamplePoints(self, originalPoints, sampledPoints, samplingDistance,
closedCurve):
if (not originalPoints or not sampledPoints or samplingDistance <= 0):
print("ResamplePoints failed: invalid inputs")
return False
if (originalPoints.GetNumberOfPoints() < 2):
sampledPoints.DeepCopy(originalPoints)
return True
distanceFromLastSampledPoint = 0
previousCurvePoint = originalPoints.GetPoint(0)
sampledPoints.Reset()
sampledPoints.InsertNextPoint(
previousCurvePoint) # First point in new set is always point 0
numberOfOriginalPoints = originalPoints.GetNumberOfPoints()
totalSegmentLength = 0
for originalPointIndex in range(numberOfOriginalPoints):
currentCurvePoint = originalPoints.GetPoint(originalPointIndex)
segmentLength = math.sqrt(vtk.vtkMath().Distance2BetweenPoints(
currentCurvePoint, previousCurvePoint))
totalSegmentLength += segmentLength
if segmentLength <= 0:
continue
remainingSegmentLength = distanceFromLastSampledPoint + segmentLength
if round(remainingSegmentLength, 4) >= round(samplingDistance, 4):
segmentDirectionVector = np.array([
(currentCurvePoint[0] - previousCurvePoint[0]) /
segmentLength,
(currentCurvePoint[1] - previousCurvePoint[1]) /
segmentLength,
(currentCurvePoint[2] - previousCurvePoint[2]) /
segmentLength
])
# distance of new sampled point from previous curve point
distanceFromLastInterpolatedPoint = samplingDistance - distanceFromLastSampledPoint
while (round(remainingSegmentLength, 4) >= round(
samplingDistance, 4)):
newSampledPoint = np.array([
previousCurvePoint[0] + segmentDirectionVector[0] *
distanceFromLastInterpolatedPoint,
previousCurvePoint[1] + segmentDirectionVector[1] *
distanceFromLastInterpolatedPoint,
previousCurvePoint[2] + segmentDirectionVector[2] *
distanceFromLastInterpolatedPoint
])
sampledPoints.InsertNextPoint(newSampledPoint)
distanceFromLastSampledPoint = 0
distanceFromLastInterpolatedPoint += samplingDistance
remainingSegmentLength -= samplingDistance
distanceFromLastSampledPoint = remainingSegmentLength
else:
distanceFromLastSampledPoint += segmentLength
previousCurvePoint = currentCurvePoint
return True
def addVector(self, quaternion):
# make mapper for the data
arrowSource = vtk.vtkArrowSource()
arrowSource.SetShaftRadius(0.01)
arrowSource.SetTipLength(.1)
# arrowSource.SetNormalizedTipLength(0.05, 0.05, 0.05)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(arrowSource.GetOutputPort())
# create actor, set its mapper
self.modelActor.append(vtk.vtkActor())
el = len(self.modelActor) - 1
self.modelActor[el].SetMapper(mapper)
# Add the actor to the renderer, set the background and size.
self.ren.AddActor(self.modelActor[el])
#
self.mtxRot.append([[0, 0, 0], [0, 0, 0], [0, 0, 0]])
# Get center of the bounding box
origin = self.modelActor[el].GetCenter()
# Set rotation center
self.modelActor[el].SetOrigin(origin)
self.modelActor[el].SetPosition([-0.016, -0.006, -0.162])
mtxRot = np.identity(3)
vtk.vtkMath().QuaternionToMatrix3x3(quaternion, mtxRot)
# Rotation: convert 3x3 to 4x4 matrix
mtxTr = vtk.vtkMatrix4x4() # identity mtx
for i in range(3):
for j in range(3):
mtxTr.SetElement(i, j, mtxRot[i][j])
tr = vtk.vtkTransform()
tr.PreMultiply()
tr.Concatenate(mtxTr)
self.modelActor[el].SetUserTransform(tr)
def sliceClosestModel(self, point):
originalModel = None
# set up plane
normal = np.array([
float(self.sliceLogic.GetSliceNode().GetName() == name)
for name in ['Yellow', 'Green', 'Red']
])
plane = vtk.vtkPlane()
plane.SetOrigin(point) # point in plane
plane.SetNormal(normal)
# set up cutter
cutter = vtk.vtkCutter()
cutter.SetCutFunction(plane)
cutter.SetGenerateCutScalars(0)
cutter.Update()
# init point locator and output
pointsLocator = vtk.vtkPointLocator()
globalMinDistance = 1000
outPolyData = vtk.vtkPolyData()
# iterate over models in scene
nModels = slicer.mrmlScene.GetNumberOfNodesByClass('vtkMRMLModelNode')
for i in range(nModels):
model = slicer.mrmlScene.GetNthNodeByClass(i, 'vtkMRMLModelNode')
polyData = model.GetPolyData()
if model.GetDisplayNode() and model.GetDisplayNode().GetVisibility(
) and polyData.GetNumberOfCells() > 1 and model.GetName(
) != 'auxSphereModel': # model visible and cells available
cutter.SetInputData(polyData)
cutter.Update()
cutterOutput = cutter.GetOutput()
if cutterOutput.GetNumberOfCells(
): # model intersects with plane
# get distance from input point to closest point in model
pointsLocator.SetDataSet(cutterOutput)
pointsLocator.BuildLocator()
closestPoint = cutterOutput.GetPoint(
pointsLocator.FindClosestPoint(point))
localMinDistance = vtk.vtkMath().Distance2BetweenPoints(
closestPoint, point)
if localMinDistance < globalMinDistance: # new min
outPolyData.DeepCopy(cutterOutput)
globalMinDistance = localMinDistance
originalModel = model
# return in case no model found
if not originalModel:
return False, False
# generate output
triangulator = vtk.vtkContourTriangulator()
triangulator.SetInputData(outPolyData)
triangulator.Update()
slicedModel = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLModelNode')
slicedModel.SetAndObservePolyData(triangulator.GetOutput())
slicedModel.CreateDefaultDisplayNodes()
slicedModel.GetDisplayNode().SetVisibility(0)
return slicedModel, originalModel
def __init__(self, path):
reader = vtk.vtkOBJReader()
reader.SetFileName(path)
reader.Update()
self.obj = reader.GetOutput()
self.math = vtk.vtkMath()
# renderer
self.ren = vtk.vtkRenderer()
self.ren.SetBackground(ColorBackground)
self.actors = {}
def defineDistances(self, markupsNode1, landmark1Index, markupsNode2, landmark2Index):
coord1 = [-1, -1, -1]
coord2 = [-1, -1, -1]
markupsNode1.GetNthFiducialPosition(landmark1Index, coord1)
markupsNode2.GetNthFiducialPosition(landmark2Index, coord2)
print "point A: ", coord1
print "point B: ", coord2
diffRAxis = coord2[0] - coord1[0]
diffAAxis = coord2[1] - coord1[1]
diffSAxis = coord2[2] - coord1[2]
threeDDistance = math.sqrt(vtk.vtkMath().Distance2BetweenPoints(coord1, coord2))
return round(diffRAxis, self.numberOfDecimals), round(diffAAxis, self.numberOfDecimals), round(diffSAxis, self.numberOfDecimals), round(threeDDistance, self.numberOfDecimals)
def AddTimestamp( self, time, matrix, point, role ):
if ( time == self.timePrev ):
return
if ( self.timePrev == None or self.matrixPrev == None ):
self.timePrev = time
self.matrixPrev = vtk.vtkMatrix4x4()
self.matrixPrev.DeepCopy( matrix )
return
invertPrev = vtk.vtkMatrix4x4()
invertPrev.DeepCopy( self.matrixPrev )
invertPrev.Invert()
currChangeMatrix = vtk.vtkMatrix4x4()
vtk.vtkMatrix4x4().Multiply4x4( matrix, invertPrev, currChangeMatrix )
currChangeTransform = vtk.vtkTransform()
currChangeTransform.SetMatrix( currChangeMatrix )
currVelocity = [ 0, 0, 0 ]
currChangeTransform.GetPosition( currVelocity )
vtk.vtkMath().MultiplyScalar( currVelocity, 1 / ( time - self.timePrev ) )
currAbsVelocity = math.sqrt( currVelocity[ 0 ] * currVelocity[ 0 ] + currVelocity[ 1 ] * currVelocity[ 1 ] + currVelocity[ 2 ] * currVelocity[ 2 ] )
currentTestState = ( currAbsVelocity > TranslationalActions.VELOCITY_THRESHOLD )
if ( currentTestState == self.actionState ):
self.completeActionTime = time
else:
if ( ( time - self.completeActionTime ) > TranslationalActions.TIME_THRESHOLD ):
self.actionState = currentTestState
self.completeActionTime = time
if ( currentTestState == 1 ):
self.numActions += 1
self.timePrev = time
self.matrixPrev = vtk.vtkMatrix4x4()
self.matrixPrev.DeepCopy( matrix )
def feed_points_to_polydatavtk(self, xs, ys, zs):
'''
class method to load a vtk polydata object with a cloud of points
xs,ys,zs=[x,x1,...],[y,y1,...],[z,z1,...] indicating locations of nodes to be meshed
return:vtk polydata object
'''
math = vtk.vtkMath()
points = vtk.vtkPoints()
for i in range(len(xs)):
points.InsertPoint(i, xs[i], ys[i], zs[i])
profile = vtk.vtkPolyData()
profile.SetPoints(points)
return (profile)
def calcTransform(self, listLimbPoints):
startPoint = [0 for i in range(3)]
endPoint = [0 for i in range(3)]
center = [0 for i in range(3)]
normalizedX = [0 for i in range(3)]
normalizedY = [0 for i in range(3)]
normalizedZ = [0 for i in range(3)]
math = vtk.vtkMath()
arbitrary = [0 for i in range(3)]
matrix = vtk.vtkMatrix4x4()
arbitrary[0] = random.uniform(-10, 10)
arbitrary[1] = random.uniform(-10, 10)
arbitrary[2] = random.uniform(-10, 10)
transform = vtk.vtkTransform()
startPoint[0] = -listLimbPoints[0]
startPoint[1] = -listLimbPoints[1]
startPoint[2] = listLimbPoints[2]
endPoint[0] = -listLimbPoints[3]
endPoint[1] = -listLimbPoints[4]
endPoint[2] = listLimbPoints[5]
center[0] = (endPoint[0] + startPoint[0]) / 2
center[1] = (endPoint[1] + startPoint[1]) / 2
center[2] = (endPoint[2] + startPoint[2]) / 2
math.Subtract(endPoint, startPoint, normalizedX)
length = math.Norm(normalizedX)
math.Normalize(normalizedX)
math.Cross(normalizedX, arbitrary, normalizedZ)
math.Normalize(normalizedZ)
math.Cross(normalizedZ, normalizedX, normalizedY)
matrix.Identity()
for i in range(3):
matrix.SetElement(i, 0, normalizedY[i])
matrix.SetElement(i, 1, normalizedX[i])
matrix.SetElement(i, 2, normalizedZ[i])
#transform.PostMultiply()
transform.Translate(center)
transform.Concatenate(matrix)
transform.Scale(1, -1, 1)
return (transform, length)
def updateLine(self):
"""
Update the line to be near the selected point
"""
self.polyGrid = vtk.vtkUnstructuredGrid()
self.mapper.SetInput(self.polyGrid)
pts = []
pts.append((10, 105, 0))
pts.append((10, 95, 0))
pts.append((10, 100, 0))
pts.append((10 + self.widthPx, 100, 0))
pts.append((10 + self.widthPx, 105, 0))
pts.append((10 + self.widthPx, 95, 0))
n, points = self.pointsToPolyline(pts)
print "widthPx=", 100
pts2 = [(0, 0, 0), (self.widthPx, 0, 0)]
n, points2 = self.pointsToPolyline(pts2, 1)
p1, p2 = points2
m = vtk.vtkMath()
x, y, z = p1
x *= self.voxelSize[0] * 1000000
y *= self.voxelSize[1] * 1000000
z *= self.voxelSize[2] * 1000000
p1 = (x, y, z)
x, y, z = p2
x *= self.voxelSize[0] * 1000000
y *= self.voxelSize[1] * 1000000
z *= self.voxelSize[2] * 1000000
p2 = (x, y, z)
diff = m.Distance2BetweenPoints(p2, p1)
print "got diff=", diff
self.width = diff
self.textActor.SetDisplayPosition(-40 + self.widthPx / 2, 80)
self.textActor.SetInput("%.2fum" % self.width)
self.polyLine.GetPointIds().SetNumberOfIds(n)
for i in range(n):
self.polyLine.GetPointIds().SetId(i, i)
self.polyGrid.InsertNextCell(self.polyLine.GetCellType(),
self.polyLine.GetPointIds())
self.polyGrid.SetPoints(points)
def updateLine(self):
"""
Update the line to be near the selected point
"""
self.polyGrid = vtk.vtkUnstructuredGrid()
self.mapper.SetInput(self.polyGrid)
pts = []
pts.append((10, 105, 0))
pts.append((10, 95, 0))
pts.append((10, 100, 0))
pts.append((10 + self.widthPx, 100, 0))
pts.append((10 + self.widthPx, 105, 0))
pts.append((10 + self.widthPx, 95, 0))
n, points = self.pointsToPolyline(pts)
print "widthPx=", 100
pts2 = [(0, 0, 0), (self.widthPx, 0, 0)]
n, points2 = self.pointsToPolyline(pts2, 1)
p1, p2 = points2
m = vtk.vtkMath()
x, y, z = p1
x *= self.voxelSize[0] * 1000000
y *= self.voxelSize[1] * 1000000
z *= self.voxelSize[2] * 1000000
p1 = (x, y, z)
x, y, z = p2
x *= self.voxelSize[0] * 1000000
y *= self.voxelSize[1] * 1000000
z *= self.voxelSize[2] * 1000000
p2 = (x, y, z)
diff = m.Distance2BetweenPoints(p2, p1)
print "got diff=", diff
self.width = diff
self.textActor.SetDisplayPosition(-40 + self.widthPx / 2, 80)
self.textActor.SetInput("%.2fum" % self.width)
self.polyLine.GetPointIds().SetNumberOfIds(n)
for i in range(n):
self.polyLine.GetPointIds().SetId(i, i)
self.polyGrid.InsertNextCell(self.polyLine.GetCellType(),
self.polyLine.GetPointIds())
self.polyGrid.SetPoints(points)
def calc_seg_perp_vector(Xpts, Ypts, Zpts, direction):
math = vtk.vtkMath()
#Initiate vecs for cross product
vec1 = [Xpts[1] - Xpts[0], Ypts[1] - Ypts[0], Zpts[1] - Zpts[0]]
vec2 = [Xpts[2] - Xpts[0], Ypts[2] - Ypts[2], Zpts[2] - Zpts[0]]
perp = [0.0, 0.0, 0.0]
dirl = [0.0, 0.0, 0.0]
for i in range(3):
dirl[i] = direction[i]
math.Cross(vec1, vec2, perp)
dotval = math.Dot(perp, dirl)
if (dotval < 0):
for i in range(3):
perp[i] = -1.0 * perp[i]
return perp
def calc_seg_perp_vector(Xpts,Ypts,Zpts,direction): math = vtk.vtkMath() #Initiate vecs for cross product vec1 = [Xpts[1]-Xpts[0],Ypts[1]-Ypts[0],Zpts[1]-Zpts[0]] vec2 = [Xpts[2]-Xpts[0],Ypts[2]-Ypts[2],Zpts[2]-Zpts[0]] perp = [0.0,0.0,0.0] dirl = [0.0,0.0,0.0] for i in range(3): dirl[i] = direction[i] math.Cross(vec1,vec2,perp) dotval = math.Dot(perp,dirl) if (dotval < 0): for i in range(3): perp[i] = -1.0*perp[i] return perp
def colorCells():
randomColorGenerator = vtk.vtkMath()
input = randomColors.GetInput()
output = randomColors.GetOutput()
numCells = input.GetNumberOfCells()
colors = vtk.vtkFloatArray()
colors.SetNumberOfTuples(numCells)
i = 0
while i < numCells:
colors.SetValue(i, randomColorGenerator.Random(0, 1))
i = i + 1
output.GetCellData().CopyScalarsOff()
output.GetCellData().PassData(input.GetCellData())
output.GetCellData().SetScalars(colors)
del colors
# reference counting - it's ok
del randomColorGenerator
def colorCells (__vtk__temp0=0,__vtk__temp1=0):
randomColorGenerator = vtk.vtkMath()
input = randomColors.GetInput()
output = randomColors.GetOutput()
numCells = input.GetNumberOfCells()
colors = vtk.vtkFloatArray()
colors.SetNumberOfTuples(numCells)
i = 0
while i < numCells:
colors.SetValue(i,randomColorGenerator.Random(0,1))
i = i + 1
output.GetCellData().CopyScalarsOff()
output.GetCellData().PassData(input.GetCellData())
output.GetCellData().SetScalars(colors)
del colors
#reference counting - it's ok
del randomColorGenerator
def execute(self, obj, event):
for body_type in self.data:
for body in body_type:
body.trans.Identity()
# Quaternion stuff
yaw = body.angles[2]
pitch = body.angles[1]
roll = body.angles[0]
cy = np.cos(yaw * 0.5)
sy = np.sin(yaw * 0.5)
cp = np.cos(pitch * 0.5)
sp = np.sin(pitch * 0.5)
cr = np.cos(roll * 0.5)
sr = np.sin(roll * 0.5)
w = cy * cp * cr + sy * sp * sr
x = cy * cp * sr - sy * sp * cr
y = sy * cp * sr + cy * sp * cr
z = sy * cp * cr - cy * sp * sr
body_quaternion = np.quaternion(w, x, y, z)
# Convert to 4x4 vtkMatrix
vtkmath = vtk.vtkMath()
rot_mat_3x3 = np.zeros((3, 3))
vtkmath.QuaternionToMatrix3x3(body_quaternion.components,
rot_mat_3x3)
rot_mat_4x4 = np.zeros((4, 4))
rot_mat_4x4[0:3, 0:3] = rot_mat_3x3[:, :]
rot_mat_4x4[-1, -1] = 1
vtk_matrix = vtk.vtkMatrix4x4()
m, n = rot_mat_4x4.shape
for i in range(m):
for j in range(n):
vtk_matrix.SetElement(i, j, rot_mat_4x4[i][j])
body.trans.SetMatrix(vtk_matrix)
body.actor.SetUserTransform(body.trans)
print(body.angles, '\n')
obj.GetRenderWindow().Render()
def findClosestPointsTwoLists(X_source, X_target):
'''return the closest points indexes in X_source from the X_target points,
indexes output has the same length than X_target'''
listPoints = X_source
points = vtk.vtkPoints()
points.SetDataTypeToDouble()
listProbePoints = X_target
probePoints = vtk.vtkPoints()
probePoints.SetDataTypeToDouble()
for [x, y] in listPoints:
points.InsertNextPoint(x, y, 0.)
for [x, y] in listProbePoints:
probePoints.InsertNextPoint(x, y, 0.)
polydata = vtk.vtkPolyData()
polydata.SetPoints(points)
points.ComputeBounds()
staticLocator = vtk.vtkStaticPointLocator()
staticLocator.SetDataSet(polydata)
staticLocator.SetNumberOfPointsPerBucket(5)
staticLocator.AutomaticOn()
staticLocator.BuildLocator()
staticClosestN = vtk.vtkIdList()
ind = np.zeros(len(X_target), dtype=np.int)
D = np.zeros(len(X_target))
math = vtk.vtkMath()
x = [0, 0, 0]
p = [0, 0, 0]
staticClosestN = vtk.vtkIdList()
for i in range(len(X_target)):
staticLocator.FindClosestNPoints(1, probePoints.GetPoint(i),
staticClosestN)
ind[i] = staticClosestN.GetId(0) # we then select the closest point
points.GetPoint(ind[i], x)
probePoints.GetPoint(i, p)
D[i] = math.Distance2BetweenPoints(x, p)**0.5
return ind, D
def drawArrow(start_point, end_point):
math = vtk.vtkMath()
# X-Axis is a vector from start to end
normX = np.subtract(start_point, end_point)
length = np.linalg.norm(normX)
normX = np.divide(normX, length)
# Z axis is an arbitrary vector cross X
arbitrary = [0.0, 0.0, 1.0]
normZ = np.cross(normX, arbitrary)
# Y-Axis is Z cross X
normY = np.cross(normZ, normX)
tVec_at_b0_mat = vtk.vtkMatrix4x4()
tVec_at_b0_mat.Identity()
for i in range(3):
tVec_at_b0_mat.SetElement(i, 0, normX[i])
tVec_at_b0_mat.SetElement(i, 1, normY[i])
tVec_at_b0_mat.SetElement(i, 2, normZ[i])
arrowBase = vtk.vtkArrowSource()
arrowBase.Update()
print(arrowBase.GetTipLength())
print(arrowBase.GetTipRadius())
print(arrowBase.GetTipResolution())
print(arrowBase.GetShaftRadius())
print(arrowBase.GetShaftResolution())
arrow_transform = vtk.vtkTransform()
arrow_transform.Translate(start_point)
arrow_transform.Concatenate(tVec_at_b0_mat)
arrow_transform.Scale(length, length, length)
arrow_transform.Update()
transformPD = vtk.vtkTransformPolyDataFilter()
transformPD.SetInputData(arrowBase.GetOutput())
transformPD.SetTransform(arrow_transform)
transformPD.Update()
return transformPD.GetOutput()
def opyfFindClosestPointandDistance3D(X):
staticLocator, points, probePoints = opyfBuildLocatorandStuff3D(X)
staticClosestN = vtk.vtkIdList()
ind = np.zeros(len(X), dtype=np.int)
D = np.zeros(len(X))
math = vtk.vtkMath()
x = [0, 0, 0]
p = [0, 0, 0]
staticClosestN = vtk.vtkIdList()
for i in range(len(X)):
staticLocator.FindClosestNPoints(2, probePoints.GetPoint(i),
staticClosestN)
ind[i] = staticClosestN.GetId(1) # we then select the furthest point
points.GetPoint(ind[i], x)
points.GetPoint(i, p)
D[i] = math.Distance2BetweenPoints(x, p)**0.5
return ind, D
def find_final_cut(self, normal, centroid):
final_plane = vtk.vtkPlane()
final_plane.SetOrigin(centroid)
final_plane.SetNormal(normal)
final_cutter = vtk.vtkCutter()
final_cutter.SetInputData(self.pred_surface)
final_cutter.SetCutFunction(final_plane)
final_cutter.GenerateCutScalarsOff()
final_stripper = vtk.vtkStripper()
final_stripper.SetInputConnection(final_cutter.GetOutputPort())
final_stripper.Update()
MaxCutNumber = 0
area = 0
minDist = np.inf
minIDX = -1
minIDXarea = 0
for i in range(final_stripper.GetOutput().GetNumberOfCells()):
final_pd = final_stripper.GetOutput().GetCell(i).GetPoints()
final_CM = self.vtkCenterOfMass(final_pd)
final_d2 = vtk.vtkMath().Distance2BetweenPoints(final_CM, centroid)
if final_d2 < minDist:
minDist = final_d2
minIDX = i
# Final cut
finalCut = vtk.vtkPolyData()
finalCut.DeepCopy(final_stripper.GetOutput())
final_line = finalCut.GetCell(minIDX)
points = final_line.GetPoints()
#cells = vtk.vtkCellArray()
#cells.InsertNextCell(final_line)
# pd_finalCut = vtk.vtkPolyData()
# pd_finalCut.SetPoints(points)
# pd_finalCut.SetLines(cells)
return points
def distanceAfterRegistration(self, initialModel, inputModel, fidList, transformNode):
# Computes the distance between the models following registration
# computes the distance between the entire models but if the code below is
# uncommented then only the distance between the breasts will be computed
breastBoundPolyData = vtk.vtkPolyData()
self.FiducialsToPolyData(fidList, breastBoundPolyData)
# Create plane of best fit from input breast boundary fiducials
plane = vtk.vtkPlane()
self.LeastSquaresPlane(inputModel, breastBoundPolyData, plane)
#Compute the mean distance after registration
# If above is uncommented comment out the two lines following
sourcePolyData = initialModel.GetPolyData()
targetPolyData = inputModel.GetPolyData()
cellId = vtk.mutable(0)
subId = vtk.mutable(0)
dist2 = vtk.mutable(0.0)
locator = vtk.vtkCellLocator()
locator.SetDataSet(targetPolyData)
locator.SetNumberOfCellsPerBucket(1)
locator.BuildLocator()
totalDistance = 0.0
sourcePoints = sourcePolyData.GetPoints()
n = sourcePoints.GetNumberOfPoints()
m = vtk.vtkMath()
for sourcePointIndex in xrange(n):
sourcePointPos = [0, 0, 0]
sourcePoints.GetPoint(sourcePointIndex, sourcePointPos)
transformedSourcePointPos = [0, 0, 0, 1]
sourcePointPos.append(1)
transformNode.GetTransformToParent().MultiplyPoint(sourcePointPos, transformedSourcePointPos)
surfacePoint = [0, 0, 0]
transformedSourcePointPos.pop()
locator.FindClosestPoint(transformedSourcePointPos, surfacePoint, cellId, subId, dist2)
totalDistance = totalDistance + math.sqrt(dist2)
return (round((totalDistance/n),2))
def geodesic_distance(poly, start, end):
'''
The mesh must be a manifold
'''
d_graph = vtk.vtkDijkstraGraphGeodesicPath()
d_graph.SetInputData(poly)
d_graph.SetStartVertex(start)
d_graph.SetEndVertex(end)
d_graph.Update()
id_list = d_graph.GetIdList()
if id_list.GetNumberOfIds() == 0:
return float("inf")
distance = 0.
points = poly.GetPoints()
for i in range(id_list.GetNumberOfIds() - 1):
i_curr = id_list.GetId(i)
i_next = id_list.GetId(i + 1)
dist = vtk.vtkMath()
distance += dist.Distance2BetweenPoints(points.GetPoint(i_curr),
points.GetPoint(i_next))
return distance
def __init__(self, sim, pos, dims, density, fixed=False):
# ODE initialization
x, y, z = pos # initial pos
lx, ly, lz = dims # dimensions
self.sim = sim # link to the sim object
self.body = ode.Body(self.sim.world) # ode body
mass = ode.Mass() # mass object
mass.setBox(density, lx, ly, lz) # calculate mass
self.body.setMass(mass) # link mass to body
self.body.setPosition(pos) # set the initial pos
self.geom = ode.GeomBox(self.sim.space, lengths=dims) # geometry
self.geom.setBody(self.body) # link geometry and body
if fixed:
self.fixedJoint = ode.FixedJoint(self.sim.world)
self.fixedJoint.attach(self.body,self.sim.space.getBody())
self.fixedJoint.setFixed()
# VTK initialization
self.math = vtk.vtkMath()
self.cube = vtk.vtkCubeSource()
self.cube.SetXLength(lx)
self.cube.SetYLength(ly)
self.cube.SetZLength(lz)
self.cube.SetCenter((0.0,0.0,0.0))
self.reader = vtk.vtkJPEGReader()
self.reader.SetFileName(ROBOT_IMAGE)
self.texture = vtk.vtkTexture()
transform = vtk.vtkTransform()
transform.Scale(1.0,1.0,1.0)
self.texture.SetTransform(transform)
self.texture.SetInput(self.reader.GetOutput())
self.mapper = vtk.vtkPolyDataMapper()
self.mapper.SetInput(self.cube.GetOutput())
self.actor = vtk.vtkActor()
self.actor.SetMapper(self.mapper)
self.actor.SetTexture(self.texture)
sim.renderer.AddActor(self.actor)
# Self-include in the bodies for visualization
sim.bodies.append(self)
def _get_transform(startPoint, endPoint, f):
# Compute a basis
normalized_x = [0 for i in range(3)]
normalized_y = [0 for i in range(3)]
normalized_z = [0 for i in range(3)]
# The X axis is a vector from start to end
math = vtk.vtkMath()
math.Subtract(endPoint, startPoint, normalized_x)
length = math.Norm(normalized_x)
math.Normalize(normalized_x)
# The Z axis is an arbitrary vector cross X
arbitrary = [0 for i in range(3)]
arbitrary[0] = random.uniform(-10, 10)
arbitrary[1] = random.uniform(-10, 10)
arbitrary[2] = random.uniform(-10, 10)
math.Cross(normalized_x, arbitrary, normalized_z)
math.Normalize(normalized_z)
# The Y axis is Z cross X
math.Cross(normalized_z, normalized_x, normalized_y)
matrix = vtk.vtkMatrix4x4()
# Create the direction cosine matrix
matrix.Identity()
for i in range(3):
matrix.SetElement(i, 0, normalized_x[i])
matrix.SetElement(i, 1, normalized_y[i])
matrix.SetElement(i, 2, normalized_z[i])
# Apply the transforms
transform = vtk.vtkTransform()
transform.Translate(startPoint)
transform.Concatenate(matrix)
transform.Scale(length * f, length * f, length * f)
return transform
def generateVTK2DFromPoints(listOfPoints, name):
math = vtk.vtkMath()
points = vtk.vtkPoints()
for elt in listOfPoints:
(i,x,y) = elt
points.InsertPoint(i,x,y,0)
profile = vtk.vtkPolyData()
profile.SetPoints(points)
delny = vtk.vtkDelaunay2D()
delny.SetInputData(profile)
delny.SetTolerance(0.0001)
delny.SetAlpha(0)
print("alpha :",delny.GetAlpha())
print("Output :", delny.GetOutput())
delny.BoundingTriangulationOff()
toSave = vtk.vtkPolyDataWriter()
toSave.SetInputConnection(delny.GetOutputPort())
toSave.SetFileName(name)
toSave.Write()
def geodesic_distance_map(poly, start, threshold, max_depth=3000):
'''
compute the geodesic distance map on a polydata from a starting point
'''
count = 0
dist_arr = np.ones(poly.GetNumberOfPoints()) * np.inf
vtk_math = vtk.vtkMath()
points = poly.GetPoints()
pt_queue = [start]
dist_queue = [0.]
visited_list = [start]
while pt_queue and count < max_depth:
count += 1
print("debug: ", pt_queue)
node = pt_queue.pop(0)
dist = dist_queue.pop(0)
dist_arr[node] = dist
tmplt_list = vtk.vtkIdList()
poly.GetPointCells(node, tmplt_list)
for i in range(tmplt_list.GetNumberOfIds()):
tmplt_pt_list = vtk.vtkIdList()
poly.GetCellPoints(tmplt_list.GetId(i), tmplt_pt_list)
for j in range(tmplt_pt_list.GetNumberOfIds()):
p_id = tmplt_pt_list.GetId(j)
if not p_id in visited_list:
visited_list.append(p_id)
cum_dist = np.linalg.norm(
np.array(points.GetPoint(node)) -
np.array(points.GetPoint(p_id))) + dist
print("dist: ", cum_dist)
if cum_dist < threshold:
pt_queue.append(p_id)
dist_queue.append(cum_dist)
print("count: ", count)
return dist_arr
def generateVTKFromPoints(listOfPoints):
math = vtk.vtkMath()
points = vtk.vtkPoints()
for elt in listOfPoints:
(i,x,y,z) = elt
points.InsertPoint(i,x,y,z)
profile = vtk.vtkPolyData()
profile.SetPoints(points)
delny = vtk.vtkDelaunay3D()
delny.SetInputData(profile)
delny.SetTolerance(0.0001)
delny.SetAlpha(0)
print("alpha :",delny.GetAlpha())
print("Output :", delny.GetOutput())
delny.BoundingTriangulationOff()
toSave = vtk.vtkUnstructuredGridWriter()
toSave.SetInputConnection(delny.GetOutputPort())
toSave.SetFileName("Cube"+str(len(listOfPoints))+".vtk")
toSave.Write()
def Execute(self):
if self.Mesh == None:
self.PrintError('Error: No input mesh.')
if not self.CellEntityIdsArrayName:
self.PrintError('Error: No input CellEntityIdsArrayName.')
return
cellEntityIdsArray = self.Mesh.GetCellData().GetArray(self.CellEntityIdsArrayName)
#cut off the volumetric elements
wallThreshold = vtk.vtkThreshold()
wallThreshold.SetInputData(self.Mesh)
wallThreshold.ThresholdByUpper(self.SurfaceCellEntityId-0.5)
wallThreshold.SetInputArrayToProcess(0,0,0,1,self.CellEntityIdsArrayName)
wallThreshold.Update()
meshToSurface = vmtkscripts.vmtkMeshToSurface()
meshToSurface.Mesh = wallThreshold.GetOutput()
meshToSurface.Execute()
#Compute the normals for this surface, orientation should be right because the surface is closed
#TODO: Add option for cell normals in vmtksurfacenormals
normalsFilter = vtk.vtkPolyDataNormals()
normalsFilter.SetInputData(meshToSurface.Surface)
normalsFilter.SetAutoOrientNormals(1)
normalsFilter.SetFlipNormals(0)
normalsFilter.SetConsistency(1)
normalsFilter.SplittingOff()
normalsFilter.ComputePointNormalsOff()
normalsFilter.ComputeCellNormalsOn()
normalsFilter.Update()
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = normalsFilter.GetOutput()
surfaceToMesh.Execute()
#Save the current normals
wallWithBoundariesMesh = surfaceToMesh.Mesh
savedNormals = vtk.vtkDoubleArray()
savedNormals.DeepCopy(wallWithBoundariesMesh.GetCellData().GetNormals())
savedNormals.SetName('SavedNormals')
wallWithBoundariesMesh.GetCellData().AddArray(savedNormals)
#cut off the boundaries and other surfaces
extrudeThresholdLower = vtk.vtkThreshold()
extrudeThresholdLower.SetInputData(wallWithBoundariesMesh)
extrudeThresholdLower.ThresholdByLower(self.ExtrudeCellEntityId+0.5)
extrudeThresholdLower.SetInputArrayToProcess(0,0,0,1,self.CellEntityIdsArrayName)
extrudeThresholdLower.Update()
extrudeThresholdUpper = vtk.vtkThreshold()
extrudeThresholdUpper.SetInputConnection(extrudeThresholdLower.GetOutputPort())
extrudeThresholdUpper.ThresholdByUpper(self.ExtrudeCellEntityId-0.5)
extrudeThresholdUpper.SetInputArrayToProcess(0,0,0,1,self.CellEntityIdsArrayName)
extrudeThresholdUpper.Update()
meshToSurface = vmtkscripts.vmtkMeshToSurface()
meshToSurface.Mesh = extrudeThresholdUpper.GetOutput()
meshToSurface.Execute()
#Compute cell normals without boundaries
normalsFilter = vtk.vtkPolyDataNormals()
normalsFilter.SetInputData(meshToSurface.Surface)
normalsFilter.SetAutoOrientNormals(1)
normalsFilter.SetFlipNormals(0)
normalsFilter.SetConsistency(1)
normalsFilter.SplittingOff()
normalsFilter.ComputePointNormalsOn()
normalsFilter.ComputeCellNormalsOn()
normalsFilter.Update()
wallWithoutBoundariesSurface = normalsFilter.GetOutput()
normals = wallWithoutBoundariesSurface.GetCellData().GetNormals()
savedNormals = wallWithoutBoundariesSurface.GetCellData().GetArray('SavedNormals')
math = vtk.vtkMath()
#If the normal are inverted, recompute the normals with flipping on
if normals.GetNumberOfTuples() > 0 and math.Dot(normals.GetTuple3(0),savedNormals.GetTuple3(0)) < 0:
normalsFilter = vtk.vtkPolyDataNormals()
normalsFilter.SetInputData(meshToSurface.Surface)
normalsFilter.SetAutoOrientNormals(1)
normalsFilter.SetFlipNormals(1)
normalsFilter.SetConsistency(1)
normalsFilter.SplittingOff()
normalsFilter.ComputePointNormalsOn()
normalsFilter.ComputeCellNormalsOn()
normalsFilter.Update()
wallWithoutBoundariesSurface = normalsFilter.GetOutput()
wallWithoutBoundariesSurface.GetPointData().GetNormals().SetName('Normals')
wallWithoutBoundariesSurface.GetCellData().RemoveArray('SavedNormals')
surfaceToMesh = vmtkscripts.vmtkSurfaceToMesh()
surfaceToMesh.Surface = wallWithoutBoundariesSurface
surfaceToMesh.Execute()
#Offset to apply to the array
wallOffset = 0
if self.IncludeSurfaceCells or self.IncludeOriginalSurfaceCells:
wallOffset += 1
if self.IncludeSurfaceCells or self.IncludeExtrudedSurfaceCells:
wallOffset+=1
boundaryLayer = vmtkscripts.vmtkBoundaryLayer2()
boundaryLayer.Mesh = surfaceToMesh.Mesh
boundaryLayer.WarpVectorsArrayName = 'Normals'
boundaryLayer.NegateWarpVectors = False
boundaryLayer.ThicknessArrayName = self.ThicknessArrayName
boundaryLayer.ConstantThickness = self.ConstantThickness
boundaryLayer.IncludeSurfaceCells = self.IncludeSurfaceCells
boundaryLayer.NumberOfSubLayers = self.NumberOfSubLayers
boundaryLayer.SubLayerRatio = self.SubLayerRatio
boundaryLayer.Thickness = self.Thickness
boundaryLayer.ThicknessRatio = self.Thickness
boundaryLayer.MaximumThickness = self.MaximumThickness
boundaryLayer.CellEntityIdsArrayName = self.CellEntityIdsArrayName
boundaryLayer.IncludeExtrudedOpenProfilesCells = self.IncludeExtrudedOpenProfilesCells
boundaryLayer.IncludeExtrudedSurfaceCells = self.IncludeExtrudedSurfaceCells
boundaryLayer.IncludeOriginalSurfaceCells = self.IncludeOriginalSurfaceCells
boundaryLayer.LayerEntityId = self.SurfaceCellEntityId
boundaryLayer.SurfaceEntityId = self.InletOutletCellEntityId + 1
if cellEntityIdsArray != None:
#Append the new surface ids
idRange = cellEntityIdsArray.GetRange()
boundaryLayer.OpenProfilesEntityId = idRange[1] + wallOffset + 2
boundaryLayer.Execute()
if cellEntityIdsArray != None:
#offset the previous cellentityids to make room for the new ones
arrayCalculator = vtk.vtkArrayCalculator()
arrayCalculator.SetInputData(self.Mesh)
if vtk.vtkVersion.GetVTKMajorVersion()>=9 or (vtk.vtkVersion.GetVTKMajorVersion()>=8 and vtk.vtkVersion.GetVTKMinorVersion()>=1):
arrayCalculator.SetAttributeTypeToCellData()
else:
arrayCalculator.SetAttributeModeToUseCellData()
arrayCalculator.AddScalarVariable("entityid",self.CellEntityIdsArrayName,0)
arrayCalculator.SetFunction("if( entityid > " + str(self.InletOutletCellEntityId-1) +", entityid + " + str(wallOffset) + ", entityid)")
arrayCalculator.SetResultArrayName('CalculatorResult')
arrayCalculator.Update()
#This need to be copied in order to be of the right type (int)
cellEntityIdsArray.DeepCopy(arrayCalculator.GetOutput().GetCellData().GetArray('CalculatorResult'))
arrayCalculator.SetFunction("if( entityid > " + str(self.SurfaceCellEntityId-1) +", entityid + 1, entityid)")
arrayCalculator.Update()
##This need to be copied in order to be of the right type (int)
cellEntityIdsArray.DeepCopy(arrayCalculator.GetOutput().GetCellData().GetArray('CalculatorResult'))
appendFilter = vtkvmtk.vtkvmtkAppendFilter()
appendFilter.AddInput(self.Mesh)
appendFilter.AddInput(boundaryLayer.Mesh)
appendFilter.Update()
self.Mesh = appendFilter.GetOutput()
def testSkinOrder(self):
# Create the RenderWindow, Renderer and Interactor
#
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
RESOLUTION = 64
START_SLICE = 50
END_SLICE = 60
PIXEL_SIZE = 3.2
centerX = RESOLUTION / 2
centerY = RESOLUTION / 2
centerZ = (END_SLICE - START_SLICE) / 2
endX = RESOLUTION - 1
endY = RESOLUTION - 1
endZ = END_SLICE - 1
origin = (RESOLUTION / 2.0) * PIXEL_SIZE * -1.0
math = vtk.vtkMath()
orders = ["ap", "pa", "si", "iss", "lr", "rl"]
sliceOrder = SliceOrder.SliceOrder()
reader = list()
iso = list()
mapper = list()
actor = list()
skinColors = [
[0.875950, 0.598302, 0.656878],
[0.641134, 0.536594, 0.537889],
[0.804079, 0.650506, 0.558249],
[0.992896, 0.603716, 0.660385],
[0.589101, 0.513448, 0.523095],
[0.650247, 0.700527, 0.752458],
]
for idx, order in enumerate(orders):
reader.append(vtk.vtkVolume16Reader())
reader[idx].SetDataDimensions(RESOLUTION, RESOLUTION)
reader[idx].SetFilePrefix(VTK_DATA_ROOT + "/Data/headsq/quarter")
reader[idx].SetDataSpacing(PIXEL_SIZE, PIXEL_SIZE, 1.5)
reader[idx].SetDataOrigin(origin, origin, 1.5)
reader[idx].SetImageRange(START_SLICE, END_SLICE)
if order == "ap":
reader[idx].SetTransform(sliceOrder.ap)
elif order == "pa":
reader[idx].SetTransform(sliceOrder.pa)
elif order == "si":
reader[idx].SetTransform(sliceOrder.si)
elif order == "iss":
reader[idx].SetTransform(sliceOrder.iss)
elif order == "lr":
reader[idx].SetTransform(sliceOrder.lr)
elif order == "rl":
reader[idx].SetTransform(sliceOrder.rl)
else:
s = "No such transform exists."
raise Exception(s)
reader[idx].SetHeaderSize(0)
reader[idx].SetDataMask(0x7FFF)
reader[idx].SetDataByteOrderToLittleEndian()
reader[idx].GetExecutive().SetReleaseDataFlag(0, 1)
iso.append(vtk.vtkContourFilter())
iso[idx].SetInputConnection(reader[idx].GetOutputPort())
iso[idx].SetValue(0, 550.5)
iso[idx].ComputeScalarsOff()
iso[idx].ReleaseDataFlagOn()
mapper.append(vtk.vtkPolyDataMapper())
mapper[idx].SetInputConnection(iso[idx].GetOutputPort())
mapper[idx].ImmediateModeRenderingOn()
actor.append(vtk.vtkActor())
actor[idx].SetMapper(mapper[idx])
# r = math.Random(.5, 1)
# g = math.Random(.5, 1)
# b = math.Random(.5, 1)
# print r, g, b
actor[idx].GetProperty().SetDiffuseColor(
# math.Random(.5, 1), math.Random(.5, 1), math.Random(.5, 1))
# r, g, b)
skinColors[idx]
)
ren.AddActor(actor[idx])
renWin.SetSize(300, 300)
ren.ResetCamera()
ren.GetActiveCamera().Azimuth(210)
ren.GetActiveCamera().Elevation(30)
ren.GetActiveCamera().Dolly(1.2)
ren.ResetCameraClippingRange()
ren.SetBackground(0.8, 0.8, 0.8)
# render and interact with data
iRen = vtk.vtkRenderWindowInteractor()
iRen.SetRenderWindow(renWin)
renWin.Render()
img_file = "skinOrder.png"
vtk.test.Testing.compareImage(iRen.GetRenderWindow(), vtk.test.Testing.getAbsImagePath(img_file), threshold=25)
vtk.test.Testing.interact()
def __init__(self, ren):
self.ren1 = ren
# Get random numbers
self.math = vtk.vtkMath()
self.math.RandomSeed(1)
import vtk
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the RenderWindow, Renderer and both Actors
#
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# create some points on a sphere such that the data is not in the form
# of z = f(x,y)
#
math1 = vtk.vtkMath()
points = vtk.vtkPoints()
vectors = vtk.vtkFloatArray()
vectors.SetNumberOfComponents(3)
i = 0
while i < 100:
theta = math1.Random(0.31415, 2.8)
phi = math1.Random(0.31415, 2.8)
points.InsertPoint(i, math.cos(theta) * math.sin(phi),
math.sin(theta) * math.sin(phi), math.cos(phi))
vectors.InsertTuple3(i, math.cos(theta) * math.sin(phi),
math.sin(theta) * math.sin(phi), math.cos(phi))
i = i + 1
profile = vtk.vtkPolyData()
profile.SetPoints(points)
def SetRandomSeed(caller, eventId):
#print "Restart random number generator"
raMath = vtk.vtkMath()
raMath.RandomSeed(6)
def AddTimestamp( self, time, matrix, point, role ):
if ( time == self.timePrev1 or time == self.timePrev2 or time == self.timePrev3 ):
return
if ( self.pointPrev3 == None or self.timePrev3 == None ):
if ( self.pointPrev2 != None and self.timePrev2 != None ):
self.pointPrev3 = self.pointPrev2[:]
self.timePrev3 = self.timePrev2
if ( self.pointPrev1 != None ):
self.pointPrev2 = self.pointPrev1[:]
self.timePrev2 = self.timePrev1
if ( point != None ):
self.pointPrev1 = point[:]
self.timePrev1 = time
return
# Note that we are using backward difference formulas here
# We might use central difference formulas for better accuracy, but it couldn't be extensible to real-time
timeDiff01 = time - self.timePrev1
timeDiff12 = self.timePrev1 - self.timePrev2
timeDiff23 = self.timePrev2 - self.timePrev3
velocity0 = [ 0, 0, 0 ]
vtk.vtkMath().Subtract( point[0:3], self.pointPrev1[0:3], velocity0 )
velocity0 = [ velocity0[ 0 ] / timeDiff01, velocity0[ 1 ] / timeDiff01, velocity0[ 2 ] / timeDiff01 ]
velocity1 = [ 0, 0, 0 ]
vtk.vtkMath().Subtract( self.pointPrev1[0:3], self.pointPrev2[0:3], velocity1 )
velocity1 = [ velocity1[ 0 ] / timeDiff12, velocity1[ 1 ] / timeDiff12, velocity1[ 2 ] / timeDiff12 ]
velocity2 = [ 0, 0, 0 ]
vtk.vtkMath().Subtract( self.pointPrev2[0:3], self.pointPrev3[0:3], velocity2 )
velocity2 = [ velocity2[ 0 ] / timeDiff23, velocity2[ 1 ] / timeDiff23, velocity2[ 2 ] / timeDiff23 ]
acceleration0 = [ 0, 0, 0 ]
vtk.vtkMath().Subtract( velocity0, velocity1, acceleration0 )
acceleration0 = [ acceleration0[ 0 ] / timeDiff01, acceleration0[ 1 ] / timeDiff01, acceleration0[ 2 ] / timeDiff01 ]
acceleration1 = [ 0, 0, 0 ]
vtk.vtkMath().Subtract( velocity1, velocity2, acceleration1 )
acceleration1 = [ acceleration1[ 0 ] / timeDiff12, acceleration1[ 1 ] / timeDiff12, acceleration1[ 2 ] / timeDiff12 ]
jerk = [ 0, 0, 0 ]
vtk.vtkMath().Subtract( acceleration0, acceleration1, jerk )
jerk = [ jerk[ 0 ] / timeDiff01, jerk[ 1 ] / timeDiff01, jerk[ 2 ] / timeDiff01 ]
jerkMagnitude = math.pow( jerk[ 0 ], 2 ) + math.pow( jerk[ 1 ], 2 ) + math.pow( jerk[ 2 ], 2 )
self.squaredJerk += jerkMagnitude * timeDiff01
self.pointPrev3 = self.pointPrev2[:] # Require element copy
self.timePrev3 = self.timePrev2
self.pointPrev2 = self.pointPrev1[:] # Require element copy
self.timePrev2 = self.timePrev1
self.pointPrev1 = point[:] # Require element copy
self.timePrev1 = time
def testParametricFunctions(self):
# ------------------------------------------------------------
# Get a texture
# ------------------------------------------------------------
textureReader = vtk.vtkJPEGReader()
textureReader.SetFileName(VTK_DATA_ROOT + "/Data/beach.jpg")
texture = vtk.vtkTexture()
texture.SetInputConnection(textureReader.GetOutputPort())
# ------------------------------------------------------------
# For each parametric surface:
# 1) Create it
# 2) Assign mappers and actors
# 3) Position this object
# 5) Add a label
# ------------------------------------------------------------
# ------------------------------------------------------------
# Create a torus
# ------------------------------------------------------------
torus = vtk.vtkParametricTorus()
torusSource = vtk.vtkParametricFunctionSource()
torusSource.SetParametricFunction(torus)
torusSource.SetScalarModeToPhase()
torusMapper = vtk.vtkPolyDataMapper()
torusMapper.SetInputConnection(torusSource.GetOutputPort())
torusMapper.SetScalarRange(0, 360)
torusActor = vtk.vtkActor()
torusActor.SetMapper(torusMapper)
torusActor.SetPosition(0, 12, 0)
torusTextMapper = vtk.vtkTextMapper()
torusTextMapper.SetInput("Torus")
torusTextMapper.GetTextProperty().SetJustificationToCentered()
torusTextMapper.GetTextProperty().SetVerticalJustificationToCentered()
torusTextMapper.GetTextProperty().SetColor(1, 0, 0)
torusTextMapper.GetTextProperty().SetFontSize(14)
torusTextActor = vtk.vtkActor2D()
torusTextActor.SetMapper(torusTextMapper)
torusTextActor.GetPositionCoordinate().SetCoordinateSystemToWorld()
torusTextActor.GetPositionCoordinate().SetValue(0, 9.5, 0)
# ------------------------------------------------------------
# Create a klein bottle
# ------------------------------------------------------------
klein = vtk.vtkParametricKlein()
kleinSource = vtk.vtkParametricFunctionSource()
kleinSource.SetParametricFunction(klein)
kleinSource.SetScalarModeToU0V0()
kleinMapper = vtk.vtkPolyDataMapper()
kleinMapper.SetInputConnection(kleinSource.GetOutputPort())
kleinMapper.SetScalarRange(0, 3)
kleinActor = vtk.vtkActor()
kleinActor.SetMapper(kleinMapper)
kleinActor.SetPosition(8, 10.5, 0)
kleinTextMapper = vtk.vtkTextMapper()
kleinTextMapper.SetInput("Klein")
kleinTextMapper.GetTextProperty().SetJustificationToCentered()
kleinTextMapper.GetTextProperty().SetVerticalJustificationToCentered()
kleinTextMapper.GetTextProperty().SetColor(1, 0, 0)
kleinTextMapper.GetTextProperty().SetFontSize(14)
kleinTextActor = vtk.vtkActor2D()
kleinTextActor.SetMapper(kleinTextMapper)
kleinTextActor.GetPositionCoordinate().SetCoordinateSystemToWorld()
kleinTextActor.GetPositionCoordinate().SetValue(8, 9.5, 0)
# ------------------------------------------------------------
# Create a Figure-8 Klein
# ------------------------------------------------------------
klein2 = vtk.vtkParametricFigure8Klein()
klein2Source = vtk.vtkParametricFunctionSource()
klein2Source.SetParametricFunction(klein2)
klein2Source.GenerateTextureCoordinatesOn()
klein2Mapper = vtk.vtkPolyDataMapper()
klein2Mapper.SetInputConnection(klein2Source.GetOutputPort())
klein2Mapper.SetScalarRange(0, 3)
klein2Actor = vtk.vtkActor()
klein2Actor.SetMapper(klein2Mapper)
klein2Actor.SetPosition(16, 12, 0)
klein2Actor.SetTexture(texture)
fig8KleinTextMapper = vtk.vtkTextMapper()
fig8KleinTextMapper.SetInput("Fig-8.Klein")
fig8KleinTextMapper.GetTextProperty().SetJustificationToCentered()
fig8KleinTextMapper.GetTextProperty().SetVerticalJustificationToCentered()
fig8KleinTextMapper.GetTextProperty().SetColor(1, 0, 0)
fig8KleinTextMapper.GetTextProperty().SetFontSize(14)
fig8KleinTextActor = vtk.vtkActor2D()
fig8KleinTextActor.SetMapper(fig8KleinTextMapper)
fig8KleinTextActor.GetPositionCoordinate().SetCoordinateSystemToWorld()
fig8KleinTextActor.GetPositionCoordinate().SetValue(16, 9.5, 0)
# ------------------------------------------------------------
# Create a mobius strip
# ------------------------------------------------------------
mobius = vtk.vtkParametricMobius()
mobiusSource = vtk.vtkParametricFunctionSource()
mobiusSource.SetParametricFunction(mobius)
mobiusSource.GenerateTextureCoordinatesOn()
mobiusMapper = vtk.vtkPolyDataMapper()
mobiusMapper.SetInputConnection(mobiusSource.GetOutputPort())
mobiusActor = vtk.vtkActor()
mobiusActor.SetMapper(mobiusMapper)
mobiusActor.RotateX(45)
mobiusActor.SetPosition(24, 12, 0)
mobiusActor.SetTexture(texture)
mobiusTextMapper = vtk.vtkTextMapper()
mobiusTextMapper.SetInput("Mobius")
mobiusTextMapper.GetTextProperty().SetJustificationToCentered()
mobiusTextMapper.GetTextProperty().SetVerticalJustificationToCentered()
mobiusTextMapper.GetTextProperty().SetColor(1, 0, 0)
mobiusTextMapper.GetTextProperty().SetFontSize(14)
mobiusTextActor = vtk.vtkActor2D()
mobiusTextActor.SetMapper(mobiusTextMapper)
mobiusTextActor.GetPositionCoordinate().SetCoordinateSystemToWorld()
mobiusTextActor.GetPositionCoordinate().SetValue(24, 9.5, 0)
# ------------------------------------------------------------
# Create a super toroid
# ------------------------------------------------------------
toroid = vtk.vtkParametricSuperToroid()
toroid.SetN1(2)
toroid.SetN2(3)
toroidSource = vtk.vtkParametricFunctionSource()
toroidSource.SetParametricFunction(toroid)
toroidSource.SetScalarModeToU()
toroidMapper = vtk.vtkPolyDataMapper()
toroidMapper.SetInputConnection(toroidSource.GetOutputPort())
toroidMapper.SetScalarRange(0, 6.28)
toroidActor = vtk.vtkActor()
toroidActor.SetMapper(toroidMapper)
toroidActor.SetPosition(0, 4, 0)
superToroidTextMapper = vtk.vtkTextMapper()
superToroidTextMapper.SetInput("Super.Toroid")
superToroidTextMapper.GetTextProperty().SetJustificationToCentered()
superToroidTextMapper.GetTextProperty().SetVerticalJustificationToCentered()
superToroidTextMapper.GetTextProperty().SetColor(1, 0, 0)
superToroidTextMapper.GetTextProperty().SetFontSize(14)
superToroidTextActor = vtk.vtkActor2D()
superToroidTextActor.SetMapper(superToroidTextMapper)
superToroidTextActor.GetPositionCoordinate().SetCoordinateSystemToWorld()
superToroidTextActor.GetPositionCoordinate().SetValue(0, 1.5, 0)
# ------------------------------------------------------------
# Create a super ellipsoid
# ------------------------------------------------------------
superEllipsoid = vtk.vtkParametricSuperEllipsoid()
superEllipsoid.SetXRadius(1.25)
superEllipsoid.SetYRadius(1.5)
superEllipsoid.SetZRadius(1.0)
superEllipsoid.SetN1(1.1)
superEllipsoid.SetN2(1.75)
superEllipsoidSource = vtk.vtkParametricFunctionSource()
superEllipsoidSource.SetParametricFunction(superEllipsoid)
superEllipsoidSource.SetScalarModeToV()
superEllipsoidMapper = vtk.vtkPolyDataMapper()
superEllipsoidMapper.SetInputConnection(superEllipsoidSource.GetOutputPort())
superEllipsoidMapper.SetScalarRange(0, 3.14)
superEllipsoidActor = vtk.vtkActor()
superEllipsoidActor.SetMapper(superEllipsoidMapper)
superEllipsoidActor.SetPosition(8, 4, 0)
superEllipsoidTextMapper = vtk.vtkTextMapper()
superEllipsoidTextMapper.SetInput("Super.Ellipsoid")
superEllipsoidTextMapper.GetTextProperty().SetJustificationToCentered()
superEllipsoidTextMapper.GetTextProperty().SetVerticalJustificationToCentered()
superEllipsoidTextMapper.GetTextProperty().SetColor(1, 0, 0)
superEllipsoidTextMapper.GetTextProperty().SetFontSize(14)
superEllipsoidTextActor = vtk.vtkActor2D()
superEllipsoidTextActor.SetMapper(superEllipsoidTextMapper)
superEllipsoidTextActor.GetPositionCoordinate().SetCoordinateSystemToWorld()
superEllipsoidTextActor.GetPositionCoordinate().SetValue(8, 1.5, 0)
# ------------------------------------------------------------
# Create an open 1D spline
# ------------------------------------------------------------
math = vtk.vtkMath()
inputPoints = vtk.vtkPoints()
for i in range(0, 10):
x = math.Random(-1, 1)
y = math.Random(-1, 1)
z = math.Random(-1, 1)
inputPoints.InsertPoint(i,x,y,z)
spline = vtk.vtkParametricSpline()
spline.SetPoints(inputPoints)
spline.ClosedOff()
splineSource = vtk.vtkParametricFunctionSource()
splineSource.SetParametricFunction(spline)
splineMapper = vtk.vtkPolyDataMapper()
splineMapper.SetInputConnection(splineSource.GetOutputPort())
splineActor = vtk.vtkActor()
splineActor.SetMapper(splineMapper)
splineActor.SetPosition(16, 4, 0)
splineActor.GetProperty().SetColor(0, 0, 0)
splineTextMapper = vtk.vtkTextMapper()
splineTextMapper.SetInput("Open.Spline")
splineTextMapper.GetTextProperty().SetJustificationToCentered()
splineTextMapper.GetTextProperty().SetVerticalJustificationToCentered()
splineTextMapper.GetTextProperty().SetColor(1, 0, 0)
splineTextMapper.GetTextProperty().SetFontSize(14)
splineTextActor = vtk.vtkActor2D()
splineTextActor.SetMapper(splineTextMapper)
splineTextActor.GetPositionCoordinate().SetCoordinateSystemToWorld()
splineTextActor.GetPositionCoordinate().SetValue(16, 1.5, 0)
# ------------------------------------------------------------
# Create a closed 1D spline
# ------------------------------------------------------------
spline2 = vtk.vtkParametricSpline()
spline2.SetPoints(inputPoints)
spline2.ClosedOn()
spline2Source = vtk.vtkParametricFunctionSource()
spline2Source.SetParametricFunction(spline2)
spline2Mapper = vtk.vtkPolyDataMapper()
spline2Mapper.SetInputConnection(spline2Source.GetOutputPort())
spline2Actor = vtk.vtkActor()
spline2Actor.SetMapper(spline2Mapper)
spline2Actor.SetPosition(24, 4, 0)
spline2Actor.GetProperty().SetColor(0, 0, 0)
spline2TextMapper = vtk.vtkTextMapper()
spline2TextMapper.SetInput("Closed.Spline")
spline2TextMapper.GetTextProperty().SetJustificationToCentered()
spline2TextMapper.GetTextProperty().SetVerticalJustificationToCentered()
spline2TextMapper.GetTextProperty().SetColor(1, 0, 0)
spline2TextMapper.GetTextProperty().SetFontSize(14)
spline2TextActor = vtk.vtkActor2D()
spline2TextActor.SetMapper(spline2TextMapper)
spline2TextActor.GetPositionCoordinate().SetCoordinateSystemToWorld()
spline2TextActor.GetPositionCoordinate().SetValue(24, 1.5, 0)
# ------------------------------------------------------------
# Create a spiral conic
# ------------------------------------------------------------
sconic = vtk.vtkParametricConicSpiral()
sconic.SetA(0.8)
sconic.SetB(2.5)
sconic.SetC(0.4)
sconicSource = vtk.vtkParametricFunctionSource()
sconicSource.SetParametricFunction(sconic)
sconicSource.SetScalarModeToDistance()
sconicMapper = vtk.vtkPolyDataMapper()
sconicMapper.SetInputConnection(sconicSource.GetOutputPort())
sconicActor = vtk.vtkActor()
sconicActor.SetMapper(sconicMapper)
sconicMapper.SetScalarRange(0, 9)
sconicActor.SetPosition(0, -4, 0)
sconicActor.SetScale(1.2, 1.2, 1.2)
sconicTextMapper = vtk.vtkTextMapper()
sconicTextMapper.SetInput("Spiral.Conic")
sconicTextMapper.GetTextProperty().SetJustificationToCentered()
sconicTextMapper.GetTextProperty().SetVerticalJustificationToCentered()
sconicTextMapper.GetTextProperty().SetColor(1, 0, 0)
sconicTextMapper.GetTextProperty().SetFontSize(14)
sconicTextActor = vtk.vtkActor2D()
sconicTextActor.SetMapper(sconicTextMapper)
sconicTextActor.GetPositionCoordinate().SetCoordinateSystemToWorld()
sconicTextActor.GetPositionCoordinate().SetValue(0, -6.5, 0)
# ------------------------------------------------------------
# Create Boy's surface
# ------------------------------------------------------------
boy = vtk.vtkParametricBoy()
boySource = vtk.vtkParametricFunctionSource()
boySource.SetParametricFunction(boy)
boySource.SetScalarModeToModulus()
boyMapper = vtk.vtkPolyDataMapper()
boyMapper.SetInputConnection(boySource.GetOutputPort())
boyMapper.SetScalarRange(0, 2)
boyActor = vtk.vtkActor()
boyActor.SetMapper(boyMapper)
boyActor.SetPosition(8, -4, 0)
boyActor.SetScale(1.5, 1.5, 1.5)
boyTextMapper = vtk.vtkTextMapper()
boyTextMapper.SetInput("Boy")
boyTextMapper.GetTextProperty().SetJustificationToCentered()
boyTextMapper.GetTextProperty().SetVerticalJustificationToCentered()
boyTextMapper.GetTextProperty().SetColor(1, 0, 0)
boyTextMapper.GetTextProperty().SetFontSize(14)
boyTextActor = vtk.vtkActor2D()
boyTextActor.SetMapper(boyTextMapper)
boyTextActor.GetPositionCoordinate().SetCoordinateSystemToWorld()
boyTextActor.GetPositionCoordinate().SetValue(8, -6.5, 0)
# ------------------------------------------------------------
# Create a cross cap
# ------------------------------------------------------------
crossCap = vtk.vtkParametricCrossCap()
crossCapSource = vtk.vtkParametricFunctionSource()
crossCapSource.SetParametricFunction(crossCap)
crossCapSource.SetScalarModeToY()
crossCapMapper = vtk.vtkPolyDataMapper()
crossCapMapper.SetInputConnection(crossCapSource.GetOutputPort())
crossCapActor = vtk.vtkActor()
crossCapActor.SetMapper(crossCapMapper)
crossCapActor.RotateX(65)
crossCapActor.SetPosition(16, -4, 0)
crossCapActor.SetScale(1.5, 1.5, 1.5)
crossCapTextMapper = vtk.vtkTextMapper()
crossCapTextMapper.SetInput("Cross.Cap")
crossCapTextMapper.GetTextProperty().SetJustificationToCentered()
crossCapTextMapper.GetTextProperty().SetVerticalJustificationToCentered()
crossCapTextMapper.GetTextProperty().SetColor(1, 0, 0)
crossCapTextMapper.GetTextProperty().SetFontSize(14)
crossCapTextActor = vtk.vtkActor2D()
crossCapTextActor.SetMapper(crossCapTextMapper)
crossCapTextActor.GetPositionCoordinate().SetCoordinateSystemToWorld()
crossCapTextActor.GetPositionCoordinate().SetValue(16, -6.5, 0)
# ------------------------------------------------------------
# Create Dini's surface
# ------------------------------------------------------------
dini = vtk.vtkParametricDini()
diniSource = vtk.vtkParametricFunctionSource()
diniSource.SetScalarModeToDistance()
diniSource.SetParametricFunction(dini)
diniMapper = vtk.vtkPolyDataMapper()
diniMapper.SetInputConnection(diniSource.GetOutputPort())
diniActor = vtk.vtkActor()
diniActor.SetMapper(diniMapper)
diniActor.RotateX(-90)
diniActor.SetPosition(24, -3, 0)
diniActor.SetScale(1.5, 1.5, 0.5)
diniTextMapper = vtk.vtkTextMapper()
diniTextMapper.SetInput("Dini")
diniTextMapper.GetTextProperty().SetJustificationToCentered()
diniTextMapper.GetTextProperty().SetVerticalJustificationToCentered()
diniTextMapper.GetTextProperty().SetColor(1, 0, 0)
diniTextMapper.GetTextProperty().SetFontSize(14)
diniTextActor = vtk.vtkActor2D()
diniTextActor.SetMapper(diniTextMapper)
diniTextActor.GetPositionCoordinate().SetCoordinateSystemToWorld()
diniTextActor.GetPositionCoordinate().SetValue(24, -6.5, 0)
# ------------------------------------------------------------
# Create Enneper's surface
# ------------------------------------------------------------
enneper = vtk.vtkParametricEnneper()
enneperSource = vtk.vtkParametricFunctionSource()
enneperSource.SetParametricFunction(enneper)
enneperSource.SetScalarModeToQuadrant()
enneperMapper = vtk.vtkPolyDataMapper()
enneperMapper.SetInputConnection(enneperSource.GetOutputPort())
enneperMapper.SetScalarRange(1, 4)
enneperActor = vtk.vtkActor()
enneperActor.SetMapper(enneperMapper)
enneperActor.SetPosition(0, -12, 0)
enneperActor.SetScale(0.25, 0.25, 0.25)
enneperTextMapper = vtk.vtkTextMapper()
enneperTextMapper.SetInput("Enneper")
enneperTextMapper.GetTextProperty().SetJustificationToCentered()
enneperTextMapper.GetTextProperty().SetVerticalJustificationToCentered()
enneperTextMapper.GetTextProperty().SetColor(1, 0, 0)
enneperTextMapper.GetTextProperty().SetFontSize(14)
enneperTextActor = vtk.vtkActor2D()
enneperTextActor.SetMapper(enneperTextMapper)
enneperTextActor.GetPositionCoordinate().SetCoordinateSystemToWorld()
enneperTextActor.GetPositionCoordinate().SetValue(0, -14.5, 0)
# ------------------------------------------------------------
# Create an ellipsoidal surface
# ------------------------------------------------------------
ellipsoid = vtk.vtkParametricEllipsoid()
ellipsoid.SetXRadius(1)
ellipsoid.SetYRadius(0.75)
ellipsoid.SetZRadius(0.5)
ellipsoidSource = vtk.vtkParametricFunctionSource()
ellipsoidSource.SetParametricFunction(ellipsoid)
ellipsoidSource.SetScalarModeToZ()
ellipsoidMapper = vtk.vtkPolyDataMapper()
ellipsoidMapper.SetInputConnection(ellipsoidSource.GetOutputPort())
ellipsoidMapper.SetScalarRange(-0.5, 0.5)
ellipsoidActor = vtk.vtkActor()
ellipsoidActor.SetMapper(ellipsoidMapper)
ellipsoidActor.SetPosition(8, -12, 0)
ellipsoidActor.SetScale(1.5, 1.5, 1.5)
ellipsoidTextMapper = vtk.vtkTextMapper()
ellipsoidTextMapper.SetInput("Ellipsoid")
ellipsoidTextMapper.GetTextProperty().SetJustificationToCentered()
ellipsoidTextMapper.GetTextProperty().SetVerticalJustificationToCentered()
ellipsoidTextMapper.GetTextProperty().SetColor(1, 0, 0)
ellipsoidTextMapper.GetTextProperty().SetFontSize(14)
ellipsoidTextActor = vtk.vtkActor2D()
ellipsoidTextActor.SetMapper(ellipsoidTextMapper)
ellipsoidTextActor.GetPositionCoordinate().SetCoordinateSystemToWorld()
ellipsoidTextActor.GetPositionCoordinate().SetValue(8, -14.5, 0)
# ------------------------------------------------------------
# Create an surface with random hills on it.
# Note that for testing, we will disable the
# random generation of the surfaces. This is
# because random number generators do not
# return the same result on different operating
# systems.
# ------------------------------------------------------------
randomHills = vtk.vtkParametricRandomHills()
randomHills.AllowRandomGenerationOff()
randomHills.GenerateTheHills()
randomHillsSource = vtk.vtkParametricFunctionSource()
randomHillsSource.SetParametricFunction(randomHills)
randomHillsSource.GenerateTextureCoordinatesOn()
randomHillsMapper = vtk.vtkPolyDataMapper()
randomHillsMapper.SetInputConnection(randomHillsSource.GetOutputPort())
randomHillsActor = vtk.vtkActor()
randomHillsActor.SetMapper(randomHillsMapper)
randomHillsActor.SetPosition(16, -14, 0)
randomHillsActor.SetScale(0.2, 0.2, 0.2)
randomHillsActor.SetTexture(texture)
randomHillsTextMapper = vtk.vtkTextMapper()
randomHillsTextMapper.SetInput("Random.Hills")
randomHillsTextMapper.GetTextProperty().SetJustificationToCentered()
randomHillsTextMapper.GetTextProperty().SetVerticalJustificationToCentered()
randomHillsTextMapper.GetTextProperty().SetColor(1, 0, 0)
randomHillsTextMapper.GetTextProperty().SetFontSize(14)
randomHillsTextActor = vtk.vtkActor2D()
randomHillsTextActor.SetMapper(randomHillsTextMapper)
randomHillsTextActor.GetPositionCoordinate().SetCoordinateSystemToWorld()
randomHillsTextActor.GetPositionCoordinate().SetValue(16, -14.5, 0)
# ------------------------------------------------------------
# Create an Steiner's Roman Surface.
# ------------------------------------------------------------
roman = vtk.vtkParametricRoman()
roman.SetRadius(1.5)
romanSource = vtk.vtkParametricFunctionSource()
romanSource.SetParametricFunction(roman)
romanSource.SetScalarModeToX()
romanMapper = vtk.vtkPolyDataMapper()
romanMapper.SetInputConnection(romanSource.GetOutputPort())
romanActor = vtk.vtkActor()
romanActor.SetMapper(romanMapper)
romanActor.SetPosition(24, -12, 0)
romanTextMapper = vtk.vtkTextMapper()
romanTextMapper.SetInput("Roman")
romanTextMapper.GetTextProperty().SetJustificationToCentered()
romanTextMapper.GetTextProperty().SetVerticalJustificationToCentered()
romanTextMapper.GetTextProperty().SetColor(1, 0, 0)
romanTextMapper.GetTextProperty().SetFontSize(14)
romanTextActor = vtk.vtkActor2D()
romanTextActor.SetMapper(romanTextMapper)
romanTextActor.GetPositionCoordinate().SetCoordinateSystemToWorld()
romanTextActor.GetPositionCoordinate().SetValue(24, -14.5, 0)
# ------------------------------------------------------------
# Create the RenderWindow, Renderer and both Actors
# ------------------------------------------------------------
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# add actors
ren.AddViewProp(torusActor)
ren.AddViewProp(kleinActor)
ren.AddViewProp(klein2Actor)
ren.AddViewProp(toroidActor)
ren.AddViewProp(superEllipsoidActor)
ren.AddViewProp(mobiusActor)
ren.AddViewProp(splineActor)
ren.AddViewProp(spline2Actor)
ren.AddViewProp(sconicActor)
ren.AddViewProp(boyActor)
ren.AddViewProp(crossCapActor)
ren.AddViewProp(diniActor)
ren.AddViewProp(enneperActor)
ren.AddViewProp(ellipsoidActor)
ren.AddViewProp(randomHillsActor)
ren.AddViewProp(romanActor)
#add text actors
ren.AddViewProp(torusTextActor)
ren.AddViewProp(kleinTextActor)
ren.AddViewProp(fig8KleinTextActor)
ren.AddViewProp(mobiusTextActor)
ren.AddViewProp(superToroidTextActor)
ren.AddViewProp(superEllipsoidTextActor)
ren.AddViewProp(splineTextActor)
ren.AddViewProp(spline2TextActor)
ren.AddViewProp(sconicTextActor)
ren.AddViewProp(boyTextActor)
ren.AddViewProp(crossCapTextActor)
ren.AddViewProp(diniTextActor)
ren.AddViewProp(enneperTextActor)
ren.AddViewProp(ellipsoidTextActor)
ren.AddViewProp(randomHillsTextActor)
ren.AddViewProp(romanTextActor)
ren.SetBackground(0.7, 0.8, 1)
renWin.SetSize(500, 500)
ren.ResetCamera()
ren.GetActiveCamera().Zoom(1.3)
iren.Initialize()
renWin.Render()
#iren.Start()
img_file = "TestParametricFunctions.png"
vtk.test.Testing.compareImage(iren.GetRenderWindow(),vtk.test.Testing.getAbsImagePath(img_file),threshold=25)
vtk.test.Testing.interact()
var_name += repr(arg)
return var_name
#init Tk
try:
import Tkinter
pythonTk = Tkinter.Tk()
pythonTk.withdraw()
except:
pythonTk = None
pass #no hassles if Tk is not present.
# setup some common things for testing
rtTempObject = vtk.vtkObject()
rtExMath = vtk.vtkMath()
rtExMath.RandomSeed(6)
# create the testing class to do the work
rtTester = vtk.vtkTesting()
for arg in sys.argv[2:]:
rtTester.AddArgument(arg)
VTK_DATA_ROOT = rtTester.GetDataRoot()
if rtTester.IsInteractiveModeSpecified() == 0:
vtk.vtkRenderWindowInteractor = vtkTestingInteractor
# load in the script
test_script = sys.argv[1]
def testPlatonicSolids(self):
# Create five instances of vtkPlatonicSolidSource
# corresponding to each of the five Platonic solids.
#
tet = vtk.vtkPlatonicSolidSource()
tet.SetSolidTypeToTetrahedron()
tetMapper = vtk.vtkPolyDataMapper()
tetMapper.SetInputConnection(tet.GetOutputPort())
tetActor = vtk.vtkActor()
tetActor.SetMapper(tetMapper)
cube = vtk.vtkPlatonicSolidSource()
cube.SetSolidTypeToCube()
cubeMapper = vtk.vtkPolyDataMapper()
cubeMapper.SetInputConnection(cube.GetOutputPort())
cubeActor = vtk.vtkActor()
cubeActor.SetMapper(cubeMapper)
cubeActor.AddPosition(2.0, 0, 0)
oct = vtk.vtkPlatonicSolidSource()
oct.SetSolidTypeToOctahedron()
octMapper = vtk.vtkPolyDataMapper()
octMapper.SetInputConnection(oct.GetOutputPort())
octActor = vtk.vtkActor()
octActor.SetMapper(octMapper)
octActor.AddPosition(4.0, 0, 0)
icosa = vtk.vtkPlatonicSolidSource()
icosa.SetSolidTypeToIcosahedron()
icosaMapper = vtk.vtkPolyDataMapper()
icosaMapper.SetInputConnection(icosa.GetOutputPort())
icosaActor = vtk.vtkActor()
icosaActor.SetMapper(icosaMapper)
icosaActor.AddPosition(6.0, 0, 0)
dode = vtk.vtkPlatonicSolidSource()
dode.SetSolidTypeToDodecahedron()
dodeMapper = vtk.vtkPolyDataMapper()
dodeMapper.SetInputConnection(dode.GetOutputPort())
dodeActor = vtk.vtkActor()
dodeActor.SetMapper(dodeMapper)
dodeActor.AddPosition(8.0, 0, 0)
# Create rendering stuff
#
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
# Add the actors to the renderer, set the background and size
#
ren.AddActor(tetActor)
ren.AddActor(cubeActor)
ren.AddActor(octActor)
ren.AddActor(icosaActor)
ren.AddActor(dodeActor)
colors = self.Colors()
# Create a lookup table with colors for each face
#
math = vtk.vtkMath()
lut = vtk.vtkLookupTable()
lut.SetNumberOfColors(20)
lut.Build()
lut.SetTableValue(0, colors.GetRGBAColor("red"))
lut.SetTableValue(1, colors.GetRGBAColor("lime"))
lut.SetTableValue(2, colors.GetRGBAColor("yellow"))
lut.SetTableValue(3, colors.GetRGBAColor("blue"))
lut.SetTableValue(4, colors.GetRGBAColor("magenta"))
lut.SetTableValue(5, colors.GetRGBAColor("cyan"))
lut.SetTableValue(6, colors.GetRGBAColor("spring_green"))
lut.SetTableValue(7, colors.GetRGBAColor("lavender"))
lut.SetTableValue(8, colors.GetRGBAColor("mint_cream"))
lut.SetTableValue(9, colors.GetRGBAColor("violet"))
lut.SetTableValue(10, colors.GetRGBAColor("ivory_black"))
lut.SetTableValue(11, colors.GetRGBAColor("coral"))
lut.SetTableValue(12, colors.GetRGBAColor("pink"))
lut.SetTableValue(13, colors.GetRGBAColor("salmon"))
lut.SetTableValue(14, colors.GetRGBAColor("sepia"))
lut.SetTableValue(15, colors.GetRGBAColor("carrot"))
lut.SetTableValue(16, colors.GetRGBAColor("gold"))
lut.SetTableValue(17, colors.GetRGBAColor("forest_green"))
lut.SetTableValue(18, colors.GetRGBAColor("turquoise"))
lut.SetTableValue(19, colors.GetRGBAColor("plum"))
lut.SetTableRange(0, 19)
tetMapper.SetLookupTable(lut)
tetMapper.SetScalarRange(0, 19)
cubeMapper.SetLookupTable(lut)
cubeMapper.SetScalarRange(0, 19)
octMapper.SetLookupTable(lut)
octMapper.SetScalarRange(0, 19)
icosaMapper.SetLookupTable(lut)
icosaMapper.SetScalarRange(0, 19)
dodeMapper.SetLookupTable(lut)
dodeMapper.SetScalarRange(0, 19)
cam = ren.GetActiveCamera()
cam.SetPosition(3.89696, 7.20771, 1.44123)
cam.SetFocalPoint(3.96132, 0, 0)
cam.SetViewUp(-0.0079335, 0.196002, -0.980571)
cam.SetClippingRange(5.42814, 9.78848)
ren.SetBackground(colors.GetRGBColor("black"))
renWin.SetSize(400, 150)
# render and interact with data
iRen = vtk.vtkRenderWindowInteractor()
iRen.SetRenderWindow(renWin);
renWin.Render()
img_file = "TestPlatonicSolids.png"
vtk.test.Testing.compareImage(iRen.GetRenderWindow(), vtk.test.Testing.getAbsImagePath(img_file), threshold=25)
vtk.test.Testing.interact()
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Generate random planes to form a convex polyhedron.
# Create a polyhedral representation of the planes.
# get the interactor ui
# create some points laying between 1<=r<5 (r is radius)
# the points also have normals pointing away from the origin.
#
mathObj = vtk.vtkMath()
points = vtk.vtkPoints()
normals = vtk.vtkFloatArray()
normals.SetNumberOfComponents(3)
i = 0
while i < 100:
radius = 1.0
theta = mathObj.Random(0,360)
phi = mathObj.Random(0,180)
x = expr.expr(globals(), locals(),["radius","*","sin","(","phi",")*","cos","(","theta",")"])
y = expr.expr(globals(), locals(),["radius","*","sin","(","phi",")*","sin","(","theta",")"])
z = expr.expr(globals(), locals(),["radius","*","cos","(","phi",")"])
points.InsertPoint(i,x,y,z)
normals.InsertTuple3(i,x,y,z)
i = i + 1
planes = vtk.vtkPlanes()
planes.SetPoints(points)
planes.SetNormals(normals)
def GetSemiUniDistnaceGrid(
self, m_holePerSlice, m_numberOfSlice, m_errorTolerance=1, m_startPadding=0, m_endPadding=0, m_bufferDeg=40
):
"""
Obtain a set of coordinates roughly equal to a projection of periodic square grid vertex on the arm
surface. The gird also can arbitrarily has a buffer zone where no holes are drilled.
:param m_holePerSlice: [int] Desired number of holes per slice
:param m_numberOfSlice: [int] Desired number of slices
:param m_errorTolerance: [float] The maximum allowed deviation of hole coordinate from idea grid
:param m_startPadding: [int] Starting side padding where no holes will be drilled
:param m_endPadding: [int] Ending side padding where no holes will be drilled
:param m_bufferDeg: [float] Angle between planes where buffers zones are in between. Default to 40
:return: [list] List of hole coordinates
"""
vtkmath = vtk.vtkMath()
if not self._centerLine._IS_READ_FLAG:
self._centerLine.Read()
if self._bufferAngle != None:
m_bufferDeg = self._bufferAngle
m_totalDistance = 0
for i in xrange(
1 + int(m_startPadding / 0.3), self._centerLine._data.GetNumberOfPoints() - int(m_endPadding / 0.3)
):
m_totalDistance += self._centerLine.GetDistance(i, i - 1)
# Shrink the distance a bit before deviding it so that all intervals will lie in the padded segment
m_sliceSpacing = (m_totalDistance) * 0.98 / (m_numberOfSlice)
m_intervalIndexes = self._centerLine.GetEqualDistanceIntervalsIndex(
m_sliceSpacing, m_startPadding, m_endPadding
)
self._centerLineIntervals = m_intervalIndexes
m_tangents = []
for k in xrange(len(m_intervalIndexes)):
m_tmp = self._centerLine.GetNormalizedTangent(m_intervalIndexes[k], range=12, step=3)
m_tangents.append(m_tmp)
m_average = [sum([m_tangents[i][j] for i in xrange(3)]) / float(len(m_tangents)) for j in xrange(3)]
m_openingList = []
m_holeList = []
m_alphaNormal = None
m_masterPt = self._centerLine.GetPoint(m_intervalIndexes[0])
# Define cast opening zone and start drilling zone
if m_bufferDeg != None and self._openingMarker != None:
m_kdtree = vtk.vtkKdTreePointLocator()
m_kdtree.SetDataSet(self._centerLine._data)
m_kdtree.BuildLocator()
m_closestCenterlinePointId = m_kdtree.FindClosestPoint(self._openingMarker)
m_closestCenterlinePoint = self._centerLine.GetPoint(m_closestCenterlinePointId)
m_masterPt = m_closestCenterlinePoint
# Drill along intervals
for i in xrange(len(m_intervalIndexes)):
l_sliceCenter = self._centerLine.GetPoint(m_intervalIndexes[i])
l_slice = self.SliceSurface(l_sliceCenter, m_average)
if i == 0:
# Define the starting vector for all slice
# l_ringAlphaPt = l_slice.GetPoint(i)
l_ringAlphaVect = [self._openingMarker[j] - m_masterPt[j] for j in xrange(3)]
m_alphaNormal = [0, 0, 0]
vtkmath.Cross(m_average, l_ringAlphaVect, m_alphaNormal)
m_alphaNormalMag = sum([m_alphaNormal[i] for i in xrange(3)])
m_alphaNormal = [m_alphaNormal[i] / m_alphaNormalMag for i in xrange(3)]
# Define an initial accuracy which relax if no suitable points is found, affects calculation speed
m_loopAccuracy = 0.25
m_ringSliceAlphaVect = None
while m_ringSliceAlphaVect == None:
for j in xrange(l_slice.GetNumberOfPoints()):
l_ringSliceAlphaVect = [l_slice.GetPoint(j)[k] - l_sliceCenter[k] for k in xrange(3)]
# l_ringSliceMasterVect = [l_slice.GetPoint(j)[k] - m_masterPt[k] for k in xrange(3)]
if (
math.fabs(vtkmath.Dot(l_ringSliceAlphaVect, m_alphaNormal)) < m_loopAccuracy
and vtkmath.Dot(l_ringSliceAlphaVect, l_ringAlphaVect) > 0
):
m_ringSliceAlphaVect = l_ringSliceAlphaVect
break
m_loopAccuracy *= 2
if m_loopAccuracy >= 10:
raise ValueError("Slice Alpha Vector search reaches maximum tolerance")
break
l_uniformSectionDegree = (360.0 - m_bufferDeg) / m_holePerSlice
l_sectionDegree = (360.0 - m_bufferDeg) / m_holePerSlice
l_loopbreak = 0
m_openingList.append(
[l_ringSliceAlphaVect[k] + l_sliceCenter[k] for k in xrange(3)]
) # Include first vector
l_holeList = []
while len(l_holeList) < m_holePerSlice - 1:
if len(l_holeList) == 0:
l_sectionDegree += m_bufferDeg / 2
for j in xrange(l_slice.GetNumberOfPoints()):
l_p1 = [0.0, 0.0, 0.0]
l_ringVect = [l_slice.GetPoint(j)[k] - l_sliceCenter[k] for k in xrange(3)]
vtkmath.Cross(l_ringSliceAlphaVect, l_ringVect, l_p1)
l_p2 = vtkmath.Dot(l_p1, m_average)
l_angleBetweenRunningAndInitialVector = vtkmath.AngleBetweenVectors(
l_ringSliceAlphaVect, l_ringVect
)
if (
l_angleBetweenRunningAndInitialVector
> vtkmath.RadiansFromDegrees(l_sectionDegree - m_errorTolerance / 2)
and l_angleBetweenRunningAndInitialVector
< vtkmath.RadiansFromDegrees(l_sectionDegree + m_errorTolerance / 2.0)
and l_p2 > 0
):
l_ringSliceAlphaVect = l_ringVect
l_holeList.append([l_ringVect[k] + l_sliceCenter[k] for k in xrange(3)])
l_sectionDegree += l_uniformSectionDegree - vtkmath.DegreesFromRadians(
l_angleBetweenRunningAndInitialVector
)
break
if l_loopbreak == m_holePerSlice:
raise RuntimeError("Current error tolerence setting is to low to produce anything.")
l_loopbreak += 1
m_holeList.extend(l_holeList)
self._openingList = m_openingList
return m_holeList
t.Translate(1.1,0,0)
tf = vtk.vtkTransformFilter()
tf.SetTransform(t)
tf.SetInputConnection(disk.GetOutputPort())
strips = vtk.vtkStripper()
strips.SetInputConnection(tf.GetOutputPort())
strips.Update()
app = vtk.vtkAppendPolyData()
app.AddInputData(disk.GetOutput())
app.AddInputData(strips.GetOutput())
app.Update()
model = app.GetOutput()
extrude = vtk.vtkLinearExtrusionFilter()
extrude.SetInputData(model)
# create random cell scalars for the model before extrusion.
rn = vtk.vtkMath()
rn.RandomSeed(1230)
cellColors = vtk.vtkUnsignedCharArray()
cellColors.SetNumberOfComponents(3)
cellColors.SetNumberOfTuples(model.GetNumberOfCells())
i = 0
while i < model.GetNumberOfCells():
cellColors.InsertComponent(i,0,rn.Random(100,255))
cellColors.InsertComponent(i,1,rn.Random(100,255))
cellColors.InsertComponent(i,2,rn.Random(100,255))
i = i + 1
model.GetCellData().SetScalars(cellColors)
# Lets test the arrow source instead of creating another test.
arrow1 = vtk.vtkArrowSource()
mapper1 = vtk.vtkPolyDataMapper()
def distance2(pnt1,pnt2):
return vtk.vtkMath().Distance2BetweenPoints(pnt1,pnt2)
def myMain(controller,args):
fname=args.fname
controller=args.controller
myid = controller.GetLocalProcessId();
numProcs = controller.GetNumberOfProcesses();
pts=np.loadtxt(fname)
sf=100
paint=rgbPainter()
r,t,z = rec2cyl(pts[:,0],pts[:,1],pts[:,2])
#im=np.abs(getGeomImperfection(r,z,np.mean(r)))
if pts.shape[1] == 4:
im=pts[:,3]
else:
im=getGeomImperfection(r,z,np.mean(r))
rid=r-im
xx,yy,zz=cyl2rec(rid+im*sf,t,z)
math = vtk.vtkMath()
points = vtk.vtkPoints()
colors =vtk.vtkUnsignedCharArray()
colors.SetNumberOfComponents(3);
colors.SetName("Colors");
for i in range(0,pts.shape[0]):
#points.InsertPoint(i,pts[i][0],pts[i][1],pts[i][2] )
points.InsertPoint(i,xx[i],yy[i],zz[i] )
polydata = vtk.vtkPolyData()
polydata.SetPoints(points)
polydata.GetPointData().SetScalars(colors)
polydata.Update()
surf =vtk.vtkSurfaceReconstructionFilter()
surf.SetInput(polydata)
surf.SetNeighborhoodSize(40)
#surf.SetSampleSpacing(6.0)
if (myid != 0):
controller.AddRMI(surf.Update,'',200)
controller.ProcessRMIs();
else:
contourFilter = vtk.vtkContourFilter()
contourFilter.SetInputConnection(surf.GetOutputPort())
reverse = vtk.vtkReverseSense()
reverse.SetInputConnection(contourFilter.GetOutputPort())
reverse.ReverseCellsOn()
reverse.ReverseNormalsOn()
reverse.Update()
outputPolyData=reverse.GetOutput()
#for i in range(0,pts.shape[0]):
# dcolor=np.zeros(3)
# colorLookupTable.GetColor(im[i],dcolor)
# cc=dcolor*255.0
# colors.InsertNextTupleValue(cc)
#outputPolyData.GetPointData().SetScalars(polydata.GetPointData().GetScalars() );
newSurf = transform_back( points, reverse.GetOutput());
pts2=np.zeros((newSurf.GetNumberOfPoints(),3))
for i in range(0,newSurf.GetNumberOfPoints()):
pts2[i,:]=newSurf.GetPoint(i)
r2,t2,z2 = rec2cyl(pts2[:,0],pts2[:,1],pts2[:,2])
im2=getGeomImperfection(r2,z2,np.mean(r2))
#im2-=np.min(im2)
#im2=np.abs(im2)
paint.setValue(np.min(im2))
paint.setValue(np.max(im2))
for i in range(0,newSurf.GetNumberOfPoints()):
colors.InsertNextTupleValue(paint.getRGB(im2[i]))
newSurf.GetPointData().SetScalars(colors );
mapper = vtk.vtkPolyDataMapper();
mapper.InterpolateScalarsBeforeMappingOn()
#mapper.SetInputConnection(outputPolyData.GetProducerPort())
mapper.SetInputConnection(newSurf.GetProducerPort())
mapper.SetScalarModeToUsePointData()
mapper.ScalarVisibilityOn();
surfaceActor = vtk.vtkActor();
surfaceActor.SetMapper(mapper);
ren = vtk.vtkRenderer();
renWin = vtk.vtkRenderWindow();
renWin.AddRenderer(ren);
iren = vtk.vtkRenderWindowInteractor();
iren.SetRenderWindow(renWin);
style = vtk.vtkInteractorStyleTrackballCamera()
iren.SetInteractorStyle(style)
ren.AddActor(surfaceActor);
ren.SetBackground(1, 1, 1);
renWin.SetSize(800, 600);
prn=1000.
pc=-prn
plXY = vtk.vtkPlaneSource()
plXY.SetPoint1(prn,-prn,0)
plXY.SetPoint2(-prn,prn,0)
plXY.SetOrigin(pc,pc,0)
plXY.SetCenter(0,0,0)
plXYmap = vtk.vtkPolyDataMapper()
plXYmap.SetInput(plXY.GetOutput())
plXYact = vtk.vtkActor()
plXYact.SetMapper(plXYmap)
plXYact.GetProperty().SetOpacity(0.1)
plYZ = vtk.vtkPlaneSource()
plYZ.SetCenter(0,pc,pc)
plYZ.SetPoint1(0,prn,-prn)
plYZ.SetPoint2(0,-prn,prn)
plYZmap = vtk.vtkPolyDataMapper()
plYZmap.SetInput(plYZ.GetOutput())
plYZact = vtk.vtkActor()
plYZact.SetMapper(plYZmap)
plYZact.GetProperty().SetOpacity(0.1)
plZX = vtk.vtkPlaneSource()
plZX.SetCenter(pc,0,pc)
plZX.SetPoint1(prn,0,-prn)
plZX.SetPoint2(-prn,0,prn)
plZXmap = vtk.vtkPolyDataMapper()
plZXmap.SetInput(plZX.GetOutput())
plZXact = vtk.vtkActor()
plZXact.SetMapper(plZXmap)
plZXact.GetProperty().SetOpacity(0.1)
ren.AddActor(plXYact)
ren.AddActor(plYZact)
ren.AddActor(plZXact)
ax=vtk.vtkAxesActor()
ax.GetXAxisCaptionActor2D().GetProperty().SetColor(0,0,0)
ax.GetYAxisCaptionActor2D().GetProperty().SetColor(0,0,0)
ax.GetZAxisCaptionActor2D().GetProperty().SetColor(0,0,0)
ow=vtk.vtkOrientationMarkerWidget()
ow.SetOrientationMarker(ax)
ow.SetInteractor(iren)
ow.SetViewport( 0.0, 0.0, 0.4, 0.4 )
ow.SetEnabled( 1 )
ow.InteractiveOn()
lut=vtk.vtkLookupTable()
lut.SetHueRange( 0.66667, 0.0 )
lut.SetSaturationRange (1.0, 1.0)
lut.SetNumberOfColors(50)# len(self.plotables))
lut.SetTableRange(paint.getMinValue(),paint.getMaxValue())
lut.Build()
scalar_bar = vtk.vtkScalarBarActor()
scalar_bar.SetOrientationToHorizontal()
scalar_bar.SetLookupTable(lut)
scalar_bar.SetTitle("Imperfection value");
scalar_bar.SetNumberOfLabels(11)
scalar_bar_widget = vtk.vtkScalarBarWidget()
scalar_bar_widget.SetInteractor(iren)
scalar_bar_widget.SetScalarBarActor(scalar_bar)
scalar_bar_widget.On()
iren.Initialize();
renWin.Render();
iren.Start();
imageSource = vtk.vtkRTAnalyticSource()
imageSource.SetWholeExtent(extent[0], extent[1], extent[2], extent[3],
extent[4], extent[5])
imageSource.SetCenter(center)
imageSource.Update()
img = imageSource.GetOutput()
scalarRange = img.GetScalarRange()
origin = img.GetOrigin()
spacing = img.GetSpacing()
# create an unstructured grid by generating a point cloud and
# applying Delaunay triangulation on it.
vtk.vtkMath().RandomSeed(0) # vtkPointSource internally uses vtkMath::Random()
pointSource = vtk.vtkPointSource()
pointSource.SetCenter(center)
pointSource.SetRadius(center[0])
pointSource.SetNumberOfPoints(24 * 24 * 24)
delaunay3D = vtk.vtkDelaunay3D()
delaunay3D.SetInputConnection(pointSource.GetOutputPort())
# probe into img using unstructured grif geometry
probe1 = vtk.vtkProbeFilter()
probe1.SetSourceData(img)
probe1.SetInputConnection(delaunay3D.GetOutputPort())
# probe into the unstructured grid using ImageData geometry
outputData = vtk.vtkImageData()
def get_actors(args = None): # This will be used later to get random numbers. math = vtk.vtkMath() # Total number of points. numberOfInputPoints = 20 # One spline for each direction. aSplineX = vtk.vtkCardinalSpline() aSplineY = vtk.vtkCardinalSpline() aSplineZ = vtk.vtkCardinalSpline() # Generate random (pivot) points and add the corresponding # coordinates to the splines. # aSplineX will interpolate the x values of the points # aSplineY will interpolate the y values of the points # aSplineZ will interpolate the z values of the points inputPoints = vtk.vtkPoints() for i in range(0, numberOfInputPoints): x = math.Random(0, 1) y = math.Random(0, 1) z = math.Random(0, 1) aSplineX.AddPoint(i, x) aSplineY.AddPoint(i, y) aSplineZ.AddPoint(i, z) inputPoints.InsertPoint(i, x, y, z) # The following section will create glyphs for the pivot points # in order to make the effect of the spline more clear. # Create a polydata to be glyphed. inputData = vtk.vtkPolyData() inputData.SetPoints(inputPoints) # Use sphere as glyph source. balls = vtk.vtkSphereSource() balls.SetRadius(.01) balls.SetPhiResolution(10) balls.SetThetaResolution(10) glyphPoints = vtk.vtkGlyph3D() glyphPoints.SetInput(inputData) glyphPoints.SetSource(balls.GetOutput()) glyphMapper = vtk.vtkPolyDataMapper() glyphMapper.SetInputConnection(glyphPoints.GetOutputPort()) glyph = vtk.vtkActor() glyph.SetMapper(glyphMapper) glyph.GetProperty().SetDiffuseColor(tomato) glyph.GetProperty().SetSpecular(.3) glyph.GetProperty().SetSpecularPower(30) # Generate the polyline for the spline. points = vtk.vtkPoints() profileData = vtk.vtkPolyData() # Number of points on the spline numberOfOutputPoints = 400 # Interpolate x, y and z by using the three spline filters and # create new points for i in range(0, numberOfOutputPoints): t = (numberOfInputPoints-1.0)/(numberOfOutputPoints-1.0)*i points.InsertPoint(i, aSplineX.Evaluate(t), aSplineY.Evaluate(t), aSplineZ.Evaluate(t)) # Create the polyline. lines = vtk.vtkCellArray() lines.InsertNextCell(numberOfOutputPoints) for i in range(0, numberOfOutputPoints): lines.InsertCellPoint(i) profileData.SetPoints(points) profileData.SetLines(lines) # Add thickness to the resulting line. profileTubes = vtk.vtkTubeFilter() profileTubes.SetNumberOfSides(8) profileTubes.SetInput(profileData) profileTubes.SetRadius(.005) profileMapper = vtk.vtkPolyDataMapper() profileMapper.SetInputConnection(profileTubes.GetOutputPort()) profile = vtk.vtkActor() profile.SetMapper(profileMapper) profile.GetProperty().SetDiffuseColor(banana) profile.GetProperty().SetSpecular(.3) profile.GetProperty().SetSpecularPower(30) return (glyph, profile)
def uniformFn(NPts,points):
math = vtk.vtkMath()
math.RandomSeed(27183)
for i in range(0,NPts):
points.SetPoint(i,math.Random(0,1),math.Random(0,1),0.0)
#!/usr/bin/env python
import vtk
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Interpolate onto a volume
# Parameters for debugging
NPts = 100 #Keep test small
math = vtk.vtkMath()
math.RandomSeed(31415)
res = 50
polyData = vtk.vtkPolyData()
pts = vtk.vtkPoints()
pts.SetDataTypeToFloat()
pts.SetNumberOfPoints(NPts)
for i in range(0,NPts):
pts.SetPoint(i,math.Random(-1,1),math.Random(-1,1),math.Random(-1,1))
polyData.SetPoints(pts);
# Generate signed distance function and contour it
dist = vtk.vtkUnsignedDistance()
dist.SetInputData(polyData)
dist.SetRadius(0.25) #how far out to propagate distance calculation
dist.SetDimensions(res,res,res)
dist.CappingOn()
dist.AdjustBoundsOn()
dist.SetAdjustDistance(0.01)
# Extract the surface with modified flying edges
def display(data, datascalevec=None, radius=None, color=None, shape_type=None):
"""display(data, radius=1, datascalevec=.5):
or
r = random.randn(10,3)
d = {1:r,2:r+2}
plotvtk.display(d,color=[[255,0,0],[0,0,255]],radius=[[.004],[.01]])
or
radius={'0':.004,'1':.004}
color={'0':[255,0,0],'1':[0,0,255]}
plotvtk.display(d,color=color,radius=radius)
"""
try:
if shape(data)[0] == 3 and shape(data)[1] != 3:
print "array is probably transposed wrong. transposing"
data = transpose(data)
except IndexError: # it probably a dictionary
pass
for i in data.keys():
if len(shape(data[i])) == 1:
# data 1D array
pass
elif shape(data[i])[0] == 3 and shape(data[i])[1] != 3:
print "dictionary array is probably transposed wrong. transposing"
data[i] = transpose(data[i])
# set some defaults if nothing defined
defcolor = array([[255, 0, 0]]) # red
defradius = array([[0.004]])
# Adding feature to handle a single array or a dictionary of arrays
# so as to handle multiple data.
if type(data) == dict:
for d in data.keys():
numdata = len(data[d])
if color == None:
# color = red
print "making default color scheme"
color = array(
[
arange(0, 255, 255 / len(data[d]))[::-1],
arange(0, 255, 255 / len(data[d])),
arange(0, 255, 255 / len(data[d])),
]
).T
if radius == None:
radius = tile([defradius], len(data[d])).T
else:
print "data in non dict form"
data = {1: data}
radius = defradius
color = defcolor
[ren, renWin, iren] = vtkwindow()
print "ln", len(data.keys())
for k in range(0, len(data.keys())):
print shape(data[data.keys()[k]]) # , len(data[k]), shape(color)
if k == -1:
[sdata, scalefactor] = scaledata(float_(data[data.keys()[k]]))
print "scaled data"
else:
sdata = float_(data[data.keys()[k]])
points = vtk.vtkPoints()
math = vtk.vtkMath()
# some 2 pnts of fake data at 0,0,0
pointsfake = vtk.vtkPoints()
pointsfake.InsertNextPoint(0, 0, 0)
pointsfake.InsertNextPoint(0, 0, 0)
pointsfake.InsertNextPoint(0, 0, 0)
ballActor, profile = vtkpoints(pointsfake, color=[0, 255, 0], radius=0.0000) # radius[k])
ren.AddActor(ballActor) # Add the actors to the renderer, set the background and size
# end of fake data
print "lengthofdata", len(sdata)
if len(shape(sdata)) == 1: # add dimension
sdata = array([sdata])
if len(sdata) < 3: # tile to fix some bug where no points plotted unless = or greater than 3 points
sdata = tile(sdata, [3 - len(sdata) + 1, 1])
print "len", len(sdata)
for i in range(len(sdata)):
points.InsertNextPoint(sdata[i, 0], sdata[i, 1], sdata[i, 2])
# make color and radius dictonaries.
if type(color) == list and type(radius) == list:
c = {}
r = {}
for cr in range(0, len(color)):
c[cr] = color[cr]
for cr in range(len(radius)):
r[cr] = radius[cr]
color = c
radius = r
print k
# print shape_type.keys()[k]#shape_type[shape_type.keys()[k]]
try:
if shape_type.keys()[k] == "points":
ballActor, profile = vtkpoints(points, color=color[color.keys()[k]], radius=radius[radius.keys()[k]])
ren.AddActor(ballActor) # Add the actors to the renderer, set the background and size
if shape_type.keys()[k] == "disks":
print "trying disk plot"
disk_pos = data[data.keys()[k]]
disk_dir = shape_type[shape_type.keys()[k]]
for i in range(0, size(disk_pos, 0)):
d = disk_dir[i] * 90
diskactor = vtkdisk(c=(0, 0, 0))
diskactor.RotateX(90)
diskactor.SetPosition(disk_pos[i][0], disk_pos[i][1], disk_pos[i][2])
diskactor.RotateZ(d[0])
diskactor.RotateX(d[1])
ren.AddActor(diskactor)
print "done disk"
except AttributeError:
pass
ballActor, profile = vtkpoints(points, color=color[color.keys()[k]], radius=radius[radius.keys()[k]])
ren.AddActor(ballActor) # Add the actors to the renderer, set the background and size
# outline = vtk.vtkOutlineFilter()
# outline.SetInput(mapBalls.GetOutput())
# outlineMapper = vtk.vtkPolyDataMapper()
# outlineMapper.SetInput(outline.GetOutput())
# outlineActor = vtk.vtkActor()
# outlineActor.SetMapper(outlineMapper)
# outlineActor.GetProperty().SetColor(1,1,1)
iren.Initialize()
ren.ResetCamera()
renWin.Render()
iren.Start()