def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkXMLRectilinearGridReader(), 'Reading vtkXMLRectilinearGrid.',
(), ('vtkXMLRectilinearGrid',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
# extract commandline arguments
(opts, args) = p.parse_args()
if len(args) < 2:
sys.stderr.write("Number of arguments incorrect\n")
sys.exit(1)
vtr_files = args[0:-1]
grid_file = args[-1]
# read vtr data
r = {}
for vtr_file in vtr_files:
if opts.verbose: sys.stdout.write("Reading " + vtr_file + "\n");
if vtr_file.endswith(".vtr"):
r[vtr_file] = vtk.vtkXMLRectilinearGridReader()
else:
sys.stderr.write("Not currently configured to read file of type " + vtr_file + "\n");
sys.exit(2)
r[vtr_file].SetFileName(vtr_file)
r[vtr_file].Update()
r[vtr_file] = r[vtr_file].GetOutput()
# get function_vals and check it exists
if opts.verbose: sys.stdout.write("Extracting function_vals\n")
fcn_vals = {}
for vtr_file in vtr_files:
fcn_vals[vtr_file] = r[vtr_file].GetPointData().GetArray("function_vals")
if not fcn_vals[vtr_file]:
sys.stderr.write(vtr_file + " does not have PointData called function_vals\n")
# get the com filename
if len(args) != 1:
p.print_help()
sys.exit(1)
in_file = args[0]
if opts.verbose: print "Reading", in_file
if in_file.endswith(".vtp"):
indata = vtk.vtkXMLPolyDataReader()
writer = vtk.vtkXMLPolyDataWriter()
elif in_file.endswith(".vtu"):
indata = vtk.vtkXMLUnstructuredGridReader()
writer = vtk.vtkXMLUnstructuredGridWriter()
elif in_file.endswith(".vtr"):
indata = vtk.vtkXMLRectilinearGridReader()
writer = vtk.vtkXMLRectilinearGridWriter()
else:
print "This program has not yet been configured to read files of type", in_file
sys.exit(2)
indata.SetFileName(in_file)
indata.Update()
indata = indata.GetOutput()
if opts.verbose: print "Generating", opts.name
yf = vtk.vtkDoubleArray()
yf.SetName(opts.name)
yf.SetNumberOfValues(indata.GetNumberOfPoints())
sphere = vtk.vtkSphere()
sphere.SetCenter(0.0, 0.0, 0.0)
sphere.SetRadius(0.25)
sample = vtk.vtkSampleFunction()
sample.SetImplicitFunction(sphere)
sample.SetModelBounds(-0.5, 0.5, -0.5, 0.5, -0.5, 0.5)
sample.SetSampleDimensions(res, res, res)
sample.Update()
# Converts image data to structured grid
convert = vtk.vtkImageDataToPointSet()
convert.SetInputConnection(sample.GetOutputPort())
convert.Update()
cthvtr = vtk.vtkXMLRectilinearGridReader()
cthvtr.SetFileName("" + str(VTK_DATA_ROOT) + "/Data/cth.vtr")
cthvtr.CellArrayStatus = ['Pressure', 'Void Volume Fraction', 'X Velocity', 'Y Velocity', 'Z Velocity', 'Volume Fraction for Armor Plate', 'Mass for Armor Plate', 'Volume Fraction for Body, Nose', 'Mass for Body, Nose']
cthvtr.Update()
input = cthvtr.GetOutput()
# Create a cutting plane
plane = vtk.vtkPlane()
plane.SetOrigin(input.GetCenter())
plane.SetNormal(1, 1, 1)
# First create the usual cutter
cutter = vtk.vtkCutter()
cutter.SetInputData(input)
cutter.SetCutFunction(plane)
import vtk
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.animation as animation
from mpl_toolkits.axes_grid1 import make_axes_locatable
plt.rcParams['animation.ffmpeg_path'] = '/usr/bin/ffmpeg'
from vtk.util.numpy_support import vtk_to_numpy
reader = vtk.vtkXMLRectilinearGridReader()
fig, ax = plt.subplots()
NrTs = 1500
ims = []
for k in np.arange(0, NrTs, 1):
# create the filename from sequence number
if k < 10:
filename = "tmp/Et_000000000" + str(k) + '.vtr'
elif k < 100:
filename = "tmp/Et_00000000" + str(k) + '.vtr'
elif k < 1000:
filename = "tmp/Et_0000000" + str(k) + '.vtr'
reader.SetFileName(filename)
reader.Update()
Efield = reader.GetOutput().GetPointData().GetArray(0)
u = vtk_to_numpy(Efield)
im = ax.imshow(u, interpolation='nearest')
a = im.get_axes()
def readVTRFile(fileName): '''Function to read vtk structured grid (vtr) and return a grid object.''' Reader = vtk.vtkXMLRectilinearGridReader() Reader.SetFileName(fileName) Reader.Update() return Reader.GetOutput()
# get the com filename
if len(args) != 1:
p.print_help()
sys.exit(1)
in_file = args[0]
if opts.verbose: print "Reading", in_file
if in_file.endswith(".vtp"):
indata = vtk.vtkXMLPolyDataReader()
writer = vtk.vtkXMLPolyDataWriter()
elif in_file.endswith(".vtu"):
indata = vtk.vtkXMLUnstructuredGridReader()
writer = vtk.vtkXMLUnstructuredGridWriter()
elif in_file.endswith(".vtr"):
indata = vtk.vtkXMLRectilinearGridReader()
writer = vtk.vtkXMLRectilinearGridWriter()
else:
print "This program has not yet been configured to read files of type", in_file
sys.exit(2)
indata.SetFileName(in_file)
indata.Update()
indata = indata.GetOutput()
if opts.verbose: print "Generating", opts.name
yf = vtk.vtkDoubleArray()
yf.SetName(opts.name)
yf.SetNumberOfValues(indata.GetNumberOfPoints())
def _load_file(filename, c, alpha, threshold, spacing, unpack):
fl = filename.lower()
################################################################# other formats:
if fl.endswith(".xml") or fl.endswith(".xml.gz") or fl.endswith(".xdmf"):
# Fenics tetrahedral file
actor = loadDolfin(filename)
elif fl.endswith(".neutral") or fl.endswith(
".neu"): # neutral tetrahedral file
actor = loadNeutral(filename)
elif fl.endswith(".gmsh"): # gmesh file
actor = loadGmesh(filename)
elif fl.endswith(".pcd"): # PCL point-cloud format
actor = loadPCD(filename)
actor.GetProperty().SetPointSize(2)
elif fl.endswith(".off"):
actor = loadOFF(filename)
elif fl.endswith(".3ds"): # 3ds format
actor = load3DS(filename)
elif fl.endswith(".wrl"):
importer = vtk.vtkVRMLImporter()
importer.SetFileName(filename)
importer.Read()
importer.Update()
actors = importer.GetRenderer().GetActors() #vtkActorCollection
actors.InitTraversal()
wacts = []
for i in range(actors.GetNumberOfItems()):
act = actors.GetNextActor()
wacts.append(act)
actor = Assembly(wacts)
################################################################# volumetric:
elif fl.endswith(".tif") or fl.endswith(".slc") or fl.endswith(".vti") \
or fl.endswith(".mhd") or fl.endswith(".nrrd") or fl.endswith(".nii") \
or fl.endswith(".dem"):
img = loadImageData(filename, spacing)
if threshold is False:
if c is None and alpha == 1:
c = ['b', 'lb', 'lg', 'y',
'r'] # good for blackboard background
alpha = (0.0, 0.0, 0.2, 0.4, 0.8, 1)
actor = Volume(img, c, alpha)
else:
actor = Volume(img).isosurface(threshold=threshold)
actor.color(c).alpha(alpha)
################################################################# 2D images:
elif fl.endswith(".png") or fl.endswith(".jpg") or fl.endswith(
".bmp") or fl.endswith(".jpeg"):
if ".png" in fl:
picr = vtk.vtkPNGReader()
elif ".jpg" in fl or ".jpeg" in fl:
picr = vtk.vtkJPEGReader()
elif ".bmp" in fl:
picr = vtk.vtkBMPReader()
picr.SetFileName(filename)
picr.Update()
actor = Picture() # object derived from vtk.vtkImageActor()
actor.SetInputData(picr.GetOutput())
if alpha is None:
alpha = 1
actor.SetOpacity(alpha)
################################################################# multiblock:
elif fl.endswith(".vtm") or fl.endswith(".vtmb"):
read = vtk.vtkXMLMultiBlockDataReader()
read.SetFileName(filename)
read.Update()
mb = read.GetOutput()
if unpack:
acts = []
for i in range(mb.GetNumberOfBlocks()):
b = mb.GetBlock(i)
if isinstance(b,
(vtk.vtkPolyData, vtk.vtkImageData,
vtk.vtkUnstructuredGrid, vtk.vtkStructuredGrid,
vtk.vtkRectilinearGrid)):
acts.append(b)
return acts
else:
return mb
################################################################# numpy:
elif fl.endswith(".npy"):
acts = loadNumpy(filename)
if unpack == False:
return Assembly(acts)
return acts
elif fl.endswith(".geojson") or fl.endswith(".geojson.gz"):
return loadGeoJSON(fl)
################################################################# polygonal mesh:
else:
if fl.endswith(".vtk"): # read all legacy vtk types
#output can be:
# PolyData, StructuredGrid, StructuredPoints, UnstructuredGrid, RectilinearGrid
reader = vtk.vtkDataSetReader()
reader.ReadAllScalarsOn()
reader.ReadAllVectorsOn()
reader.ReadAllTensorsOn()
reader.ReadAllFieldsOn()
reader.ReadAllNormalsOn()
reader.ReadAllColorScalarsOn()
elif fl.endswith(".ply"):
reader = vtk.vtkPLYReader()
elif fl.endswith(".obj"):
reader = vtk.vtkOBJReader()
elif fl.endswith(".stl"):
reader = vtk.vtkSTLReader()
elif fl.endswith(".byu") or fl.endswith(".g"):
reader = vtk.vtkBYUReader()
elif fl.endswith(".foam"): # OpenFoam
reader = vtk.vtkOpenFOAMReader()
elif fl.endswith(".pvd"):
reader = vtk.vtkXMLGenericDataObjectReader()
elif fl.endswith(".vtp"):
reader = vtk.vtkXMLPolyDataReader()
elif fl.endswith(".vts"):
reader = vtk.vtkXMLStructuredGridReader()
elif fl.endswith(".vtu"):
reader = vtk.vtkXMLUnstructuredGridReader()
elif fl.endswith(".vtr"):
reader = vtk.vtkXMLRectilinearGridReader()
elif fl.endswith(".pvtk"):
reader = vtk.vtkPDataSetReader()
elif fl.endswith(".pvtr"):
reader = vtk.vtkXMLPRectilinearGridReader()
elif fl.endswith("pvtu"):
reader = vtk.vtkXMLPUnstructuredGridReader()
elif fl.endswith(".txt") or fl.endswith(".xyz"):
reader = vtk.vtkParticleReader() # (format is x, y, z, scalar)
elif fl.endswith(".facet"):
reader = vtk.vtkFacetReader()
else:
return None
reader.SetFileName(filename)
reader.Update()
routput = reader.GetOutput()
if not routput:
colors.printc("~noentry Unable to load", filename, c=1)
return None
actor = Actor(routput, c, alpha)
if fl.endswith(".txt") or fl.endswith(".xyz"):
actor.GetProperty().SetPointSize(4)
actor.filename = filename
return actor
def readVTK(fname):
reader = vtkXMLRectilinearGridReader()
reader.SetFileName(fname)
reader.Update()
grid = reader.GetOutput(0)
return grid
def readVTRFile(fileName):
'''Function to read vtk structured grid (vtr) and return a grid object.'''
Reader = vtk.vtkXMLRectilinearGridReader()
Reader.SetFileName(fileName)
Reader.Update()
return Reader.GetOutput()
# work out readers and writers to use
if datafn.endswith(".vtu"):
old_mesh_reader = vtk.vtkXMLUnstructuredGridReader()
elif datafn.endswith(".vtp"):
old_mesh_reader = vtk.vtkXMLPolyDataReader()
else:
print "Program not yet configured for type of input file", datafn
sys.exit(2)
if meshfn.endswith(".vtu"):
new_mesh_reader = vtk.vtkXMLUnstructuredGridReader()
elif meshfn.endswith(".vtp"):
new_mesh_reader = vtk.vtkXMLPolyDataReader()
elif meshfn.endswith(".vtr"):
new_mesh_reader = vtk.vtkXMLRectilinearGridReader()
else:
print "Program not yet configured for type of input file", meshfn
sys.exit(2)
if outputfn.endswith(".vtu"):
writer = vtk.vtkXMLUnstructuredGridWriter()
elif outputfn.endswith(".vtp"):
writer = vtk.vtkXMLPolyDataWriter()
else:
print "Program not yet configured for type of output file", outputfn
sys.exit(2)
# to get rid of z values
flattener = vtk.vtkTransform()
flattener.Scale(1.0, 1.0, 0.0)