def TestXdmfConversion(dataInput, fileName):
global CleanUpGood, timer
fileName = OutputDir + fileName
xdmfFile = fileName + ".xmf"
hdf5File = fileName + ".h5"
vtkFile = fileName + ".vtk"
xWriter = vtk.vtkXdmf3Writer()
xWriter.SetLightDataLimit(LightDataLimit)
xWriter.WriteAllTimeStepsOn()
xWriter.SetFileName(xdmfFile)
xWriter.SetInputData(dataInput)
timer.StartTimer()
xWriter.Write()
timer.StopTimer()
print "vtkXdmf3Writer took", timer.GetElapsedTime(), "seconds to write",\
xdmfFile
ds = vtk.vtkDataSet.SafeDownCast(dataInput)
if ds:
dsw = vtk.vtkDataSetWriter()
dsw.SetFileName(vtkFile)
dsw.SetInputData(ds)
dsw.Write()
if not DoFilesExist(xdmfFile, None, None, False):
message = "Writer did not create " + xdmfFile
raiseErrorAndExit(message)
xReader = vtk.vtkXdmf3Reader()
xReader.SetFileName(xdmfFile)
timer.StartTimer()
xReader.Update()
timer.StopTimer()
print "vtkXdmf3Reader took", timer.GetElapsedTime(), "seconds to read",\
xdmfFile
rOutput = xReader.GetOutputDataObject(0)
fail = DoDataObjectsDiffer(dataInput, rOutput)
if fail:
raiseErrorAndExit("Xdmf conversion test failed")
else:
if ds:
DoFilesExist(xdmfFile, hdf5File, vtkFile, CleanUpGood)
else:
DoFilesExist(xdmfFile, hdf5File, None, CleanUpGood)
def TestXdmfConversion(dataInput, fileName):
global CleanUpGood, timer
fileName = OutputDir + fileName
xdmfFile = fileName + ".xmf"
hdf5File = fileName + ".h5"
vtkFile = fileName + ".vtk"
xWriter = vtk.vtkXdmf3Writer()
xWriter.SetLightDataLimit(LightDataLimit)
xWriter.WriteAllTimeStepsOn()
xWriter.SetFileName(xdmfFile)
xWriter.SetInputData(dataInput)
timer.StartTimer()
xWriter.Write()
timer.StopTimer()
print "vtkXdmf3Writer took", timer.GetElapsedTime(), "seconds to write",\
xdmfFile
ds = vtk.vtkDataSet.SafeDownCast(dataInput)
if ds:
dsw = vtk.vtkDataSetWriter()
dsw.SetFileName(vtkFile)
dsw.SetInputData(ds)
dsw.Write()
if not DoFilesExist(xdmfFile, None, None, False):
message = "Writer did not create " + xdmfFile
raiseErrorAndExit(message)
xReader = vtk.vtkXdmf3Reader()
xReader.SetFileName(xdmfFile)
timer.StartTimer()
xReader.Update()
timer.StopTimer()
print "vtkXdmf3Reader took", timer.GetElapsedTime(), "seconds to read",\
xdmfFile
rOutput = xReader.GetOutputDataObject(0)
fail = DoDataObjectsDiffer(dataInput, rOutput)
if fail:
raiseErrorAndExit("Xdmf conversion test failed")
else:
if ds:
DoFilesExist(xdmfFile, hdf5File, vtkFile, CleanUpGood)
else:
DoFilesExist(xdmfFile, hdf5File, None, CleanUpGood)
"Iron/Iron_Protein.ImageData.Collection.xmf",
"Iron/Iron_Protein.RectilinearGrid.xmf",
"Iron/Iron_Protein.RectilinearGrid.Collection.xmf",
"Iron/Iron_Protein.StructuredGrid.xmf",
"Iron/Iron_Protein.StructuredGrid.Collection.xmf",
"Big/Scenario1_p1.xmf",
]
testfilenames = smallFiles
import sys
if "--do_big_files" in sys.argv:
testfilenames = smallFiles + largeFiles
if __name__ == "__main__":
for fname in testfilenames:
xr = vtk.vtkXdmf3Reader()
afname = "" + str(VTK_DATA_ROOT) + "/Data/XDMF/" + fname
print "Trying ", afname
xr.CanReadFile(afname)
xr.SetFileName(afname)
xr.UpdateInformation()
xr.Update()
ds = xr.GetOutputDataObject(0)
if not ds:
print "Got zero output from known good file"
sys.exit(vtk.VTK_ERROR)
#if res != vtk.VTK_OK:
# print "Could not read", afname
# sys.exit(vtk.VTK_ERROR)
"""
This test verifies that vtk's Xdmf reader will read a polyhedron sample file.
"""
import os, sys
import vtk
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
if __name__ == "__main__":
fnameIn = "" + str(VTK_DATA_ROOT) + "/Data/XDMF/polyhedron.xmf"
xr = vtk.vtkXdmf3Reader()
xr.CanReadFile(fnameIn)
xr.SetFileName(fnameIn)
xr.UpdateInformation()
xr.Update()
ds = xr.GetOutputDataObject(0)
if not ds:
print "Got zero output from known good file"
sys.exit(vtk.VTK_ERROR)
print ds.GetCells()
print ds.GetPoints()
def read(filetype, filename):
import vtk
from vtk.util import numpy_support
def _read_data(data):
"""Extract numpy arrays from a VTK data set.
"""
# Go through all arrays, fetch data.
out = {}
for k in range(data.GetNumberOfArrays()):
array = data.GetArray(k)
if array:
array_name = array.GetName()
out[array_name] = numpy.copy(
vtk.util.numpy_support.vtk_to_numpy(array))
return out
def _read_cells(vtk_mesh):
data = numpy.copy(
vtk.util.numpy_support.vtk_to_numpy(vtk_mesh.GetCells().GetData()))
offsets = numpy.copy(
vtk.util.numpy_support.vtk_to_numpy(
vtk_mesh.GetCellLocationsArray()))
types = numpy.copy(
vtk.util.numpy_support.vtk_to_numpy(vtk_mesh.GetCellTypesArray()))
# `data` is a one-dimensional vector with
# (num_points0, p0, p1, ... ,pk, numpoints1, p10, p11, ..., p1k, ...
# Translate it into the cells dictionary.
cells = {}
for vtk_type, meshio_type in vtk_to_meshio_type.items():
# Get all offsets for vtk_type
os = offsets[numpy.argwhere(types == vtk_type).transpose()[0]]
num_cells = len(os)
if num_cells > 0:
if meshio_type == "polygon":
for idx_cell in range(num_cells):
num_pts = data[os[idx_cell]]
cell = data[os[idx_cell] + 1:os[idx_cell] + 1 +
num_pts]
key = meshio_type + str(num_pts)
if key in cells:
cells[key] = numpy.vstack([cells[key], cell])
else:
cells[key] = cell
else:
num_pts = data[os[0]]
# instantiate the array
arr = numpy.empty((num_cells, num_pts), dtype=int)
# store the num_pts entries after the offsets into the columns
# of arr
for k in range(num_pts):
arr[:, k] = data[os + k + 1]
cells[meshio_type] = arr
return cells
if filetype in ["vtk", "vtk-ascii", "vtk-binary"]:
reader = vtk.vtkUnstructuredGridReader()
reader.SetFileName(filename)
reader.SetReadAllNormals(1)
reader.SetReadAllScalars(1)
reader.SetReadAllTensors(1)
reader.SetReadAllVectors(1)
reader.Update()
vtk_mesh = reader.GetOutput()
elif filetype in ["vtu", "vtu-ascii", "vtu-binary"]:
reader = vtk.vtkXMLUnstructuredGridReader()
reader.SetFileName(filename)
reader.Update()
vtk_mesh = reader.GetOutput()
elif filetype in ["xdmf", "xdmf2"]:
reader = vtk.vtkXdmfReader()
reader.SetFileName(filename)
reader.SetReadAllColorScalars(1)
reader.SetReadAllFields(1)
reader.SetReadAllNormals(1)
reader.SetReadAllScalars(1)
reader.SetReadAllTCoords(1)
reader.SetReadAllTensors(1)
reader.SetReadAllVectors(1)
reader.Update()
vtk_mesh = reader.GetOutputDataObject(0)
elif filetype == "xdmf3":
reader = vtk.vtkXdmf3Reader()
reader.SetFileName(filename)
reader.SetReadAllColorScalars(1)
reader.SetReadAllFields(1)
reader.SetReadAllNormals(1)
reader.SetReadAllScalars(1)
reader.SetReadAllTCoords(1)
reader.SetReadAllTensors(1)
reader.SetReadAllVectors(1)
reader.Update()
vtk_mesh = reader.GetOutputDataObject(0)
else:
assert filetype == "exodus", "Unknown file type '{}'.".format(filename)
reader = vtk.vtkExodusIIReader()
reader.SetFileName(filename)
vtk_mesh = _read_exodusii_mesh(reader)
# Explicitly extract points, cells, point data, field data
points = numpy.copy(
numpy_support.vtk_to_numpy(vtk_mesh.GetPoints().GetData()))
cells = _read_cells(vtk_mesh)
point_data = _read_data(vtk_mesh.GetPointData())
field_data = _read_data(vtk_mesh.GetFieldData())
cell_data = _read_data(vtk_mesh.GetCellData())
# split cell_data by the cell type
cd = {}
index = 0
for cell_type in cells:
num_cells = len(cells[cell_type])
cd[cell_type] = {}
for name, array in cell_data.items():
cd[cell_type][name] = array[index:index + num_cells]
index += num_cells
cell_data = cd
return Mesh(points,
cells,
point_data=point_data,
cell_data=cell_data,
field_data=field_data)
def RunTest():
fail = False
print "TEST SET 1 - verify reader/writer work for range of canonical datasets"
print MemUsage("Before starting TEST SET 1")
dog = vtk.vtkDataObjectGenerator()
i = 0
for testObject in testObjects:
fileName = "xdmfIOtest_" + str(i)
print "Test vtk object", testObject
dog.SetProgram(testObject)
dog.Update()
TestXdmfConversion(dog.GetOutput(), fileName)
i += 1
print "TEST SET 2 - verify reader/writer work for Graphs"
print MemUsage("Before starting TEST SET 2")
print "Test Graph data"
gsrc = vtk.vtkRandomGraphSource()
gsrc.DirectedOn()
gsrc.Update()
gFilePrefix = "xdmfIOtest_Graph"
gFileName = OutputDir + gFilePrefix + ".xdmf"
ghFileName = OutputDir + gFilePrefix + ".h5"
xWriter = vtk.vtkXdmf3Writer()
xWriter.SetLightDataLimit(LightDataLimit)
xWriter.SetFileName(gFileName)
xWriter.SetInputConnection(0, gsrc.GetOutputPort(0))
timer.StartTimer()
xWriter.Write()
timer.StopTimer()
print "vtkXdmf3Writer took", timer.GetElapsedTime(), "seconds to write",\
gFileName
xReader = vtk.vtkXdmf3Reader()
xReader.SetFileName(gFileName)
xReader.Update()
rOutput = xReader.GetOutputDataObject(0)
fail = DoDataObjectsDiffer(gsrc.GetOutputDataObject(0),
xReader.GetOutputDataObject(0))
if fail:
raiseErrorAndExit("Failed graph conversion test")
if not DoFilesExist(gFileName, ghFileName, None, CleanUpGood):
raiseErrorAndExit("Failed to write Graph file")
print "TEST SET 3 - verify reader/writer handle time varying data"
print MemUsage("Before starting TEST SET 3")
print "Test temporal data"
tsrc = vtk.vtkTimeSourceExample()
tsrc.GrowingOn()
tsrc.SetXAmplitude(2.0)
tFilePrefix = "xdmfIOTest_Temporal"
tFileName = OutputDir + tFilePrefix + ".xdmf"
thFileName = OutputDir + tFilePrefix + ".h5"
xWriter = vtk.vtkXdmf3Writer()
xWriter.SetLightDataLimit(LightDataLimit)
xWriter.WriteAllTimeStepsOn()
xWriter.SetFileName(tFileName)
xWriter.SetInputConnection(0, tsrc.GetOutputPort(0))
timer.StartTimer()
xWriter.Write()
timer.StopTimer()
print "vtkXdmf3Writer took", timer.GetElapsedTime(), "seconds to write",\
tFileName
xReader = vtk.vtkXdmf3Reader()
xReader.SetFileName(tFileName)
xReader.UpdateInformation()
oi = xReader.GetOutputInformation(0)
timerange = oi.Get(vtk.vtkCompositeDataPipeline.TIME_STEPS())
ii = tsrc.GetOutputInformation(0)
correcttimes = ii.Get(vtk.vtkCompositeDataPipeline.TIME_STEPS())
#compare number of and values for temporal range
if len(timerange) != len(correcttimes):
print "timesteps failed"
print timerange, "!=", correcttimes
raiseErrorAndExit("Failed to get same times")
for i in xrange(0, len(correcttimes)):
if abs(abs(timerange[i]) - abs(correcttimes[i])) > 0.000001:
print "time result failed"
print timerange, "!=", correcttimes
raiseErrorAndExit("Failed to get same times")
#exercise temporal processing and compare geometric bounds at each tstep
indices = range(0, len(timerange)) + range(len(timerange) - 2, -1, -1)
for x in indices:
xReader.GetExecutive().SetUpdateTimeStep(0, timerange[x])
xReader.Update()
obds = xReader.GetOutputDataObject(0).GetBounds()
tsrc.GetExecutive().SetUpdateTimeStep(
0, timerange[x] + 0.0001) #workaround a precision bug in TSE
tsrc.Update()
ibds = tsrc.GetOutputDataObject(0).GetBounds()
print timerange[x], obds
for i in (0, 1, 2, 3, 4, 5):
if abs(abs(obds[i]) - abs(ibds[i])) > 0.000001:
print "time result failed"
print obds, "!=", ibds
raiseErrorAndExit("Failed to get same data for this timestep")
fail = DoFilesExist(tFileName, thFileName, None, CleanUpGood)
if not fail:
raiseErrorAndExit("Failed Temporal Test")
print MemUsage("End of Testing")
def read(filetype, filename):
# pylint: disable=import-error
import vtk
from vtk.util import numpy_support
def _read_data(data):
'''Extract numpy arrays from a VTK data set.
'''
# Go through all arrays, fetch data.
out = {}
for k in range(data.GetNumberOfArrays()):
array = data.GetArray(k)
if array:
array_name = array.GetName()
out[array_name] = numpy.copy(
vtk.util.numpy_support.vtk_to_numpy(array)
)
return out
def _read_cells(vtk_mesh):
data = numpy.copy(vtk.util.numpy_support.vtk_to_numpy(
vtk_mesh.GetCells().GetData()
))
offsets = numpy.copy(vtk.util.numpy_support.vtk_to_numpy(
vtk_mesh.GetCellLocationsArray()
))
types = numpy.copy(vtk.util.numpy_support.vtk_to_numpy(
vtk_mesh.GetCellTypesArray()
))
vtk_to_meshio_type = {
vtk.VTK_VERTEX: 'vertex',
vtk.VTK_LINE: 'line',
vtk.VTK_TRIANGLE: 'triangle',
vtk.VTK_QUAD: 'quad',
vtk.VTK_TETRA: 'tetra',
vtk.VTK_HEXAHEDRON: 'hexahedron',
vtk.VTK_WEDGE: 'wedge',
vtk.VTK_PYRAMID: 'pyramid'
}
# `data` is a one-dimensional vector with
# (num_points0, p0, p1, ... ,pk, numpoints1, p10, p11, ..., p1k, ...
# Translate it into the cells dictionary.
cells = {}
for vtk_type, meshio_type in vtk_to_meshio_type.items():
# Get all offsets for vtk_type
os = offsets[numpy.argwhere(types == vtk_type).transpose()[0]]
num_cells = len(os)
if num_cells > 0:
num_pts = data[os[0]]
# instantiate the array
arr = numpy.empty((num_cells, num_pts), dtype=int)
# sort the num_pts entries after the offsets into the columns
# of arr
for k in range(num_pts):
arr[:, k] = data[os+k+1]
cells[meshio_type] = arr
return cells
if filetype in ['vtk', 'vtk-ascii', 'vtk-binary']:
reader = vtk.vtkUnstructuredGridReader()
reader.SetFileName(filename)
reader.Update()
vtk_mesh = reader.GetOutput()
elif filetype in ['vtu', 'vtu-ascii', 'vtu-binary']:
reader = vtk.vtkXMLUnstructuredGridReader()
reader.SetFileName(filename)
reader.Update()
vtk_mesh = reader.GetOutput()
elif filetype in ['xdmf', 'xdmf2']:
reader = vtk.vtkXdmfReader()
reader.SetFileName(filename)
reader.Update()
vtk_mesh = reader.GetOutputDataObject(0)
elif filetype == 'xdmf3':
reader = vtk.vtkXdmf3Reader()
reader.SetFileName(filename)
reader.Update()
vtk_mesh = reader.GetOutputDataObject(0)
else:
assert filetype == 'exodus', \
'Unknown file type \'{}\'.'.format(filename)
reader = vtk.vtkExodusIIReader()
reader.SetFileName(filename)
vtk_mesh = _read_exodusii_mesh(reader)
# Explicitly extract points, cells, point data, field data
points = numpy.copy(numpy_support.vtk_to_numpy(
vtk_mesh.GetPoints().GetData()
))
cells = _read_cells(vtk_mesh)
point_data = _read_data(vtk_mesh.GetPointData())
field_data = _read_data(vtk_mesh.GetFieldData())
cell_data = _read_data(vtk_mesh.GetCellData())
# split cell_data by the cell type
cd = {}
index = 0
for cell_type in cells:
num_cells = len(cells[cell_type])
cd[cell_type] = {}
for name, array in cell_data.items():
cd[cell_type][name] = array[index:index+num_cells]
index += num_cells
cell_data = cd
return points, cells, point_data, cell_data, field_data
def RunTest():
fail = False
print "TEST SET 1 - verify reader/writer work for range of canonical datasets"
print MemUsage("Before starting TEST SET 1")
dog = vtk.vtkDataObjectGenerator()
i = 0
for testObject in testObjects:
fileName = "xdmfIOtest_" + str(i)
print "Test vtk object", testObject
dog.SetProgram(testObject)
dog.Update()
TestXdmfConversion(dog.GetOutput(), fileName)
i += 1
print "TEST SET 2 - verify reader/writer work for Graphs"
print MemUsage("Before starting TEST SET 2")
print "Test Graph data"
gsrc = vtk.vtkRandomGraphSource()
gsrc.DirectedOn()
gsrc.Update()
gFilePrefix = "xdmfIOtest_Graph"
gFileName = OutputDir + gFilePrefix + ".xdmf"
ghFileName = OutputDir + gFilePrefix + ".h5"
xWriter = vtk.vtkXdmf3Writer()
xWriter.SetLightDataLimit(LightDataLimit)
xWriter.SetFileName(gFileName)
xWriter.SetInputConnection(0, gsrc.GetOutputPort(0))
timer.StartTimer()
xWriter.Write()
timer.StopTimer()
print "vtkXdmf3Writer took", timer.GetElapsedTime(), "seconds to write",\
gFileName
xReader = vtk.vtkXdmf3Reader()
xReader.SetFileName(gFileName)
xReader.Update()
rOutput = xReader.GetOutputDataObject(0)
fail = DoDataObjectsDiffer(gsrc.GetOutputDataObject(0), xReader.GetOutputDataObject(0))
if fail:
raiseErrorAndExit("Failed graph conversion test")
if not DoFilesExist(gFileName, ghFileName, None, CleanUpGood):
raiseErrorAndExit("Failed to write Graph file")
print "TEST SET 3 - verify reader/writer handle time varying data"
print MemUsage("Before starting TEST SET 3")
print "Test temporal data"
tsrc = vtk.vtkTimeSourceExample()
tsrc.GrowingOn()
tsrc.SetXAmplitude(2.0)
tFilePrefix = "xdmfIOTest_Temporal"
tFileName = OutputDir + tFilePrefix + ".xdmf"
thFileName = OutputDir + tFilePrefix + ".h5"
xWriter = vtk.vtkXdmf3Writer()
xWriter.SetLightDataLimit(LightDataLimit)
xWriter.WriteAllTimeStepsOn()
xWriter.SetFileName(tFileName)
xWriter.SetInputConnection(0, tsrc.GetOutputPort(0))
timer.StartTimer()
xWriter.Write()
timer.StopTimer()
print "vtkXdmf3Writer took", timer.GetElapsedTime(), "seconds to write",\
tFileName
xReader = vtk.vtkXdmf3Reader()
xReader.SetFileName(tFileName)
xReader.UpdateInformation()
oi = xReader.GetOutputInformation(0)
timerange = oi.Get(vtk.vtkCompositeDataPipeline.TIME_STEPS())
ii = tsrc.GetOutputInformation(0)
correcttimes = ii.Get(vtk.vtkCompositeDataPipeline.TIME_STEPS())
#compare number of and values for temporal range
if len(timerange) != len(correcttimes):
print "timesteps failed"
print timerange, "!=", correcttimes
raiseErrorAndExit("Failed to get same times")
for i in xrange(0, len(correcttimes)):
if abs(abs(timerange[i])-abs(correcttimes[i])) > 0.000001:
print "time result failed"
print timerange, "!=", correcttimes
raiseErrorAndExit("Failed to get same times")
#exercise temporal processing and compare geometric bounds at each tstep
indices = range(0,len(timerange)) + range(len(timerange)-2,-1,-1)
for x in indices:
xReader.UpdateTimeStep(timerange[x])
obds = xReader.GetOutputDataObject(0).GetBounds()
tsrc.Update(timerange[x]+0.0001) #workaround a precision bug in TSE
ibds = tsrc.GetOutputDataObject(0).GetBounds()
print timerange[x], obds
for i in (0,1,2,3,4,5):
if abs(abs(obds[i])-abs(ibds[i])) > 0.000001:
print "time result failed"
print obds, "!=", ibds
raiseErrorAndExit("Failed to get same data for this timestep")
fail = DoFilesExist(tFileName, thFileName, None, CleanUpGood)
if not fail:
raiseErrorAndExit("Failed Temporal Test")
print MemUsage("End of Testing")
