def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
InputArrayChoiceMixin.__init__(self)
self._config.scaleFactor = 1
configList = [
('Scale factor:', 'scaleFactor', 'base:float', 'text',
'The warping will be scaled by this factor'),
('Vectors selection:', 'vectorsSelection', 'base:str', 'choice',
'The attribute that will be used as vectors for the warping.',
(self._defaultVectorsSelectionString, self._userDefinedString))]
self._warpVector = vtk.vtkWarpVector()
ScriptedConfigModuleMixin.__init__(
self, configList,
{'Module (self)' : self,
'vtkWarpVector' : self._warpVector})
module_utils.setup_vtk_object_progress(self, self._warpVector,
'Warping points.')
self.sync_module_logic_with_config()
def run_vtk(hdf5_filename: str, scale: float):
#alg = HDF5Source()
alg = H5NastranReader()
alg.SetFileName(hdf5_filename)
#cf = vtk.vtkContourFilter()
#cf.SetInputConnection(alg.GetOutputPort())
#cf.SetValue(0, 200)
model, ugrid, root, alt_grids = get_nastran_ugrid(hdf5_filename)
ugrid = alt_grids['main']
warp = vtk.vtkWarpVector()
warp.SetScaleFactor(scale)
warp.SetInputData(ugrid)
warp.Update()
#warp = ugrid
grid_mapper = vtk.vtkDataSetMapper()
if 0:
grid_mapper.SetInputData(ugrid)
else:
grid_mapper.SetInputData(warp.GetOutput())
#grid_mapper = vtk.vtkPolyDataMapper()
#grid_mapper.SetInputConnection(ugrid.GetOutputPort())
actor = vtk.vtkLODActor()
actor.SetMapper(grid_mapper)
add_actor_to_renderer(actor)
print('go')
def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
InputArrayChoiceMixin.__init__(self)
self._config.scaleFactor = 1
configList = [
('Scale factor:', 'scaleFactor', 'base:float', 'text',
'The warping will be scaled by this factor'),
('Vectors selection:', 'vectorsSelection', 'base:str', 'choice',
'The attribute that will be used as vectors for the warping.',
(self._defaultVectorsSelectionString, self._userDefinedString))
]
self._warpVector = vtk.vtkWarpVector()
ScriptedConfigModuleMixin.__init__(self, configList, {
'Module (self)': self,
'vtkWarpVector': self._warpVector
})
module_utils.setup_vtk_object_progress(self, self._warpVector,
'Warping points.')
self.sync_module_logic_with_config()
def apply_modes(self, modes_with_scales):
for mode, scale in modes_with_scales.items():
print('Applying ' + mode + ' multiplied by ' + str(scale))
self.mesh.GetOutput().GetPointData().SetActiveVectors(mode)
warp_vector = vtk.vtkWarpVector()
warp_vector.SetInputConnection(self.mesh.GetOutputPort())
warp_vector.SetScaleFactor(scale)
warp_vector.Update()
self.mesh = warp_vector
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkWarpVector(),
'Processing.', ('vtkPointSet', ),
('vtkPointSet', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def main():
file_name, color_scheme = get_program_parameters()
colors = vtk.vtkNamedColors()
# Read a vtk file
#
plate = vtk.vtkPolyDataReader()
plate.SetFileName(file_name)
plate.SetVectorsName("mode8")
plate.Update()
warp = vtk.vtkWarpVector()
warp.SetInputConnection(plate.GetOutputPort())
warp.SetScaleFactor(0.5)
normals = vtk.vtkPolyDataNormals()
normals.SetInputConnection(warp.GetOutputPort())
color = vtk.vtkVectorDot()
color.SetInputConnection(normals.GetOutputPort())
lut = vtk.vtkLookupTable()
MakeLUT(color_scheme, lut)
plateMapper = vtk.vtkDataSetMapper()
plateMapper.SetInputConnection(color.GetOutputPort())
plateMapper.SetLookupTable(lut)
plateMapper.SetScalarRange(-1, 1)
plateActor = vtk.vtkActor()
plateActor.SetMapper(plateMapper)
# Create the RenderWindow, Renderer and both Actors
#
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Add the actors to the renderer, set the background and size
#
ren.AddActor(plateActor)
ren.SetBackground(colors.GetColor3d("Wheat"))
renWin.SetSize(512, 512)
ren.GetActiveCamera().SetPosition(13.3991, 14.0764, 9.97787)
ren.GetActiveCamera().SetFocalPoint(1.50437, 0.481517, 4.52992)
ren.GetActiveCamera().SetViewAngle(30)
ren.GetActiveCamera().SetViewUp(-0.120861, 0.458556, -0.880408)
ren.GetActiveCamera().SetClippingRange(12.5724, 26.8374)
# Render the image.
renWin.Render()
iren.Start()
def getWarpedMesh(mesh, displacement_field_name='displacement'):
mesh.GetPointData().SetActiveVectors(displacement_field_name)
warp = vtk.vtkWarpVector()
warp.SetInputData(mesh)
warp.Update()
mesh = warp.GetOutput()
return mesh
def __init__ (self, mod_m):
debug ("In WarpVectorCutPlane::__init__ ()")
Common.state.busy ()
Base.Objects.CutPlaneModule.__init__ (self, mod_m)
self.cut = vtk.vtkCutter ()
self.warp = vtk.vtkWarpVector ()
self.norm = vtk.vtkPolyDataNormals ()
self.mapper = self.map = vtk.vtkPolyDataMapper ()
self.map.SetLookupTable (self.mod_m.get_scalar_lut ())
self.actor = self.act = vtk.vtkActor ()
self.data_out = self.mod_m.GetOutput ()
self._initialize ()
self._gui_init ()
self.renwin.Render ()
Common.state.idle ()
def sliceDown(self):
# Warp using the normals
warp = vtk.vtkWarpVector()
warp.SetInputData(fixMesh(downsample(self.currentPeel))) # fixMesh here updates normals needed for warping
warp.SetInputArrayToProcess(0, 0, 0, vtk.vtkDataObject().FIELD_ASSOCIATION_POINTS,
vtk.vtkDataSetAttributes().NORMALS)
warp.SetScaleFactor(-1)
warp.Update()
out = vtk.vtkPolyData()
out = upsample(warp.GetPolyDataOutput())
out = smooth(out)
out = fixMesh(out)
out = cleanMesh(out)
self.currentPeel = out
def getMeshVolume(
mesh,
warp_mesh=1
):
if warp_mesh == 1:
warp = vtk.vtkWarpVector()
warp.SetInputData(mesh)
warp.Update()
mesh = warp.GetOutput()
polydata = myvtk.ugrid2pdata(mesh)
mass = myvtk.getMassProperties(polydata)
volume = mass.GetVolume()
return volume
def main(args):
INDIR = args.indir
FILENAME = args.input_filename
OUTDIR = args.outdir
WARP_VECTOR_NAME = args.warp_vec_name
mesh = intializeVTP(INDIR + FILENAME)
mesh.GetPointData().SetActiveVectors(WARP_VECTOR_NAME)
warpVector = vtk.vtkWarpVector()
warpVector.SetInputData(mesh)
warpVector.Update()
if (args.output_filename is None):
output_filename = OUTDIR + '/Warped_' + FILENAME
else:
output_filename = OUTDIR + args.output_filename
writeVTP(warpVector.GetOutput(), output_filename)
def _getElementMetrics(self):
for k, p in self.polydatas.items():
# create a deformed polydata object for deformed metrics
warp = vtk.vtkWarpVector()
warp.SetInputData(p)
warp.SetScaleFactor(1)
p.GetPointData().SetActiveVectors('displacement')
warp.Update()
warped = warp.GetOutput()
# Use the MeshQuality filter with the metric set to volume to quickly get cell volumes
# for reference and deformed cases.
mesh_quality = vtk.vtkMeshQuality()
mesh_quality.SetTetQualityMeasureToVolume()
mesh_quality.SetInputData(p)
mesh_quality.Update()
r_volumes = mesh_quality.GetOutput().GetCellData().GetArray("Quality")
r_volumes.SetName('Reference Volume')
p.GetCellData().AddArray(r_volumes)
mesh_quality2 = vtk.vtkMeshQuality()
mesh_quality2.SetTetQualityMeasureToVolume()
mesh_quality2.SetInputData(warped)
mesh_quality2.Update()
d_volumes = mesh_quality2.GetOutput().GetCellData().GetArray("Quality")
d_volumes.SetName('Deformed Volume')
p.GetCellData().AddArray(d_volumes)
# CellCenters filter generates new polydata with points at centroids. Grab these points
# data array and add it to polydata for reference and deformed.
cell_centers = vtk.vtkCellCenters()
cell_centers.VertexCellsOff()
cell_centers.SetInputData(p)
cell_centers.Update()
r_centroids = cell_centers.GetOutput().GetPoints().GetData()
r_centroids.SetName('Reference Centroid')
p.GetCellData().AddArray(r_centroids)
cell_centers2 = vtk.vtkCellCenters()
cell_centers2.VertexCellsOff()
cell_centers2.SetInputData(warped)
cell_centers2.Update()
d_centroids = cell_centers2.GetOutput().GetPoints().GetData()
d_centroids.SetName('Deformed Centroid')
p.GetCellData().AddArray(d_centroids)
def warpVTU(data_vtu_in, array_type, array_name):
# type: (object, object, object) -> object
if array_type == 'point':
if data_vtu_in.GetPointData().HasArray(array_name):
data_vtu_in.GetPointData().SetActiveVectors(array_name)
else:
print("Point data array '%s' does not exist" % array_name)
elif array_type == 'cell':
if data_vtu_in.GetCellData().HasArray(array_name):
data_vtu_in.GetCellData().SetActiveVectors(array_name)
else:
print("Cell data array '%s' does not exist" % array_name)
else:
print("Array type '%s' undefined" % array_type)
warpVector = vtk.vtkWarpVector()
warpVector.SetInputData(data_vtu_in)
warpVector.Update()
model_vtu_deformed = warpVector.GetOutput()
return model_vtu_deformed
fd2ad.SetInputData(do2ds.GetRectilinearGridOutput())
fd2ad.SetInputFieldToDataObjectField()
fd2ad.SetOutputAttributeDataToPointData()
fd2ad.SetVectorComponent(0, "vectors", 0)
fd2ad.SetVectorComponent(1, "vectors", 1)
fd2ad.SetVectorComponent(2, "vectors", 2)
fd2ad.SetScalarComponent(0, "scalars", 0)
fd2ad.Update()
# create pipeline
#
plane = vtk.vtkRectilinearGridGeometryFilter()
plane.SetInputData(fd2ad.GetRectilinearGridOutput())
plane.SetExtent(0, 100, 0, 100, 15, 15)
warper = vtk.vtkWarpVector()
warper.SetInputConnection(plane.GetOutputPort())
warper.SetScaleFactor(0.05)
planeMapper = vtk.vtkDataSetMapper()
planeMapper.SetInputConnection(warper.GetOutputPort())
planeMapper.SetScalarRange(0.197813, 0.710419)
planeActor = vtk.vtkActor()
planeActor.SetMapper(planeMapper)
cutPlane = vtk.vtkPlane()
cutPlane.SetOrigin(fd2ad.GetOutput().GetCenter())
cutPlane.SetNormal(1, 0, 0)
planeCut = vtk.vtkCutter()
def determineCapPerfusionVolumes(caps,cap_center_coordinates,heart):
numPts = heart.GetNumberOfPoints()
heart_data = [0]*numPts
heart_graph = Graph()
cap_heart_points = set()
for i in cap_center_coordinates:
cap_heart_points.add(heart.FindPoint(i))
heart_graph = generateGraph(heart)
heart = multipleCapSourceDistance(heart,heart_graph,100000000000,cap_heart_points)
for i in range(0,numPts):
connnectedPt_list = getConnectedVerticesNotIncludingSeed(heart,i)
for j in range(0,connnectedPt_list.GetNumberOfIds()):
# new point to decide whether to add to patch, edge, or nothing (if already in edge)
cpt = connnectedPt_list.GetId(j)
heart_graph.add_edge(i,cpt,calcDistance2Points(heart,i,cpt))
heart_graph.add_edge(cpt,i,calcDistance2Points(heart,i,cpt))
print(cap_heart_points)
for i in range(0,len(cap_center_coordinates)):
if heart.FindPoint(cap_center_coordinates[i]) in heart_graph.nodes:
visited, path = dijsktra(heart_graph,heart.FindPoint(cap_center_coordinates[i]))
data_array = vtk.vtkDoubleArray()
data_array.SetName(caps[i] + '_distance_map')
for i in range(0,numPts):
if i in visited:
data_array.InsertNextValue(visited[i])
else:
data_array.InsertNextValue(-1)
heart.GetPointData().AddArray(data_array)
writeVTU(heart,'heart_distance_mapped.vtu')
for ip in range(0,numPts):
value = image.GetPointData().GetArray(0).GetValue(image.FindPoint(heart.GetPoint(ip)))
min,min_pt_index = minDistanceBetweenPointsGraph(heart_graph, heart, ip, cap_center_coordinates)
heart_data[ip] = min_pt_index
#generate summary data array for perfusion
data_array = vtk.vtkDoubleArray()
data_array.SetName('PerfusionVolumes')
for ptID in range(0,numPts):
data_array.InsertNextValue(heart_data[ptID])
heart.GetPointData().AddArray(data_array)
perfusion_data = np.zeros((len(caps),numPts))
for ip in range(0,len(heart_data)):
if(heart_data[ip]>=0):
perfusion_data[heart_data[ip],ip] = 1
#generate separate data array for each perfusion volume
#calculate the volume of each perfused area of each cap
volumes = []
LCA_data = np.zeros(numPts)
RCA_data = np.zeros(numPts)
RSA_data = np.zeros(numPts)
CA_data = np.zeros(numPts)
cap_pt_list = vtk.vtkIdList()
for i in tqdm(range(0,len(perfusion_data))):
data = vtk.vtkDoubleArray()
data.SetName(str(i) + '_' + caps[i])
for ip in range(0,numPts):
if(perfusion_data[i,ip]>0):
cap_pt_list.InsertNextId(ip)
if(caps[i].startswith('LCA')):
LCA_data[ip] = perfusion_data[i,ip]
CA_data[ip] = 1
elif(caps[i].startswith('RCA')):
RCA_data[ip] = perfusion_data[i,ip]
CA_data[ip] = 2
elif(caps[i].startswith('RSA')):
RSA_data[ip] = perfusion_data[i,ip]
CA_data[ip] = 3
data.InsertNextValue(perfusion_data[i,ip])
heart.GetPointData().AddArray(data)
Mass = extractRegionVolume(heart,cap_pt_list)
p2c = vtk.vtkPointDataToCellData()
p2c.SetInputData(heart)
p2c.PassPointDataOn()
warp = vtk.vtkWarpVector()
warp.SetInputConnection(p2c.GetOutputPort())
thresh = vtk.vtkThreshold()
thresh.SetInputConnection(warp.GetOutputPort())
thresh.ThresholdBetween(i,i)
thresh.SetInputArrayToProcess(1, 0, 0, 0, "PerfusionVolumes")
volumes.append(Mass.GetVolume())
cap_pt_list.Reset()
heart.GetPointData().AddArray(convert_np_array_to_vtk('LCA_all',LCA_data))
heart.GetPointData().AddArray(convert_np_array_to_vtk('RCA_all',RCA_data))
heart.GetPointData().AddArray(convert_np_array_to_vtk('RSA_all',RSA_data))
heart.GetPointData().AddArray(convert_np_array_to_vtk('CA_all',CA_data))
return volumes
def generateWarpedImages(
ref_image_folder,
ref_image_basename,
sol_folder,
sol_basename,
ref_frame=0,
sol_ext="vtu",
verbose=0):
myVTK.myPrint(verbose, "*** generateWarpedImages ***")
ref_image_zfill = len(glob.glob(ref_image_folder+"/"+ref_image_basename+"_*.vti")[0].rsplit("_")[-1].split(".")[0])
ref_image_filename = ref_image_folder+"/"+ref_image_basename+"_"+str(ref_frame).zfill(ref_image_zfill)+".vti"
ref_image = myVTK.readImage(
filename=ref_image_filename)
interpolator = myVTK.createImageInterpolator(
image=ref_image)
#I = numpy.empty(1)
#interpolator.Interpolate([0.35, 0.25, 0.], I)
image = vtk.vtkImageData()
image.SetOrigin(ref_image.GetOrigin())
image.SetSpacing(ref_image.GetSpacing())
image.SetExtent(ref_image.GetExtent())
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
image.AllocateScalars(vtk.VTK_FLOAT, 1)
else:
image.SetScalarTypeToFloat()
image.SetNumberOfScalarComponents(1)
image.AllocateScalars()
scalars = image.GetPointData().GetScalars()
sol_zfill = len(glob.glob(sol_folder+"/"+sol_basename+"_*."+sol_ext)[0].rsplit("_")[-1].split(".")[0])
n_frames = len(glob.glob(sol_folder+"/"+sol_basename+"_"+"[0-9]"*sol_zfill+"."+sol_ext))
#n_frames = 1
X = numpy.empty(3)
U = numpy.empty(3)
x = numpy.empty(3)
I = numpy.empty(1)
m = numpy.empty(1)
for k_frame in xrange(n_frames):
myVTK.myPrint(verbose, "k_frame = "+str(k_frame))
mesh = myVTK.readUGrid(
filename=sol_folder+"/"+sol_basename+"_"+str(k_frame).zfill(sol_zfill)+"."+sol_ext)
#print mesh
warp = vtk.vtkWarpVector()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
warp.SetInputData(mesh)
else:
warp.SetInput(mesh)
warp.Update()
warped_mesh = warp.GetOutput()
#myVTK.writeUGrid(
#ugrid=warped_mesh,
#filename=sol_folder+"/"+sol_basename+"-warped_"+str(k_frame).zfill(sol_zfill)+"."+sol_ext)
probe = vtk.vtkProbeFilter()
if (vtk.vtkVersion.GetVTKMajorVersion() >= 6):
probe.SetInputData(image)
probe.SetSourceData(warped_mesh)
else:
probe.SetInput(image)
probe.SetSource(warped_mesh)
probe.Update()
probed_image = probe.GetOutput()
scalars_mask = probed_image.GetPointData().GetArray("vtkValidPointMask")
scalars_U = probed_image.GetPointData().GetArray("displacement")
#myVTK.writeImage(
#image=probed_image,
#filename=sol_folder+"/"+sol_basename+"_"+str(k_frame).zfill(sol_zfill)+".vti")
for k_point in xrange(image.GetNumberOfPoints()):
scalars_mask.GetTuple(k_point, m)
if (m[0] == 0):
I[0] = 0.
else:
image.GetPoint(k_point, x)
scalars_U.GetTuple(k_point, U)
X = x - U
interpolator.Interpolate(X, I)
scalars.SetTuple(k_point, I)
myVTK.writeImage(
image=image,
filename=sol_folder+"/"+sol_basename+"-warped_"+str(k_frame).zfill(sol_zfill)+".vti")
def main():
fileName, dataPoint = get_program_parameters()
colors = vtk.vtkNamedColors()
thickness = list()
displacement = list()
for i in range(0, 10):
thickness.append('thickness' + str(i))
displacement.append('displacement' + str(i))
reader = list()
warp = list()
connect = list()
mold = list()
moldMapper = list()
moldActor = list()
connect2 = list()
parison = list()
normals2 = list()
parisonMapper = list()
parisonActor = list()
cf = list()
contourMapper = list()
contours = list()
ren = list()
lut = vtk.vtkLookupTable()
lut.SetHueRange(0.0, 0.66667)
for i in range(0, 10):
# Create the reader and warp the data vith vectors.
reader.append(vtk.vtkDataSetReader())
reader[i].SetFileName(fileName)
reader[i].SetScalarsName(thickness[i])
reader[i].SetVectorsName(displacement[i])
reader[i].Update()
warp.append(vtk.vtkWarpVector())
warp[i].SetInputData(reader[i].GetUnstructuredGridOutput())
# Extract the mold from the mesh using connectivity.
connect.append(vtk.vtkConnectivityFilter())
connect[i].SetInputConnection(warp[i].GetOutputPort())
connect[i].SetExtractionModeToSpecifiedRegions()
connect[i].AddSpecifiedRegion(0)
connect[i].AddSpecifiedRegion(1)
mold.append(vtk.vtkGeometryFilter())
mold[i].SetInputConnection(connect[i].GetOutputPort())
moldMapper.append(vtk.vtkDataSetMapper())
moldMapper[i].SetInputConnection(mold[i].GetOutputPort())
moldMapper[i].ScalarVisibilityOff()
moldActor.append(vtk.vtkActor())
moldActor[i].SetMapper(moldMapper[i])
moldActor[i].GetProperty().SetColor(colors.GetColor3d("ivory_black"))
moldActor[i].GetProperty().SetRepresentationToWireframe()
# Extract the parison from the mesh using connectivity.
connect2.append(vtk.vtkConnectivityFilter())
connect2[i].SetInputConnection(warp[i].GetOutputPort())
connect2[i].SetExtractionModeToSpecifiedRegions()
connect2[i].AddSpecifiedRegion(2)
parison.append(vtk.vtkGeometryFilter())
parison[i].SetInputConnection(connect2[i].GetOutputPort())
normals2.append(vtk.vtkPolyDataNormals())
normals2[i].SetInputConnection(parison[i].GetOutputPort())
normals2[i].SetFeatureAngle(60)
parisonMapper.append(vtk.vtkPolyDataMapper())
parisonMapper[i].SetInputConnection(normals2[i].GetOutputPort())
parisonMapper[i].SetLookupTable(lut)
parisonMapper[i].SetScalarRange(0.12, 1.0)
parisonActor.append(vtk.vtkActor())
parisonActor[i].SetMapper(parisonMapper[i])
cf.append(vtk.vtkContourFilter())
cf[i].SetInputConnection(connect2[i].GetOutputPort())
cf[i].SetValue(0, 0.5)
contourMapper.append(vtk.vtkPolyDataMapper())
contourMapper[i].SetInputConnection(cf[i].GetOutputPort())
contours.append(vtk.vtkActor())
contours[i].SetMapper(contourMapper[i])
ren.append(vtk.vtkRenderer())
ren[i].AddActor(moldActor[i])
ren[i].AddActor(parisonActor[i])
ren[i].AddActor(contours[i])
ren[i].SetBackground(colors.GetColor3d("AliceBlue"))
ren[i].GetActiveCamera().SetPosition(50.973277, 12.298821, 29.102547)
ren[i].GetActiveCamera().SetFocalPoint(0.141547, 12.298821, -0.245166)
ren[i].GetActiveCamera().SetViewUp(-0.500000, 0.000000, 0.866025)
ren[i].GetActiveCamera().SetClippingRange(36.640827, 78.614680)
# Create the RenderWindow and RenderWindowInteractor.
renWin = vtk.vtkRenderWindow()
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
rendererSizeX = 750
rendererSizeY = 400
renWinScale = 0.5
renWin.SetWindowName("Blow")
if 0 <= dataPoint < 10:
renWin.AddRenderer(ren[dataPoint])
renWin.SetSize(rendererSizeX, rendererSizeY)
else:
gridDimensionsX = 2
gridDimensionsY = 5
renWin.SetSize(int(rendererSizeX * gridDimensionsX * renWinScale),
int(rendererSizeY * gridDimensionsY * renWinScale))
# Add and position the renders to the render window.
viewPort = list()
for row in range(0, gridDimensionsY):
for col in range(0, gridDimensionsX):
idx = row * gridDimensionsX + col
x0 = float(col) / gridDimensionsX
y0 = float(gridDimensionsY - row - 1) / gridDimensionsY
x1 = float(col + 1) / gridDimensionsX
y1 = float(gridDimensionsY - row) / gridDimensionsY
viewPort[:] = []
viewPort.append(x0)
viewPort.append(y0)
viewPort.append(x1)
viewPort.append(y1)
renWin.AddRenderer(ren[idx])
ren[idx].SetViewport(viewPort)
iren.Initialize()
iren.Start()
def animate(self, pd, ind):
"""
Helper function called by **deformableRegistration** if **animate** is *True*.
Spawns a window with an interactive 3-D rendering of the current analyzed object
in its reference state. The displacements calculated from the deformable image
registration can be applied to this object to animate the deformation by pressing
the RIGHT-ARROW. Pressing the UP-ARROW will animate and also save the frames to
disk.
Parameters
----------
pd : vtkPolyData
The current analyzed object's reference geometry.
ind : int
The index of the current polydata in **rsurfs**. Necessary for naming directory created
if animation frames are saved.
"""
pd.GetPointData().SetActiveVectors("Displacement")
class vtkTimerCallback(object):
def __init__(self):
self.timer_count = 0
def execute(self, obj, event):
if self.timer_count == 10:
self.timer_count = 0
warpVector = vtk.vtkWarpVector()
warpVector.SetInputData(pd)
warpVector.SetScaleFactor(0.1 * (self.timer_count + 1))
warpVector.Update()
poly = warpVector.GetPolyDataOutput()
getScalars = vtk.vtkExtractVectorComponents()
getScalars.SetInputData(poly)
getScalars.Update()
vectorNorm = vtk.vtkVectorNorm()
vectorNorm.SetInputData(poly)
vectorNorm.Update()
scalars = []
scalars.append(getScalars.GetVzComponent())
scalars.append(vectorNorm.GetOutput())
scalars.append(getScalars.GetVxComponent())
scalars.append(getScalars.GetVyComponent())
names = ("Z", "Mag", "X", "Y")
for k, a in enumerate(self.actors):
calc = vtk.vtkArrayCalculator()
scalars[k].GetPointData().GetScalars().SetName(names[k])
calc.SetInputData(scalars[k])
calc.AddScalarArrayName(names[k])
calc.SetResultArrayName(names[k])
calc.SetFunction("%s * 0.1 * %f" %
(names[k], self.timer_count + 1))
calc.Update()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(calc.GetOutput())
mapper.SetScalarRange(calc.GetOutput().GetScalarRange())
mapper.SetScalarModeToUsePointData()
mapper.SetColorModeToMapScalars()
mapper.Update()
a.SetMapper(mapper)
cb.scalar_bars[k].SetLookupTable(mapper.GetLookupTable())
iren = obj
iren.GetRenderWindow().Render()
time.sleep(0.3)
if self.key == "Up":
try:
os.mkdir(self.directory)
except:
pass
w2i = vtk.vtkWindowToImageFilter()
w2i.SetInput(obj.GetRenderWindow())
w2i.Update()
png = vtk.vtkPNGWriter()
png.SetInputConnection(w2i.GetOutputPort())
png.SetFileName(self.directory + os.sep +
"frame{:d}.png".format(self.timer_count))
png.Update()
png.Write()
self.timer_count += 1
def Keypress(self, obj, event):
self.key = obj.GetKeySym()
if self.key == "Right" or self.key == "Up":
for i in range(10):
obj.CreateOneShotTimer(1)
renwin = vtk.vtkRenderWindow()
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renwin)
iren.Initialize()
cb = vtkTimerCallback()
xmins = (0, 0.5, 0, 0.5)
xmaxs = (0.5, 1, 0.5, 1)
ymins = (0, 0, 0.5, 0.5)
ymaxs = (0.5, 0.5, 1, 1)
titles = ('Z Displacement', 'Magnitude', 'X Displacement',
'Y Displacement')
cb.actors = []
cb.scalar_bars = []
cb.directory = str(
os.path.normpath(self._def_dir + os.sep +
"animation{:0d}".format(ind + 1)))
warpVector = vtk.vtkWarpVector()
warpVector.SetInputData(pd)
warpVector.Update()
poly = warpVector.GetPolyDataOutput()
getScalars = vtk.vtkExtractVectorComponents()
getScalars.SetInputData(poly)
getScalars.Update()
vectorNorm = vtk.vtkVectorNorm()
vectorNorm.SetInputData(poly)
vectorNorm.Update()
scalars = []
scalars.append(getScalars.GetVzComponent())
scalars.append(vectorNorm.GetOutput())
scalars.append(getScalars.GetVxComponent())
scalars.append(getScalars.GetVyComponent())
bounds = np.zeros(6, np.float32)
pd.GetBounds(bounds)
length = np.min(bounds[1::2] - bounds[0:-1:2]) * 0.2
bounds[1] = bounds[0] + length
bounds[3] = bounds[2] + length
bounds[5] = bounds[4] + length
for j in range(4):
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(scalars[j])
mapper.SetScalarRange(scalars[j].GetScalarRange())
mapper.SetScalarModeToUsePointData()
mapper.SetColorModeToMapScalars()
scalar_bar = vtk.vtkScalarBarActor()
scalar_bar.SetLookupTable(mapper.GetLookupTable())
scalar_bar.SetTitle(titles[j])
scalar_bar.SetLabelFormat("%3.3f")
cb.scalar_bars.append(scalar_bar)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
cb.actors.append(actor)
renderer = vtk.vtkRenderer()
renderer.SetBackground(0., 0., 0.)
renwin.AddRenderer(renderer)
if j == 0:
camera = renderer.GetActiveCamera()
else:
renderer.SetActiveCamera(camera)
triad = vtk.vtkCubeAxesActor()
triad.SetCamera(camera)
triad.SetFlyModeToStaticTriad()
triad.SetBounds(bounds)
triad.GetXAxesLinesProperty().SetColor(1.0, 0.0, 0.0)
triad.GetYAxesLinesProperty().SetColor(0.0, 1.0, 0.0)
triad.GetZAxesLinesProperty().SetColor(0.0, 0.0, 1.0)
triad.GetXAxesLinesProperty().SetLineWidth(3.0)
triad.GetYAxesLinesProperty().SetLineWidth(3.0)
triad.GetZAxesLinesProperty().SetLineWidth(3.0)
triad.XAxisLabelVisibilityOff()
triad.YAxisLabelVisibilityOff()
triad.ZAxisLabelVisibilityOff()
triad.XAxisTickVisibilityOff()
triad.YAxisTickVisibilityOff()
triad.ZAxisTickVisibilityOff()
triad.XAxisMinorTickVisibilityOff()
triad.YAxisMinorTickVisibilityOff()
triad.ZAxisMinorTickVisibilityOff()
renderer.SetViewport(xmins[j], ymins[j], xmaxs[j], ymaxs[j])
renderer.AddActor(actor)
renderer.AddActor2D(scalar_bar)
renderer.AddActor(triad)
renderer.ResetCamera()
renwin.Render()
iren.AddObserver('TimerEvent', cb.execute)
iren.AddObserver('KeyPressEvent', cb.Keypress)
iren.Start()
def __init__(self):
"""
Called when the logic class is instantiated. Can be used for initializing member variables.
"""
ScriptedLoadableModuleLogic.__init__(self)
self.inputCurveNode = None
self.inputCurveNodeObservations = []
self.inputSurfacePointsNode = None
self.inputSurfacePointsNodeObservations = []
self.numberOfCurveLandmarkPoints = 80
self.printThreeDViewNode = None
self.printThreeDWidget = None
self.printViewWidth = 1024
self.printViewHeight = 1024
self.printXResolutionDpi = 300
self.printYResolutionDpi = 300
self.printScale = 2.0 #TODO: Workaround for scaling problem, see https://github.com/SlicerFab/SlicerFab/issues/13
self.printTransparentBackground = False
# Create triangulated flat disk that will be warped
self.surfaceUnitDisk = vtk.vtkDiskSource()
self.surfaceUnitDisk.SetOuterRadius(1.0)
self.surfaceUnitDisk.SetInnerRadius(0.0)
self.surfaceUnitDisk.SetCircumferentialResolution(
self.numberOfCurveLandmarkPoints)
self.surfaceUnitDisk.SetRadialResolution(60)
self.surfaceTriangulator = vtk.vtkDelaunay2D()
self.surfaceTriangulator.SetTolerance(
0.01
) # get rid of the small triangles near the center of the unit disk
self.surfaceTriangulator.SetInputConnection(
self.surfaceUnitDisk.GetOutputPort())
# Prepare transform object
# points on the unit disk (circumference and surface)
self.surfaceTransformSourcePoints = vtk.vtkPoints()
self.surfaceTransformSourceCurvePoints = vtk.vtkPoints()
self.surfaceTransformSourceCurvePoints.SetNumberOfPoints(
self.numberOfCurveLandmarkPoints)
import math
angleIncrement = 2.0 * math.pi / float(
self.numberOfCurveLandmarkPoints)
for pointIndex in range(self.numberOfCurveLandmarkPoints):
angle = float(pointIndex) * angleIncrement
self.surfaceTransformSourceCurvePoints.SetPoint(
pointIndex, math.cos(angle), math.sin(angle), 0)
# points on the warped surface (curve points and surface points)
self.surfaceTransformTargetPoints = vtk.vtkPoints()
self.surfaceTransform = vtk.vtkThinPlateSplineTransform()
self.surfaceTransform.SetSourceLandmarks(
self.surfaceTransformSourcePoints)
self.surfaceTransform.SetTargetLandmarks(
self.surfaceTransformTargetPoints)
# Transform polydata
self.surfaceTransformFilter = vtk.vtkTransformPolyDataFilter()
self.surfaceTransformFilter.SetTransform(self.surfaceTransform)
self.surfaceTransformFilter.SetInputConnection(
self.surfaceTriangulator.GetOutputPort())
self.cleanPolyDataFilter = vtk.vtkCleanPolyData()
self.cleanPolyDataFilter.SetInputConnection(
self.surfaceTransformFilter.GetOutputPort())
#
self.surfacePolyDataNormalsThin = vtk.vtkPolyDataNormals()
self.surfacePolyDataNormalsThin.SetInputConnection(
self.cleanPolyDataFilter.GetOutputPort())
# There are a few triangles in the triangulated unit disk with inconsistent
# orientation. Enabling consistency check fixes them.
self.surfacePolyDataNormalsThin.ConsistencyOn(
) # TODO: check if needed, probably not
self.surfacePolyDataNormalsThin.SplittingOff(
) # this prevents stray normals at the edge TODO: check
# Add thickness to warped surface (if needed)
# self.surfacePolyDataNormals = vtk.vtkPolyDataNormals()
# self.surfacePolyDataNormals.SetInputConnection(self.cleanPolyDataFilter.GetOutputPort())
# self.surfacePolyDataNormals.SplittingOff() # this prevents stray normals at the edge TODO: check
self.surfaceOffset = vtk.vtkWarpVector()
self.surfaceOffset.SetInputConnection(
self.surfacePolyDataNormalsThin.GetOutputPort())
self.surfaceOffset.SetInputArrayToProcess(
0, 0, 0, vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS,
vtk.vtkDataSetAttributes.NORMALS)
self.surfaceExtrude = vtk.vtkLinearExtrusionFilter()
self.surfaceExtrude.SetInputConnection(
self.surfaceOffset.GetOutputPort())
self.surfaceExtrude.SetExtrusionTypeToNormalExtrusion()
self.surfacePolyDataNormalsThick = vtk.vtkPolyDataNormals()
self.surfacePolyDataNormalsThick.SetInputConnection(
self.surfaceExtrude.GetOutputPort())
self.surfacePolyDataNormalsThick.AutoOrientNormalsOn()
def interpolate_data(self, points, disp, stretch=None, shear=None, on_deformed=True, kernel_radius=3.0,
kernel_sharpness=1.0, remove_null=True, return_deformed=True):
"""
Interpolate data on the mesh. This can be used for comparing experimental and simulation data together.
on_deform selects whether to interpolate the data on the original or on the deformed configuration
"""
if stretch is None:
stretch = np.array([])
if shear is None:
shear = np.array([])
# We need nPts*3 data for vtk
if points.shape[1] == 2:
points_ = np.zeros([points.shape[0], 3])
points_[:,0:2] = points
# Deform data if needed
if on_deformed:
points_[:,0:2] = points + disp
# Generate vtk points structure with all data
vtkpoints = vtk.vtkPoints()
vtkpoints.SetData(numpy_support.numpy_to_vtk(points_))
vtkdisp = vtk.vtkDoubleArray()
vtkdisp.SetName("disp")
vtkdisp.SetNumberOfComponents(disp.shape[1])
vtkdisp.SetNumberOfTuples(disp.shape[0])
vtkdisp.SetVoidArray(disp.flatten(), disp.size, 1)
vtkstretch = vtk.vtkDoubleArray()
vtkstretch.SetName("stretch")
vtkstretch.SetNumberOfComponents(1)
vtkstretch.SetNumberOfTuples(stretch.size)
vtkstretch.SetVoidArray(stretch, stretch.size, 1)
shear = shear.reshape([-1, 4])
vtkshear = vtk.vtkDoubleArray()
vtkshear.SetName("shear")
vtkshear.SetNumberOfComponents(shear.shape[1])
vtkshear.SetNumberOfTuples(shear.shape[0])
vtkshear.SetVoidArray(shear, shear.size, 1)
vtkpointset = vtk.vtkPolyData()
vtkpointset.SetPoints(vtkpoints)
vtkpointset.GetPointData().AddArray(vtkdisp)
vtkpointset.GetPointData().AddArray(vtkstretch)
vtkpointset.GetPointData().AddArray(vtkshear)
# Build the locator for the interpolation
locator = vtk.vtkStaticPointLocator()
locator.SetDataSet(vtkpointset)
locator.BuildLocator()
# Build the Gaussian kernel
kernel = vtk.vtkGaussianKernel()
kernel.SetKernelFootprint(0)
kernel.SetRadius(kernel_radius)
kernel.SetSharpness(kernel_sharpness)
# If the interpolation is performed on the deformed configuration, warp the data
if on_deformed:
disp_ = np.zeros(self.x_nodes.shape)
disp_[:,0:2] = self.disp
warpData = vtk.vtkDoubleArray()
warpData.SetName("warp")
warpData.SetNumberOfComponents(3)
warpData.SetNumberOfTuples(self.x_nodes.shape[0])
warpData.SetVoidArray(disp_, self.x_nodes.shape[0], 1)
self.vtkmesh.GetPointData().AddArray(warpData)
self.vtkmesh.GetPointData().SetActiveVectors(warpData.GetName())
warpVector = vtk.vtkWarpVector()
warpVector.SetInputData(self.vtkmesh)
warpVector.Update()
self.vtkmesh = warpVector.GetOutput()
coarseInterpolator = vtk.vtkPointInterpolator()
coarseInterpolator.SetSourceData(vtkpointset)
coarseInterpolator.SetInputData(self.vtkmesh)
coarseInterpolator.SetKernel(kernel)
coarseInterpolator.SetLocator(locator)
coarseInterpolator.PassPointArraysOff()
coarseInterpolator.SetNullPointsStrategyToMaskPoints() # Get points with an invalid interpolation
coarseInterpolator.Update()
vtkmesh = coarseInterpolator.GetOutput()
if return_deformed:
self.x_nodes[:,0:2] += self.disp
self.disp = numpy_support.vtk_to_numpy(vtkmesh.GetPointData().GetArray("disp"))
self.stretch = numpy_support.vtk_to_numpy(vtkmesh.GetPointData().GetArray("stretch"))
self.shear = numpy_support.vtk_to_numpy(vtkmesh.GetPointData().GetArray("shear"))
if remove_null:
not_null = (numpy_support.vtk_to_numpy(vtkmesh.GetPointData().GetArray(
coarseInterpolator.GetValidPointsMaskArrayName()))).astype(bool)
idlist_old = np.arange(self.x_nodes.shape[0])[not_null]
self.x_nodes = self.x_nodes[not_null]
self.disp = self.disp[not_null]
self.stretch = self.stretch[not_null]
self.shear = self.shear[not_null]
idlist_new = np.arange(self.x_nodes.shape[0])
c1 = np.in1d(self.connec[:, 0], idlist_old)
c2 = np.in1d(self.connec[:, 1], idlist_old)
c3 = np.in1d(self.connec[:, 2], idlist_old)
self.connec = self.connec[np.logical_and(np.logical_and(c1,c2),c3)]
for i in idlist_new:
self.connec[self.connec == idlist_old[i]] = i
points = vtk.vtkPoints()
points.SetData(numpy_support.numpy_to_vtk(self.x_nodes))
vtkmesh.SetPoints(points)
cells = vtk.vtkCellArray()
cells.SetCells(self.connec.shape[0], numpy_support.numpy_to_vtkIdTypeArray(self.connec))
vtkmesh.SetPolys(cells)
self.shear = self.shear.reshape([-1, 2, 2])
#!/usr/bin/env python
import vtk
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# create reader and warp data with vectors
reader = vtk.vtkDataSetReader()
reader.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/blow.vtk")
reader.SetScalarsName("thickness9")
reader.SetVectorsName("displacement9")
castToUnstructuredGrid = vtk.vtkCastToConcrete()
castToUnstructuredGrid.SetInputConnection(reader.GetOutputPort())
castToUnstructuredGrid.Update()
warp = vtk.vtkWarpVector()
warp.SetInputData(castToUnstructuredGrid.GetUnstructuredGridOutput())
# extract mold from mesh using connectivity
connect = vtk.vtkConnectivityFilter()
connect.SetInputConnection(warp.GetOutputPort())
connect.SetExtractionModeToSpecifiedRegions()
connect.AddSpecifiedRegion(0)
connect.AddSpecifiedRegion(1)
moldMapper = vtk.vtkDataSetMapper()
moldMapper.SetInputConnection(reader.GetOutputPort())
moldMapper.ScalarVisibilityOff()
moldActor = vtk.vtkActor()
moldActor.SetMapper(moldMapper)
moldActor.GetProperty().SetColor(.2,.2,.2)
moldActor.GetProperty().SetRepresentationToWireframe()
# extract parison from mesh using connectivity
connect2 = vtk.vtkConnectivityFilter()
connect2.SetInputConnection(warp.GetOutputPort())
def execute(self, obj, event):
if self.timer_count == 10:
self.timer_count = 0
warpVector = vtk.vtkWarpVector()
warpVector.SetInputData(pd)
warpVector.SetScaleFactor(0.1 * (self.timer_count + 1))
warpVector.Update()
poly = warpVector.GetPolyDataOutput()
getScalars = vtk.vtkExtractVectorComponents()
getScalars.SetInputData(poly)
getScalars.Update()
vectorNorm = vtk.vtkVectorNorm()
vectorNorm.SetInputData(poly)
vectorNorm.Update()
scalars = []
scalars.append(
getScalars.GetVzComponent())
scalars.append(
vectorNorm.GetOutput())
scalars.append(
getScalars.GetVxComponent())
scalars.append(
getScalars.GetVyComponent())
names = ("Z", "Mag", "X", "Y")
for k, a in enumerate(self.actors):
calc = vtk.vtkArrayCalculator()
scalars[k].GetPointData().GetScalars().SetName(names[k])
calc.SetInputData(scalars[k])
calc.AddScalarArrayName(names[k])
calc.SetResultArrayName(names[k])
calc.SetFunction(
"%s * 0.1 * %f" % (names[k], self.timer_count + 1))
calc.Update()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(calc.GetOutput())
mapper.SetScalarRange(calc.GetOutput().GetScalarRange())
mapper.SetScalarModeToUsePointData()
mapper.SetColorModeToMapScalars()
mapper.Update()
a.SetMapper(mapper)
cb.scalar_bars[k].SetLookupTable(mapper.GetLookupTable())
iren = obj
iren.GetRenderWindow().Render()
time.sleep(0.3)
if self.key == "Up":
try:
os.mkdir(self.directory)
except:
pass
w2i = vtk.vtkWindowToImageFilter()
w2i.SetInput(obj.GetRenderWindow())
w2i.Update()
png = vtk.vtkPNGWriter()
png.SetInputConnection(w2i.GetOutputPort())
png.SetFileName(self.directory + os.sep +
"frame{:d}.png".format(self.timer_count))
png.Update()
png.Write()
self.timer_count += 1
def animate(self, pd, ind):
"""
Helper function called by **deformableRegistration** if **animate** is *True*.
Spawns a window with an interactive 3-D rendering of the current analyzed object
in its reference state. The displacements calculated from the deformable image
registration can be applied to this object to animate the deformation by pressing
the RIGHT-ARROW. Pressing the UP-ARROW will animate and also save the frames to
disk.
Parameters
----------
pd : vtkPolyData
The current analyzed object's reference geometry.
ind : int
The index of the current polydata in **rsurfs**. Necessary for naming directory created
if animation frames are saved.
"""
pd.GetPointData().SetActiveVectors("Displacement")
class vtkTimerCallback(object):
def __init__(self):
self.timer_count = 0
def execute(self, obj, event):
if self.timer_count == 10:
self.timer_count = 0
warpVector = vtk.vtkWarpVector()
warpVector.SetInputData(pd)
warpVector.SetScaleFactor(0.1 * (self.timer_count + 1))
warpVector.Update()
poly = warpVector.GetPolyDataOutput()
getScalars = vtk.vtkExtractVectorComponents()
getScalars.SetInputData(poly)
getScalars.Update()
vectorNorm = vtk.vtkVectorNorm()
vectorNorm.SetInputData(poly)
vectorNorm.Update()
scalars = []
scalars.append(
getScalars.GetVzComponent())
scalars.append(
vectorNorm.GetOutput())
scalars.append(
getScalars.GetVxComponent())
scalars.append(
getScalars.GetVyComponent())
names = ("Z", "Mag", "X", "Y")
for k, a in enumerate(self.actors):
calc = vtk.vtkArrayCalculator()
scalars[k].GetPointData().GetScalars().SetName(names[k])
calc.SetInputData(scalars[k])
calc.AddScalarArrayName(names[k])
calc.SetResultArrayName(names[k])
calc.SetFunction(
"%s * 0.1 * %f" % (names[k], self.timer_count + 1))
calc.Update()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(calc.GetOutput())
mapper.SetScalarRange(calc.GetOutput().GetScalarRange())
mapper.SetScalarModeToUsePointData()
mapper.SetColorModeToMapScalars()
mapper.Update()
a.SetMapper(mapper)
cb.scalar_bars[k].SetLookupTable(mapper.GetLookupTable())
iren = obj
iren.GetRenderWindow().Render()
time.sleep(0.3)
if self.key == "Up":
try:
os.mkdir(self.directory)
except:
pass
w2i = vtk.vtkWindowToImageFilter()
w2i.SetInput(obj.GetRenderWindow())
w2i.Update()
png = vtk.vtkPNGWriter()
png.SetInputConnection(w2i.GetOutputPort())
png.SetFileName(self.directory + os.sep +
"frame{:d}.png".format(self.timer_count))
png.Update()
png.Write()
self.timer_count += 1
def Keypress(self, obj, event):
self.key = obj.GetKeySym()
if self.key == "Right" or self.key == "Up":
for i in range(10):
obj.CreateOneShotTimer(1)
renwin = vtk.vtkRenderWindow()
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renwin)
iren.Initialize()
cb = vtkTimerCallback()
xmins = (0, 0.5, 0, 0.5)
xmaxs = (0.5, 1, 0.5, 1)
ymins = (0, 0, 0.5, 0.5)
ymaxs = (0.5, 0.5, 1, 1)
titles = ('Z Displacement', 'Magnitude',
'X Displacement', 'Y Displacement')
cb.actors = []
cb.scalar_bars = []
cb.directory = str(os.path.normpath(
self._def_dir + os.sep + "animation{:0d}".format(ind + 1)))
warpVector = vtk.vtkWarpVector()
warpVector.SetInputData(pd)
warpVector.Update()
poly = warpVector.GetPolyDataOutput()
getScalars = vtk.vtkExtractVectorComponents()
getScalars.SetInputData(poly)
getScalars.Update()
vectorNorm = vtk.vtkVectorNorm()
vectorNorm.SetInputData(poly)
vectorNorm.Update()
scalars = []
scalars.append(
getScalars.GetVzComponent())
scalars.append(
vectorNorm.GetOutput())
scalars.append(
getScalars.GetVxComponent())
scalars.append(
getScalars.GetVyComponent())
bounds = np.zeros(6, np.float32)
pd.GetBounds(bounds)
length = np.min(bounds[1::2] - bounds[0:-1:2]) * 0.2
bounds[1] = bounds[0] + length
bounds[3] = bounds[2] + length
bounds[5] = bounds[4] + length
for j in range(4):
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(scalars[j])
mapper.SetScalarRange(scalars[j].GetScalarRange())
mapper.SetScalarModeToUsePointData()
mapper.SetColorModeToMapScalars()
scalar_bar = vtk.vtkScalarBarActor()
scalar_bar.SetLookupTable(mapper.GetLookupTable())
scalar_bar.SetTitle(titles[j])
scalar_bar.SetLabelFormat("%3.3f")
cb.scalar_bars.append(scalar_bar)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
cb.actors.append(actor)
renderer = vtk.vtkRenderer()
renderer.SetBackground(0., 0., 0.)
renwin.AddRenderer(renderer)
if j == 0:
camera = renderer.GetActiveCamera()
else:
renderer.SetActiveCamera(camera)
triad = vtk.vtkCubeAxesActor()
triad.SetCamera(camera)
triad.SetFlyModeToStaticTriad()
triad.SetBounds(bounds)
triad.GetXAxesLinesProperty().SetColor(1.0, 0.0, 0.0)
triad.GetYAxesLinesProperty().SetColor(0.0, 1.0, 0.0)
triad.GetZAxesLinesProperty().SetColor(0.0, 0.0, 1.0)
triad.GetXAxesLinesProperty().SetLineWidth(3.0)
triad.GetYAxesLinesProperty().SetLineWidth(3.0)
triad.GetZAxesLinesProperty().SetLineWidth(3.0)
triad.XAxisLabelVisibilityOff()
triad.YAxisLabelVisibilityOff()
triad.ZAxisLabelVisibilityOff()
triad.XAxisTickVisibilityOff()
triad.YAxisTickVisibilityOff()
triad.ZAxisTickVisibilityOff()
triad.XAxisMinorTickVisibilityOff()
triad.YAxisMinorTickVisibilityOff()
triad.ZAxisMinorTickVisibilityOff()
renderer.SetViewport(xmins[j], ymins[j],
xmaxs[j], ymaxs[j])
renderer.AddActor(actor)
renderer.AddActor2D(scalar_bar)
renderer.AddActor(triad)
renderer.ResetCamera()
renwin.Render()
iren.AddObserver('TimerEvent', cb.execute)
iren.AddObserver('KeyPressEvent', cb.Keypress)
iren.Start()
def plot(self, struct):
# creates self. data1, legend, filename, fieldname, dim, has_field, tracker, revision
if not self.call_config(struct):
return
self.update_field_type('vector', True)
self.update_legend_data()
# creates self.src
if not self.call_src():
return
self.ini_data(self.src)
# si es cell data, lo transforma a point data, porque vtkWarpScalar parece ser que no soporta cell data.
if self.data1.get('fielddomain') == 'cell':
self.cdtpd = vtk.vtkCellDataToPointData()
self.cdtpd.SetInputConnection(self.src.GetOutputPort())
self.warpT = vtk.vtkWarpVector()
self.warpT.SetInputConnection(self.cdtpd.GetOutputPort())
else:
self.warpT = vtk.vtkWarpVector()
self.warpT.SetInputConnection(self.src.GetOutputPort())
self.warpT.GetOutput().GetPointData().SetVectors(self.vectors)
# print self.warpT
#Creacion de una tabla de color
lut = vtk.vtkLookupTable()
lut.SetRampToLinear()
lut.SetScaleToLinear()
# When using vector magnitude for coloring
lut.SetVectorModeToMagnitude()
if self.vectors is not None:
lutrange = self.vectors.GetRange(-1)
lut.SetTableRange(lutrange)
lut.Build()
self.wireM2 = vtk.vtkDataSetMapper()
self.wireM2.SetInputConnection(self.warpT.GetOutputPort())
#Definicion del campo y el rango para colorear
if self.vectors is not None:
self.wireM2.SelectColorArray(self.vectors.GetName())
self.wireM2.SetScalarRange(lutrange)
if self.data1.get('fielddomain') == 'cell':
self.wireM2.SetScalarModeToUseCellFieldData()
else:
self.wireM2.SetScalarModeToUsePointFieldData()
self.wireM2.ScalarVisibilityOn()
self.wireM2.SetLookupTable(lut)
self.wireM2.Update()
# print self.wireM2
self.wireA2 = vtk.vtkActor()
self.wireA2.SetMapper(self.wireM2)
self.wireA2.GetProperty().SetRepresentationToSurface()
self.wireA2.GetProperty().SetColor(Plot.edges_color)
self.add_sw_2(self.wireA2)
self.add_opacity_2([self.wireA2]) # Opacity: 100%/75%/50%/25%/0%
#Para pintar el wireframe original(sin desplazamiento)
# self.wireM = vtk.vtkDataSetMapper()
# self.wireM.SetInputConnection(self.src.GetOutputPort())
# self.wireM.ScalarVisibilityOff()
# self.wireA3 = vtk.vtkActor()
# self.wireA3.SetMapper(self.wireM)
# self.wireA3.GetProperty().SetRepresentationToWireframe()
# self.wireA3.GetProperty().SetColor(Plot.mesh_color)
# self.wireA3.GetProperty().SetEdgeColor(Plot.unselected_color)
# self.rens[0].AddActor(self.wireA3)
self.rens[0].AddActor(self.wireA2)
self.copy_params(struct)
self.warpT.Update()
# self.add_outline_2(self.src)
self.add_outline_2(self.warpT)
# reverse rainbow [red->blue] -> [blue->red]
if self.vectors is not None:
self.scalarrange.local_set(lutrange)
self.add_scalarbar_2(lut)
self.done = True
# Make sure all algorithms use the composite data pipeline
cdp = vtk.vtkCompositeDataPipeline()
reader.SetDefaultExecutivePrototype(cdp)
reader.SetCaseFileName("" + str(VTK_DATA_ROOT) +
"/Data/EnSight/RectGrid_ascii.case")
reader.Update()
toRectilinearGrid = vtk.vtkCastToConcrete()
# toRectilinearGrid SetInputConnection [reader GetOutputPort]
toRectilinearGrid.SetInputData(reader.GetOutput().GetBlock(0))
toRectilinearGrid.Update()
plane = vtk.vtkRectilinearGridGeometryFilter()
plane.SetInputData(toRectilinearGrid.GetRectilinearGridOutput())
plane.SetExtent(0, 100, 0, 100, 15, 15)
tri = vtk.vtkTriangleFilter()
tri.SetInputConnection(plane.GetOutputPort())
warper = vtk.vtkWarpVector()
warper.SetInputConnection(tri.GetOutputPort())
warper.SetScaleFactor(0.05)
planeMapper = vtk.vtkDataSetMapper()
planeMapper.SetInputConnection(warper.GetOutputPort())
planeMapper.SetScalarRange(0.197813, 0.710419)
planeActor = vtk.vtkActor()
planeActor.SetMapper(planeMapper)
cutPlane = vtk.vtkPlane()
# eval cutPlane SetOrigin [[reader GetOutput] GetCenter]
cutPlane.SetOrigin(reader.GetOutput().GetBlock(0).GetCenter())
cutPlane.SetNormal(1, 0, 0)
planeCut = vtk.vtkCutter()
planeCut.SetInputData(toRectilinearGrid.GetRectilinearGridOutput())
planeCut.SetCutFunction(cutPlane)
cutMapper = vtk.vtkDataSetMapper()
output = plane.GetOutput()
# Manually construct scalars
NPts = output.GetNumberOfPoints()
vectors = vtk.vtkDoubleArray()
vectors.SetNumberOfComponents(3)
vectors.SetNumberOfTuples(NPts)
for i in range(0, NPts):
vectors.SetTuple3(i, math.Random(0, 10), math.Random(0, 10),
math.Random(0, 10))
output.GetPointData().SetVectors(vectors)
# Output some statistics
print("Number of points: {0}".format(NPts))
# Time the warping
warpF = vtk.vtkWarpVector()
warpF.SetInputData(output)
warpF.SetScaleFactor(2.5)
# For timing the various tests
timer = vtk.vtkTimerLog()
timer.StartTimer()
warpF.Update()
timer.StopTimer()
time = timer.GetElapsedTime()
print("Warp via vector: {0}".format(time))
def main():
fileName1, fileName2 = get_program_parameters()
colors = vtk.vtkNamedColors()
# Set the background color.
colors.SetColor('BkgColor', [65, 99, 149, 255])
# Read a vtk file
#
pl3d = vtk.vtkMultiBlockPLOT3DReader()
pl3d.SetXYZFileName(fileName1)
pl3d.SetQFileName(fileName2)
pl3d.SetScalarFunctionNumber(100) # Density
pl3d.SetVectorFunctionNumber(202) # Momentum
pl3d.Update()
pl3dOutput = pl3d.GetOutput().GetBlock(0)
# What do we know about the data?
# Get the extent of the data: imin,imax, jmin,jmax, kmin,kmax
extent = pl3dOutput.GetExtent()
scalarRange = pl3dOutput.GetScalarRange()
# Planes are specified using a imin,imax, jmin,jmax, kmin,kmax coordinate
# specification. Min and max i,j,k values are clamped to 0 and maximum value.
# See the variable named extent for the values.
#
plane = vtk.vtkStructuredGridGeometryFilter()
plane.SetInputData(pl3dOutput)
plane.SetExtent(10, 10, 1, extent[3], 1, extent[5])
plane2 = vtk.vtkStructuredGridGeometryFilter()
plane2.SetInputData(pl3dOutput)
plane2.SetExtent(30, 30, 1, extent[3], 1, extent[5])
plane3 = vtk.vtkStructuredGridGeometryFilter()
plane3.SetInputData(pl3dOutput)
plane3.SetExtent(45, 45, 1, extent[3], 1, extent[5])
# We use an append filter because that way we can do the warping, etc. just
# using a single pipeline and actor.
#
appendF = vtk.vtkAppendPolyData()
appendF.AddInputConnection(plane.GetOutputPort())
appendF.AddInputConnection(plane2.GetOutputPort())
appendF.AddInputConnection(plane3.GetOutputPort())
# Warp
warp = vtk.vtkWarpVector()
warp.SetInputConnection(appendF.GetOutputPort())
warp.SetScaleFactor(0.005)
warp.Update()
normals = vtk.vtkPolyDataNormals()
normals.SetInputData(warp.GetPolyDataOutput())
normals.SetFeatureAngle(45)
planeMapper = vtk.vtkPolyDataMapper()
planeMapper.SetInputConnection(normals.GetOutputPort())
planeMapper.SetScalarRange(scalarRange)
planeActor = vtk.vtkActor()
planeActor.SetMapper(planeMapper)
# The outline provides context for the data and the planes.
outline = vtk.vtkStructuredGridOutlineFilter()
outline.SetInputData(pl3dOutput)
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
outlineActor.GetProperty().SetColor(colors.GetColor3d('Black'))
# Create the RenderWindow, Renderer and both Actors
#
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Add the actors to the renderer, set the background and size
#
ren.AddActor(planeActor)
ren.AddActor(outlineActor)
ren.SetBackground(colors.GetColor3d('BkgColor'))
renWin.SetSize(512, 512)
renWin.SetWindowName('VelocityProfile')
iren.Initialize()
renWin.Render()
ren.GetActiveCamera().SetPosition(19.8562, -31.8912, 47.0755)
ren.GetActiveCamera().SetFocalPoint(8.255, 0.147815, 29.7631)
ren.GetActiveCamera().SetViewUp(-0.0333325, 0.465756, 0.884285)
ren.GetActiveCamera().SetClippingRange(17.3078, 64.6375)
renWin.Render()
iren.Start()
moment_reader.Update() # --------------------------------------------------- # GET THE INITIAL SCALES FOR WARP VECTORS # --------------------------------------------------- axial_scale = get_scale(axial_reader) shear_scale = get_scale(shear_reader) moment_scale = get_scale(moment_reader) # --------------------------------------------------- # WARP VECTORS # --------------------------------------------------- # DEFORMED warp_deformed = vtk.vtkWarpVector() warp_deformed.SetInput(deformed_reader.GetOutput()) warp_deformed.SetScaleFactor(50) warp_deformed.Update() warp_deformed_mapper = vtk.vtkDataSetMapper() warp_deformed_mapper.SetInput(warp_deformed.GetOutput()) warp_deformed_actor = vtk.vtkActor() warp_deformed_actor.SetMapper(warp_deformed_mapper) warp_deformed_actor.SetVisibility(0) # AXIAL warp_axial = vtk.vtkWarpVector() warp_axial.SetInput(axial_reader.GetOutput()) warp_axial.SetScaleFactor(axial_scale) warp_axial.Update() warp_axial_mapper = vtk.vtkDataSetMapper() warp_axial_mapper.SetInput(warp_axial.GetOutput())
def main(argv):
if os.name == 'nt':
VTK_DATA_ROOT = "c:/VTK82/build_Release/ExternalData/Testing/"
else:
VTK_DATA_ROOT = "/home/jmh/"
if 1:
v16 = vtk.vtkMetaImageReader()
v16.SetFileName("/home/jmh/github/fis/data/Abdomen/CT-Abdomen.mhd")
v16.Update()
elif 0:
fname = os.path.join(VTK_DATA_ROOT, "Data/headsq/quarter")
v16 = vtk.vtkVolume16Reader()
v16.SetDataDimensions(64, 64)
v16.SetDataByteOrderToLittleEndian()
v16.SetImageRange(1, 93)
v16.SetDataSpacing(3.2, 3.2, 1.5)
v16.SetFilePrefix(fname)
v16.ReleaseDataFlagOn()
v16.SetDataMask(0x7fff)
v16.Update()
else:
v16 = vtk.vtkMetaImageReader()
v16.SetFileName("c:/github/fis/data/Abdomen/CT-Abdomen.mhd")
v16.Update()
rng = v16.GetOutput().GetScalarRange()
shifter = vtk.vtkImageShiftScale()
shifter.SetShift(-1.0*rng[0])
shifter.SetScale(255.0/(rng[1]-rng[0]))
shifter.SetOutputScalarTypeToUnsignedChar()
shifter.SetInputConnection(v16.GetOutputPort())
shifter.ReleaseDataFlagOff()
shifter.Update()
ImageViewer = vtk.vtkImageViewer2()
ImageViewer.SetInputData(shifter.GetOutput())
ImageViewer.SetColorLevel(127)
ImageViewer.SetColorWindow(255)
iren = vtk.vtkRenderWindowInteractor()
ImageViewer.SetupInteractor(iren)
ImageViewer.Render()
ImageViewer.GetRenderer().ResetCamera()
ImageViewer.Render()
dims = v16.GetOutput().GetDimensions()
global minArea
spacing = v16.GetOutput().GetSpacing()
minArea = ( spacing[0] * spacing[1] ) / 0.1
# Slider screen representation
SliderRepres = vtk.vtkSliderRepresentation2D()
_min = ImageViewer.GetSliceMin()
_max = ImageViewer.GetSliceMax()
SliderRepres.SetMinimumValue(_min)
SliderRepres.SetMaximumValue(_max)
SliderRepres.SetValue(int((_min + _max) / 2))
SliderRepres.SetTitleText("Slice")
SliderRepres.GetPoint1Coordinate().SetCoordinateSystemToNormalizedDisplay()
SliderRepres.GetPoint1Coordinate().SetValue(0.3, 0.05)
SliderRepres.GetPoint2Coordinate().SetCoordinateSystemToNormalizedDisplay()
SliderRepres.GetPoint2Coordinate().SetValue(0.7, 0.05)
SliderRepres.SetSliderLength(0.02)
SliderRepres.SetSliderWidth(0.03)
SliderRepres.SetEndCapLength(0.01)
SliderRepres.SetEndCapWidth(0.03)
SliderRepres.SetTubeWidth(0.005)
SliderRepres.SetLabelFormat("%3.0lf")
SliderRepres.SetTitleHeight(0.02)
SliderRepres.SetLabelHeight(0.02)
# Slider widget
SliderWidget = vtk.vtkSliderWidget()
SliderWidget.SetInteractor(iren)
SliderWidget.SetRepresentation(SliderRepres)
SliderWidget.KeyPressActivationOff()
SliderWidget.SetAnimationModeToAnimate()
SliderWidget.SetEnabled(True)
SliderCb = vtkSliderCallback()
SliderCb.SetImageViewer(ImageViewer)
SliderWidget.AddObserver(vtk.vtkCommand.InteractionEvent, SliderCb.Execute)
ImageViewer.SetSlice(int(SliderRepres.GetValue()))
# Contour representation - responsible for placement of points, calculation of lines and contour manipulation
global rep
rep = vtk.vtkOrientedGlyphContourRepresentation()
# vtkContourRepresentation has GetActiveNodeWorldPostion/Orientation
rep.GetProperty().SetOpacity(0) #1
prop = rep.GetLinesProperty()
from vtkUtils import renderLinesAsTubes
from vtk.util.colors import red, green, pink, yellow
renderLinesAsTubes(prop)
prop.SetColor(yellow)
propActive = rep.GetActiveProperty()
#propActive.SetOpacity(0) # 2
renderLinesAsTubes(propActive)
propActive.SetColor(green)
shapeActive = rep.GetActiveCursorShape()
warp = vtk.vtkWarpVector()
warp.SetInputData(shapeActive)
warp.SetInputArrayToProcess(0, 0, 0,
vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS,
vtk.vtkDataSetAttributes.NORMALS)
scale = 0.4
warp.SetScaleFactor(scale)
warp.Update()
rep.SetActiveCursorShape(warp.GetOutput())
# Use vtkContourTriangulator to fill contours
# Point placer
imageActorPointPlacer = vtk.vtkImageActorPointPlacer()
imageActorPointPlacer.SetImageActor(ImageViewer.GetImageActor())
rep.SetPointPlacer(imageActorPointPlacer)
global ContourWidget
# Contour widget - has a vtkWidgetEventTranslator which translate events to vtkContourWidget events
ContourWidget = vtk.vtkContourWidget()
ContourWidget.SetRepresentation(rep)
ContourWidget.SetInteractor(iren)
ContourWidget.SetEnabled(True)
ContourWidget.ProcessEventsOn()
ContourWidget.ContinuousDrawOn()
# Can be Initialize() using polydata
# Override methods that returns display position to get an overlay
# (display postions) instead of computing it from world position and
# the method BuildLines to interpolate using display positions
# instead of world positions
# Thinning of contour control points
# AddFinalPointAction
ContourWidget.AddObserver(vtk.vtkCommand.EndInteractionEvent, callback)
if 0:
# TODO: Make interior transparent
contour = ContourWidget.GetContourRepresentation().GetContourRepresentationAsPolyData()
tc = vtk.vtkContourTriangulator()
tc.SetInputData(contour)
tc.Update()
# Extrusion towards camera
extruder = vtk.vtkLinearExtrusionFilter()
extruder.CappingOn()
extruder.SetScalaFactor(1.0)
extruder.SetInputData(tc.GetOutput())
extruder.SetVector(0,0,1.0)
extruder.SetExtrusionTypeToNormalExtrusion()
polyMapper = vtk.vtkPolyMapper()
polyMapper.SetInputConnection(extruder.GetOutputPort())
polyMapper.ScalarVisibilityOn()
polyMapper.Update()
polyActor = vtk.vtkActor()
polyActor.SetMapper(polyMapper)
prop = polyActor.GetProperty()
prop.SetColor(0,1,0)
#prop.SetRepresentationToWireframe()
renderer.AddActor(polyActor)
renderer.GetRenderWindow().Render()
iren.Start()
def main():
points = vtk.vtkPoints()
points.InsertNextPoint(0.0, 0.0, 0.0)
points.InsertNextPoint(1.0, 0.0, 0.0)
points.InsertNextPoint(2.0, 0.0, 0.0)
points.InsertNextPoint(3.0, 0.0, 0.0)
points.InsertNextPoint(4.0, 0.0, 0.0)
lines = vtk.vtkCellArray()
line = vtk.vtkLine()
line.GetPointIds().SetId(0, 0)
line.GetPointIds().SetId(1, 1)
lines.InsertNextCell(line)
line.GetPointIds().SetId(0, 1)
line.GetPointIds().SetId(1, 2)
lines.InsertNextCell(line)
line.GetPointIds().SetId(0, 2)
line.GetPointIds().SetId(1, 3)
lines.InsertNextCell(line)
line.GetPointIds().SetId(0, 3)
line.GetPointIds().SetId(1, 4)
lines.InsertNextCell(line)
warpData = vtk.vtkDoubleArray()
warpData.SetNumberOfComponents(3)
warpData.SetName("warpData")
warp = [0.0, 0.0, 0.0]
warp[1] = 0.0
warpData.InsertNextTuple(warp)
warp[1] = 0.1
warpData.InsertNextTuple(warp)
warp[1] = 0.3
warpData.InsertNextTuple(warp)
warp[1] = 0.0
warpData.InsertNextTuple(warp)
warp[1] = 0.1
warpData.InsertNextTuple(warp)
polydata = vtk.vtkPolyData()
polydata.SetPoints(points)
polydata.SetLines(lines)
polydata.GetPointData().AddArray(warpData)
polydata.GetPointData().SetActiveVectors(warpData.GetName())
# WarpVector will use the array marked as active vector in polydata
# it has to be a 3 component array
# with the same number of tuples as points in polydata
warpVector = vtk.vtkWarpVector()
if VTK_MAJOR_VERSION <= 5:
warpVector.SetInput(polydata)
else:
warpVector.SetInputData(polydata)
warpVector.Update()
mapper = vtk.vtkPolyDataMapper()
if VTK_MAJOR_VERSION <= 5:
mapper.SetInput(warpVector.GetPolyDataOutput())
else:
mapper.SetInputData(warpVector.GetPolyDataOutput())
actor = vtk.vtkActor()
actor.SetMapper(mapper)
renderer = vtk.vtkRenderer()
renderer.AddActor(actor)
renderer.SetBackground(.3, .6, .3)
renderWindow = vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
renderWindowInteractor.SetRenderWindow(renderWindow)
renderWindow.Render()
renderWindowInteractor.Start()
return
def main():
colors = vtk.vtkNamedColors()
points = vtk.vtkPoints()
points.InsertNextPoint(0.0, 0.0, 0.0)
points.InsertNextPoint(1.0, 0.0, 0.0)
points.InsertNextPoint(2.0, 0.0, 0.0)
points.InsertNextPoint(3.0, 0.0, 0.0)
points.InsertNextPoint(4.0, 0.0, 0.0)
lines = vtk.vtkCellArray()
line = vtk.vtkLine()
line.GetPointIds().SetId(0, 0)
line.GetPointIds().SetId(1, 1)
lines.InsertNextCell(line)
line.GetPointIds().SetId(0, 1)
line.GetPointIds().SetId(1, 2)
lines.InsertNextCell(line)
line.GetPointIds().SetId(0, 2)
line.GetPointIds().SetId(1, 3)
lines.InsertNextCell(line)
line.GetPointIds().SetId(0, 3)
line.GetPointIds().SetId(1, 4)
lines.InsertNextCell(line)
warpData = vtk.vtkDoubleArray()
warpData.SetNumberOfComponents(3)
warpData.SetName("warpData")
warp = [0.0, 0.0, 0.0]
warp[1] = 0.0
warpData.InsertNextTuple(warp)
warp[1] = 0.1
warpData.InsertNextTuple(warp)
warp[1] = 0.3
warpData.InsertNextTuple(warp)
warp[1] = 0.0
warpData.InsertNextTuple(warp)
warp[1] = 0.1
warpData.InsertNextTuple(warp)
polydata = vtk.vtkPolyData()
polydata.SetPoints(points)
polydata.SetLines(lines)
polydata.GetPointData().AddArray(warpData)
polydata.GetPointData().SetActiveVectors(warpData.GetName())
# WarpVector will use the array marked as active vector in polydata
# it has to be a 3 component array
# with the same number of tuples as points in polydata
warpVector = vtk.vtkWarpVector()
warpVector.SetInputData(polydata)
warpVector.Update()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(warpVector.GetPolyDataOutput())
actor = vtk.vtkActor()
actor.SetMapper(mapper)
renderer = vtk.vtkRenderer()
renderer.AddActor(actor)
renderer.SetBackground(colors.GetColor3d('cobalt_green'))
renderWindow = vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
renderWindow.SetWindowName('WarpVector')
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
renderWindowInteractor.SetRenderWindow(renderWindow)
renderWindow.Render()
renderWindowInteractor.Start()
def main(argv):
scale = 1.0
if len(argv) > 1:
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(argv[1])
reader.Update()
inputPolyData = reader.GetOutput()
if len(argv) > 2:
scale = float(argv[2])
else:
sphereSource = vtk.vtkSphereSource()
sphereSource.SetPhiResolution(15)
sphereSource.SetThetaResolution(15)
sphereSource.Update()
inputPolyData = sphereSource.GetOutput()
clean = vtk.vtkCleanPolyData()
clean.SetInputData(inputPolyData)
# Generate normals
normals = vtk.vtkPolyDataNormals()
normals.SetInputConnection(clean.GetOutputPort())
normals.SplittingOff()
# Warp using the normals
warp = vtk.vtkWarpVector()
warp.SetInputConnection(normals.GetOutputPort())
warp.SetInputArrayToProcess(0, 0, 0,
vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS,
vtk.vtkDataSetAttributes.NORMALS)
warp.SetScaleFactor(scale)
warp.Modified()
# Visualize the original and warped models
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(warp.GetOutputPort())
mapper.ScalarVisibilityOff()
warpedActor = vtk.vtkActor()
warpedActor.SetMapper(mapper)
originalMapper = vtk.vtkPolyDataMapper()
originalMapper.SetInputConnection(normals.GetOutputPort())
originalMapper.ScalarVisibilityOff()
originalActor = vtk.vtkActor()
originalActor.SetMapper(originalMapper)
originalActor.GetProperty().SetInterpolationToFlat()
renderWindow = vtk.vtkRenderWindow()
renderWindow.SetSize(640, 480)
# Create a camera for all renderers
camera = vtk.vtkCamera()
# Define viewport ranges
# (xmin, ymin, xmax, ymax)
leftViewport = (0.0, 0.0, 0.5, 1.0)
rightViewport = (0.5, 0.0, 1.0, 1.0)
# Setup both renderers
leftRenderer = vtk.vtkRenderer()
leftRenderer.SetViewport(leftViewport)
leftRenderer.SetBackground(.6, .5, .4)
leftRenderer.SetActiveCamera(camera)
rightRenderer = vtk.vtkRenderer()
rightRenderer.SetViewport(rightViewport)
rightRenderer.SetBackground(.4, .5, .6)
rightRenderer.SetActiveCamera(camera)
leftRenderer.AddActor(originalActor)
rightRenderer.AddActor(warpedActor)
rightRenderer.ResetCamera()
renderWindow.AddRenderer(rightRenderer)
renderWindow.AddRenderer(leftRenderer)
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(renderWindow)
renderWindow.Render()
interactor.Start()
def execute(self, obj, event):
if self.timer_count == 10:
self.timer_count = 0
warpVector = vtk.vtkWarpVector()
warpVector.SetInputData(pd)
warpVector.SetScaleFactor(0.1 * (self.timer_count + 1))
warpVector.Update()
poly = warpVector.GetPolyDataOutput()
getScalars = vtk.vtkExtractVectorComponents()
getScalars.SetInputData(poly)
getScalars.Update()
vectorNorm = vtk.vtkVectorNorm()
vectorNorm.SetInputData(poly)
vectorNorm.Update()
scalars = []
scalars.append(getScalars.GetVzComponent())
scalars.append(vectorNorm.GetOutput())
scalars.append(getScalars.GetVxComponent())
scalars.append(getScalars.GetVyComponent())
names = ("Z", "Mag", "X", "Y")
for k, a in enumerate(self.actors):
calc = vtk.vtkArrayCalculator()
scalars[k].GetPointData().GetScalars().SetName(names[k])
calc.SetInputData(scalars[k])
calc.AddScalarArrayName(names[k])
calc.SetResultArrayName(names[k])
calc.SetFunction("%s * 0.1 * %f" %
(names[k], self.timer_count + 1))
calc.Update()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(calc.GetOutput())
mapper.SetScalarRange(calc.GetOutput().GetScalarRange())
mapper.SetScalarModeToUsePointData()
mapper.SetColorModeToMapScalars()
mapper.Update()
a.SetMapper(mapper)
cb.scalar_bars[k].SetLookupTable(mapper.GetLookupTable())
iren = obj
iren.GetRenderWindow().Render()
time.sleep(0.3)
if self.key == "Up":
try:
os.mkdir(self.directory)
except:
pass
w2i = vtk.vtkWindowToImageFilter()
w2i.SetInput(obj.GetRenderWindow())
w2i.Update()
png = vtk.vtkPNGWriter()
png.SetInputConnection(w2i.GetOutputPort())
png.SetFileName(self.directory + os.sep +
"frame{:d}.png".format(self.timer_count))
png.Update()
png.Write()
self.timer_count += 1
def warp_surface(args):
print("warp the surface ")
reader = vmtkscripts.vmtkSurfaceReader()
reader.InputFileName = args.surface
reader.Execute()
Surface = reader.Surface
narrays = Surface.GetPointData().GetNumberOfArrays()
has_normals = False
for i in range(narrays):
if ( Surface.GetPointData().GetArrayName(i) == "Normals"):
has_normals = True
break
if(has_normals):
normals = Surface
print("already have")
else:
get_normals = vtk.vtkPolyDataNormals()
get_normals.SetInputData(Surface)
get_normals.SetFeatureAngle(30.0) # default
get_normals.SetSplitting(True)
get_normals.Update()
get_normals.GetOutput().GetPointData().SetActiveVectors("Normals")
normals = get_normals.GetOutput()
print("normals generated")
random = vtk.vtkRandomAttributeGenerator()
random.SetInputData(normals)
random.SetDataTypeToDouble()
random.GeneratePointScalarsOn ()
random.SetComponentRange(-0.5, 0.5)
random.Update()
#n = random.GetOutput().GetPointData().GetNumberOfArrays()
#for i in range(n):
#print(random.GetOutput().GetPointData().GetArrayName(i))
calc = vtk.vtkArrayCalculator()
calc.SetInputConnection(random.GetOutputPort())
calc.AddScalarArrayName("RandomPointScalars", 0)
calc.AddVectorArrayName("Normals", 0, 1, 2)
calc.SetFunction("Normals * RandomPointScalars")
calc.SetResultArrayName("RandomLengthNormalVectors")
calc.Update()
warp = vtk.vtkWarpVector()
warp.SetInputConnection(calc.GetOutputPort())
warp.SetInputArrayToProcess(0, 0, 0,
vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS,
"RandomLengthNormalVectors");
warp.SetScaleFactor(args.fuzz_scale)
warp.Update()
writer = vmtkscripts.vmtkSurfaceWriter()
writer.OutputFileName = args.file_out
writer.Input = warp.GetOutput()
writer.Execute()
gInfo.marker = -1
path = Path(args.molecule)
obj_name = f'{path.stem}.obj'
pygamer.writeOBJ(obj_name, mesh)
# Pyvista
mesh = pv.read(obj_name)
shell = mesh.decimate(0.97, volume_preservation=True).extract_surface()
print(f'Decimation: {len(mesh.points)} -> {len(shell.points)}')
# warp each point by the normal vectors
for i in range(1, int(args.distance) + 1):
print(f'Expanding: {i}')
shell = shell.compute_normals()
warp = vtk.vtkWarpVector()
warp.SetInputData(shell)
warp.SetInputArrayToProcess(0, 0, 0,
vtk.vtkDataObject.FIELD_ASSOCIATION_POINTS,
vtk.vtkDataSetAttributes.NORMALS)
warp.SetScaleFactor(2)
warp.Update()
shell = pv.wrap(warp.GetOutput())
expanded_mesh = shell.extract_surface()
clus = pyacvd.Clustering(expanded_mesh)
clus.subdivide(3)
clus.cluster(args.points)
shell = clus.create_mesh().extract_surface()
uniform = shell
def main():
file_name = get_program_parameters()
colors = vtk.vtkNamedColors()
# Set the colors.
colors.SetColor("PlateColor", [255, 160, 140, 255])
colors.SetColor("BkgColor", [65, 99, 149, 255])
# Read a vtk file
#
plate = vtk.vtkPolyDataReader()
plate.SetFileName(file_name)
plate.Update()
bounds = [0] * 6
plate.GetOutput().GetBounds(bounds)
plate.SetVectorsName("mode2")
normals = vtk.vtkPolyDataNormals()
normals.SetInputConnection(plate.GetOutputPort())
warp = vtk.vtkWarpVector()
warp.SetInputConnection(normals.GetOutputPort())
warp.SetScaleFactor(0.5)
color = vtk.vtkVectorDot()
color.SetInputConnection(warp.GetOutputPort())
plateMapper = vtk.vtkDataSetMapper()
plateMapper.SetInputConnection(warp.GetOutputPort())
plateActor = vtk.vtkActor()
plateActor.SetMapper(plateMapper)
plateActor.GetProperty().SetColor(colors.GetColor3d("PlateColor"))
plateActor.RotateX(-90)
# Create the outline.
#
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(plate.GetOutputPort())
spikeMapper = vtk.vtkPolyDataMapper()
spikeMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(spikeMapper)
outlineActor.RotateX(-90)
outlineActor.GetProperty().SetColor(colors.GetColor3d("White"))
# Create the RenderWindow, Renderer and both Actors
#
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# Add the actors to the renderer, set the background and size
#
ren.AddActor(plateActor)
ren.AddActor(outlineActor)
renWin.SetSize(500, 500)
# Render the image.
renWin.Render()
ren.SetBackground(colors.GetColor3d("BkgColor"))
# This closely matches the original illustration.
ren.GetActiveCamera().SetPosition(-3.7, 13, 15.5)
ren.ResetCameraClippingRange()
renWin.Render()
iren.Start()
