def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkGenericDataObjectWriter(), 'Writing vtkGenericDataObject.',
('vtkGenericDataObject',), (),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def LabelToSurface(label_path, surface_path, lcc=False, smoothIterations=15,relaxationFactor=0.1):
tqdm.write("Converting segmentation label to surface file: {}".format(label_path))
# binary path
if platform == "linux" or platform == "linux2":
bin_path = "/home/jacky/Projects/CFD_intraranial/cxx/label_to_mesh/build_linux/LabelToMesh"
elif platform == "darwin":
return
elif platform == "win32":
bin_path = "D:/projects/CFD_intracranial/cxx/label_to_mesh/build/Release/LabelToMesh.exe"
# convert to binary file
command = bin_path + " " + label_path + " " + surface_path + " 1 1"
# print(command)
os.system(command)
reader = vtk.vtkGenericDataObjectReader()
reader.SetFileName(surface_path)
reader.Update()
surface = reader.GetOutput()
transform = vtk.vtkTransform()
transform.Scale(-1,-1,1)
transformFilter = vtk.vtkTransformPolyDataFilter()
transformFilter.SetInputData(surface)
transformFilter.SetTransform(transform)
transformFilter.Update()
surface = transformFilter.GetOutput()
smoothFilter = vtk.vtkSmoothPolyDataFilter()
smoothFilter.SetInputData(surface)
smoothFilter.SetNumberOfIterations(smoothIterations);
smoothFilter.SetRelaxationFactor(relaxationFactor);
smoothFilter.FeatureEdgeSmoothingOff();
smoothFilter.BoundarySmoothingOn();
smoothFilter.Update();
surface = smoothFilter.GetOutput()
if lcc:
connectedFilter = vtk.vtkConnectivityFilter()
connectedFilter.SetInputData(surface)
connectedFilter.Update()
surface = connectedFilter.GetOutput()
if pathlib.Path(surface_path).suffix == ".vtk":
writer = vtk.vtkGenericDataObjectWriter()
elif pathlib.Path(surface_path).suffix == ".vtp":
writer = vtk.vtkXMLPolyDataWriter()
elif pathlib.Path(surface_path).suffix == ".stl":
writer = vtk.vtkSTLWriter()
writer.SetFileName(surface_path)
writer.SetInputData(surface)
writer.Update()
tqdm.write("Convert segmentation label to surface file complete: {}".format(label_path))
def LabelToSurface(label_path, surface_path, lcc=False):
print("Converting segmentation label to surface file:", label_path)
# binary path
bin_path = "D:/Dr_Simon_Yu/CFD_intracranial/code/cxx/label_to_mesh/build/Release/LabelToMesh.exe"
# convert to binary file
command = bin_path + " " + label_path + " " + surface_path + " 1 1"
# print(command)
os.system(command)
reader = vtk.vtkGenericDataObjectReader()
reader.SetFileName(surface_path)
reader.Update()
surface = reader.GetOutput()
transform = vtk.vtkTransform()
transform.Scale(-1, -1, 1)
transformFilter = vtk.vtkTransformPolyDataFilter()
transformFilter.SetInputData(surface)
transformFilter.SetTransform(transform)
transformFilter.Update()
surface = transformFilter.GetOutput()
smoothFilter = vtk.vtkSmoothPolyDataFilter()
smoothFilter.SetInputData(surface)
smoothFilter.SetNumberOfIterations(15)
smoothFilter.SetRelaxationFactor(0.1)
smoothFilter.FeatureEdgeSmoothingOff()
smoothFilter.BoundarySmoothingOn()
smoothFilter.Update()
surface = smoothFilter.GetOutput()
if lcc:
connectedFilter = vtk.vtkConnectivityFilter()
connectedFilter.SetInputData(surface)
connectedFilter.Update()
surface = connectedFilter.GetOutput()
writer = vtk.vtkGenericDataObjectWriter()
writer.SetFileName(surface_path)
writer.SetInputData(surface)
writer.Update()
def write_vtk_to_file(filename, vtkdata):
"""
Write VTK file.
Parameters
----------
filename : str
Name of the VTK file.
vtkdata : VTK object
Mesh, scalar, vector and tensor data.
"""
writer = vtk.vtkGenericDataObjectWriter()
writer.SetFileName(filename)
if vtk_version < 6:
writer.SetInput(vtkdata)
else:
writer.SetInputData(vtkdata)
writer.Update()
def write_vtk_to_file(filename, vtkdata):
"""
Write VTK file.
Parameters
----------
filename : str
Name of the VTK file.
vtkdata : VTK object
Mesh, scalar, vector and tensor data.
"""
writer = vtk.vtkGenericDataObjectWriter()
writer.SetFileName(filename)
if vtk_version < 6:
writer.SetInput(vtkdata)
else:
writer.SetInputData(vtkdata)
writer.Update()
u = bgridreader.GetOutput()
GeomFilt2 = vtk.vtkGeometryFilter()
GeomFilt2.SetInput(u)
GeomFilt2.Update()
y = GeomFilt2.GetOutput()
append = vtk.vtkAppendPolyData()
append.AddInput(x)
append.AddInput(y)
data = append.GetOutput()
d = vtk.vtkDelaunay3D()
d.SetInput(data)
d.Update
d.BoundingTriangulationOff()
d.SetTolerance(0.01)
d.SetAlpha(0)
d.Update()
z = d.GetOutput()
return z
if __name__ == '__main__':
z = Create_topo()
writer = vtk.vtkGenericDataObjectWriter()
writer.SetFileName("test31.vtu")
writer.SetInput(z)
writer.Update()
writer.Write()
def Extrude(Slope,Extrusion,Plane,Model,Sediment,Start_time,End_time,Time_step,Mesh):
ugrid1 = vtk.vtkUnstructuredGrid() #1.import sloped sediment and change to polydata
gridreader1=vtk.vtkUnstructuredGridReader()
gridreader1.SetFileName(Slope) #.pvd
gridreader1.Update()
ugrid1 = gridreader1.GetOutput()
GeomFilt1 = vtk.vtkGeometryFilter()
GeomFilt1.SetInput(ugrid1)
GeomFilt1.Update()
y1 = GeomFilt1.GetOutput()
Extrude = vtk.vtkLinearExtrusionFilter() #2. extrude the polydata and save it again as polydata
Extrude.SetInput(y1)
Extrude.SetExtrusionTypeToVectorExtrusion()
Extrude.SetVector(0,0,-1)
PreliminaryExtrusion = Extrude.GetOutput()
PE = vtk.vtkPolyData()
PE = PreliminaryExtrusion
PE.Update()
ugrid2 = vtk.vtkUnstructuredGrid() #3. import in the top surface of the sediment below
gridreader2=vtk.vtkXMLUnstructuredGridReader()
gridreader2.SetFileName(Plane) # 000000.vtu
gridreader2.Update()
ugrid2 = gridreader2.GetOutput()
ExtrudedPoints = PE.GetPoints() #4. take points from the extruded polydata
PlanePoints = ugrid2.GetPoints() #5. get points from surface below
nPoints = PE.GetNumberOfPoints() #6. for first half of points determine if above or below last surface
Begin = nPoints/2 #7. if below set as the same as bottom surface (slightly above?)
#8. set second half
counter = 0
uPoints = ugrid2.GetPoints()
for p in range(Begin,nPoints):
y = uPoints.GetPoint(counter)[2:]
x = ExtrudedPoints.GetPoint(p)[:2] + y
ExtrudedPoints.SetPoint(p,x)
counter += 1
PE.Update()
writer = vtk.vtkGenericDataObjectWriter()
writer.SetFileName(Model)
writer.SetInput(PE)
writer.Update()
writer.Write()
#################################################################################################################
t = Start_time
dt = Time_step
ET = End_time
et = ET-1
Save = Sediment + str(t) +'000000.vtu'
Import = Sediment + str(t)+ '_sed_slope.pvd'
NewSave = Sediment + str(t)+ 'extruded_sed_slope.pvd'
SedimentGrid1 = vtk.vtkUnstructuredGrid() #1.import sloped sediment and change to polydata
SedimentGridreader1=vtk.vtkUnstructuredGridReader()
SedimentGridreader1.SetFileName(Import) #.pvd
SedimentGridreader1.Update()
SedimentGrid1 = SedimentGridreader1.GetOutput()
GeomFilt2 = vtk.vtkGeometryFilter()
GeomFilt2.SetInput(SedimentGrid1)
GeomFilt2.Update()
ExtrudeInput1 = GeomFilt2.GetOutput()
ExtrudeSed1 = vtk.vtkLinearExtrusionFilter() #2. extrude the polydata and save it again as polydata
ExtrudeSed1.SetInput(ExtrudeInput1)
ExtrudeSed1.SetExtrusionTypeToVectorExtrusion()
ExtrudeSed1.SetVector(0,0,-1)
PreliminarySedExtrusion1 = ExtrudeSed1.GetOutput()
PSE1 = vtk.vtkPolyData()
PSE1 = PreliminarySedExtrusion1
PSE1.Update()
PreSurface1 = vtk.vtkUnstructuredGrid() #3. import in the top surface of the sediment below
PSreader1=vtk.vtkGenericDataObjectReader()
PSreader1.SetFileName(Slope) # 000000.vtu
PSreader1.Update()
PreSurface1 = PSreader1.GetOutput()
ExtrudedSedPoints1 = PSE1.GetPoints() #4. take points from the extruded polydata
PSPoints1 = PreSurface1.GetPoints() #5. get points from surface below
SedPoints1 = PSE1.GetNumberOfPoints() #6. for first half of points determine if above or below last surface
BeginSed1 = nPoints/2
EndSed1 = BeginSed1 - 1 #7. if below set as the same as bottom surface (slightly above?
sedcounter1 = 0 #8. set second half
sedcounter2 = BeginSed1
for p in range(BeginSed1,SedPoints1):
y = PSPoints1.GetPoint(sedcounter1)[2:]
x = ExtrudedSedPoints1.GetPoint(p)[:2] + y
ExtrudedSedPoints1.SetPoint(p,x)
sedcounter1 += 1
writer = vtk.vtkGenericDataObjectWriter()
writer.SetFileName(NewSave)
writer.SetInput(PSE1)
writer.Update()
writer.Write()
#####################################################################################################################
while t <= et:
t += dt
pre = t -1
Previous = Sediment +str(pre) + '_sed_slope.pvd'
PreviousSave = Sediment + str(pre)+ 'extruded_sed_slope.pvd'
Import = Sediment + str(t)+ '_sed_slope.pvd'
NewSave = Sediment + str(t)+ 'extruded_sed_slope.pvd'
SedimentGrid2 = vtk.vtkUnstructuredGrid()
SedimentGridreader2=vtk.vtkUnstructuredGridReader()
SedimentGridreader2.SetFileName(Import) #.pvd
SedimentGridreader2.Update()
SedimentGrid2 = SedimentGridreader2.GetOutput()
GeomFilt3 = vtk.vtkGeometryFilter()
GeomFilt3.SetInput(SedimentGrid2)
GeomFilt3.Update()
ExtrudeInput = GeomFilt3.GetOutput()
ExtrudeInput2 = GeomFilt3.GetOutput()
ExtrudeSed2 = vtk.vtkLinearExtrusionFilter()
ExtrudeSed2.SetInput(ExtrudeInput2)
ExtrudeSed2.SetExtrusionTypeToVectorExtrusion()
ExtrudeSed2.SetVector(0,0,-1)
PreliminarySedExtrusion2 = ExtrudeSed2.GetOutput()
PSE2 = vtk.vtkPolyData()
PSE2 = PreliminarySedExtrusion2
PSE2.Update()
PreSurface2 = vtk.vtkUnstructuredGrid()
PSreader2=vtk.vtkGenericDataObjectReader()
PSreader2.SetFileName(PreviousSave) # 000000.vtu
PSreader2.Update()
PreSurface2 = PSreader2.GetOutput()
Append = vtk.vtkAppendPolyData()
Append.AddInput(PreSurface2)
Append.AddInput(PSE2)
DD = Append.GetOutput()
DD.Update()
ExtrudedSedPoints = PSE2.GetPoints()
PSPoints = PreSurface2.GetPoints()
SedPoints = PSE2.GetNumberOfPoints()
BeginSed = nPoints/2
EndSed = BeginSed - 1
sedcounter3 = 0
sedcounter4 = BeginSed
Data = DD.GetPoints()
mesh = Mesh
m = (mesh+1)**2
c = t
while c != 0:
c = (c -1)
e = int((c*m)*2)
ee = int(e + m)
for p in range(e,ee):
A = Data.GetPoint(p+(2*m))[2:] #New sediment height
B = Data.GetPoint(p)[2:] # old sediment height
C = Data.GetPoint(p+m)[2:] # old sediment bottom
if A < B: #If new sediment height is less than old sediment height
y = (Data.GetPoint(p)[:2] + Data.GetPoint(p+(2*m))[2:])
Data.SetPoint(p,y)
if A < C:
x = Data.GetPoint(p+m)[:2] + Data.GetPoint(p)[2:]
Data.SetPoint((p+m),x)
f = int((t*m)*2+m)
ff = int(f + m)
for p in range(f,ff):
y = Data.GetPoint((p-3*m))[2:]
x = Data.GetPoint(p)[:2] + y
Data.SetPoint(p,x)
writer = vtk.vtkGenericDataObjectWriter()
writer.SetFileName(NewSave)
writer.SetInput(DD)
writer.Update()
writer.Write()
def apply_filters(fname, df, sf, surf_type):
"""Apply the decimation and smoothing filters using the VTK library
and the user specified refinement factors. Decimation uses the
vtkDecimatePro method. Smoothing uses the vtkWindowSincPolyDataFilter
method. Both refinement processes maintain boundary vertices and
topology. If both filters are applied, smoothing will be applied first.
Input:
------
fname: string, name of the surface vtk file that will be refined
df: float or None, factor for target reduction in the decimation
process. Must be between 0 and 1. If set to None, no
decimation will be applied. A higher value indicates a
greater reduction in the number of surface triangles.
sf: float or None, smoothing factor for the smoothing process.
Must be between 0 and 1. If set to None, no smoothing will
be applied. A higher value indicates more smoothing.
surf_type: str, 'interior' or 'exterior', used to indicate if
the surface being refined is an interior or exterior surface.
Only interior surfaces will have smoothing applied if
smoothing is requested.
Return:
-------
outfile: string, name of the output file from VTK after refinement
"""
# read in surface w/ vtk as an unstructured grid
usg = vtk.vtkUnstructuredGridReader()
usg.SetFileName(fname)
usg.Update()
usgport = usg.GetOutputPort()
# convert USG to polydata
gf = vtk.vtkGeometryFilter()
gf.SetInputConnection(usgport)
gf.Update()
pdport = gf.GetOutputPort()
# only apply smoothing filter to interior surfaces to avoid smoothing
# the corners of the geometry
if sf is not None and surf_type == 'interior':
smoothfilter = vtk.vtkWindowedSincPolyDataFilter()
smoothfilter.SetInputConnection(pdport)
smoothfilter.SetNumberOfIterations(20)
smoothfilter.BoundarySmoothingOff # don't apply to boundaries
smoothfilter.NonManifoldSmoothingOff() # don't collapse topology/vols
smoothfilter.Update()
pdport = smoothfilter.GetOutputPort()
if df is not None:
# setup decimate operator
decifilter = vtk.vtkDecimatePro()
decifilter.SetInputConnection(pdport)
# set decimate options
decifilter.SetTargetReduction(df) # target reduction
# preserve topology (splitting or hole elimination not allowed)
decifilter.SetPreserveTopology(True)
decifilter.SetSplitting(False) # no mesh splitting allowed
# no boundary vertex (edge/curve) deletion allowed
decifilter.SetBoundaryVertexDeletion(False)
decifilter.Update()
pdport = decifilter.GetOutputPort()
# convert polydata back to USG
appendfilter = vtk.vtkAppendFilter()
appendfilter.SetInputConnection(pdport)
appendfilter.Update()
usg_new = vtk.vtkUnstructuredGrid()
usg_new.ShallowCopy(appendfilter.GetOutput())
outfile = fname.split('.')[0] + '_refined.vtk'
writer1 = vtk.vtkGenericDataObjectWriter()
writer1.SetFileName(outfile)
writer1.SetInputData(usg_new)
writer1.Update()
writer1.Write()
return outfile
def write_data_to_vtk(self, filename, datasets, volume_normalization=True):
"""Map data to the unstructured mesh element centroids
to create a VTK point-cloud dataset.
Parameters
----------
filename : str
Name of the VTK file to write.
datasets : dict
Dictionary whose keys are the data labels
and values are the data sets.
volume_normalization : bool
Whether or not to normalize the data by the
volume of the mesh elements
"""
import vtk
from vtk.util import numpy_support as vtk_npsup
if self.centroids is None:
raise RuntimeError("No centroid information is present on this "
"unstructured mesh. Please load this "
"information from a relevant statepoint file.")
if self.volumes is None and volume_normalization:
raise RuntimeError("No volume data is present on this "
"unstructured mesh. Please load the "
" mesh information from a statepoint file.")
# check that the data sets are appropriately sized
for label, dataset in datasets.items():
if isinstance(dataset, np.ndarray):
assert dataset.size == self.n_elements
else:
assert len(dataset) == self.n_elements
cv.check_type('label', label, str)
# create data arrays for the cells/points
cell_dim = 1
vertices = vtk.vtkCellArray()
points = vtk.vtkPoints()
for centroid in self.centroids:
# create a point for each centroid
point_id = points.InsertNextPoint(centroid)
# create a cell of type "Vertex" for each point
cell_id = vertices.InsertNextCell(cell_dim, (point_id, ))
# create a VTK data object
poly_data = vtk.vtkPolyData()
poly_data.SetPoints(points)
poly_data.SetVerts(vertices)
# strange VTK nuance:
# data must be held in some container
# until the vtk file is written
data_holder = []
# create VTK arrays for each of
# the data sets
for label, dataset in datasets.items():
dataset = np.asarray(dataset).flatten()
if volume_normalization:
dataset /= self.volumes.flatten()
array = vtk.vtkDoubleArray()
array.SetName(label)
array.SetNumberOfComponents(1)
array.SetArray(vtk_npsup.numpy_to_vtk(dataset), dataset.size, True)
data_holder.append(dataset)
poly_data.GetPointData().AddArray(array)
# set filename
if not filename.endswith(".vtk"):
filename += ".vtk"
writer = vtk.vtkGenericDataObjectWriter()
writer.SetFileName(filename)
writer.SetInputData(poly_data)
writer.Write()
reader = vtk.vtkStructuredPointsReader()
reader.SetFileName("fMag.0001.vtk")
reader.Update()
vtk_data = reader.GetOutput()
scalar_data = numpy_support.vtk_to_numpy(vtk_data.GetPointData().GetScalars())
mesh_shape = vtk_data.GetDimensions()
origin = vtk_data.GetOrigin()
spacing = vtk_data.GetSpacing()
scalar_data_vtk = numpy_support.numpy_to_vtk(scalar_data)
scalar_data_vtk.SetName('fMag')
vtk_obj = vtk.vtkStructuredPoints()
vtk_obj.SetDimensions(mesh_shape)
vtk_obj.SetOrigin(origin)
vtk_obj.SetSpacing(spacing)
vtk_obj.GetPointData().SetScalars(scalar_data_vtk)
writer = vtk.vtkGenericDataObjectWriter()
writer.SetFileName("test_out.vtk")
writer.SetInputDataObject(vtk_obj)
writer.Update()
writer.Write() # returns 1 on success, 0 on failure
### STRUCTURED_POINTS - VECTORS ###
reader = vtk.vtkStructuredPointsReader()
reader.SetFileName("u.0001.vtk")
reader.Update()
vtk_data = reader.GetOutput()
# return an n x 3 array of vectors
vector_data = numpy_support.vtk_to_numpy(vtk_data.GetPointData().GetVectors())
mesh_shape = vtk_data.GetDimensions()
origin = vtk_data.GetOrigin()
spacing = vtk_data.GetSpacing()
def main():
# input file (vtk isosurface geom)
fname = sys.argv[1] # unstructured grid vtk file
# read unstructured grid
usg = vtk.vtkUnstructuredGridReader()
usg.SetFileName(fname)
usg.Update()
usgport = usg.GetOutputPort()
# convert USG to polydata
gf = vtk.vtkGeometryFilter()
gf.SetInputConnection(usgport)
gf.Update()
pdport = gf.GetOutputPort()
# setup decimate operator
deci = vtk.vtkDecimatePro()
deci.SetInputConnection(pdport)
# set decimate options
target = 0.9
deci.SetTargetReduction(target) # target reduction
deci.SetPreserveTopology(
True) # preserve topology (splitting or hole elimination not allowed)
deci.SetSplitting(False) # no mesh splitting allowed
deci.SetBoundaryVertexDeletion(
False) # no boundary vertex (eddge/curve) deletion allowed
deci.Update()
deciport = deci.GetOutputPort()
# convert polydata back to USG
appendfilter = vtk.vtkAppendFilter()
appendfilter.SetInputConnection(deciport)
appendfilter.Update()
usg_new = vtk.vtkUnstructuredGrid()
usg_new.ShallowCopy(appendfilter.GetOutput())
# write file (USG) - needed for pymoab
outfile = fname.split('.')[0] + '-decimate-out-usg.vtk'
writer1 = vtk.vtkGenericDataObjectWriter()
writer1.SetFileName(outfile)
writer1.SetInputData(usg_new)
writer1.Update()
writer1.Write()
# write out polydata too
outpoly = fname.split('.')[0] + '-decimate-out-poly.vtk'
writer2 = vtk.vtkGenericDataObjectWriter()
writer2.SetFileName(outpoly)
writer2.SetInputConnection(deciport)
writer2.Update()
writer2.Write()
# try reading file in w/ pymoab again
mb = core.Core()
mb.load_file(outfile)
rs = mb.get_root_set()
# get entities w/ dim=2 (should be facets)
all_facets = mb.get_entities_by_dimension(rs, 2)
print(all_facets)
print(len(all_facets))
# confirm facet type (should by tris, not polygons)
facet_type = mb.type_from_handle(all_facets[0])
print(facet_type)
tris1 = mb.get_entities_by_type(rs, facet_type)
tris2 = mb.get_entities_by_type(rs, types.MBTRI)
polys = mb.get_entities_by_type(rs, types.MBPOLYGON)
print(tris1, len(tris1))
print(tris2, len(tris2))
print(polys, len(polys))