def _get_writer(filetype, filename):
import vtk
if filetype in "vtk-ascii":
logging.warning("VTK ASCII files are only meant for debugging.")
writer = vtk.vtkUnstructuredGridWriter()
writer.SetFileTypeToASCII()
elif filetype == "vtk-binary":
writer = vtk.vtkUnstructuredGridWriter()
writer.SetFileTypeToBinary()
elif filetype == "vtu-ascii":
logging.warning("VTU ASCII files are only meant for debugging.")
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetDataModeToAscii()
elif filetype == "vtu-binary":
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetDataModeToBinary()
elif filetype == "xdmf2":
writer = vtk.vtkXdmfWriter()
elif filetype == "xdmf3":
writer = vtk.vtkXdmf3Writer()
else:
assert filetype == "exodus", "Unknown file type '{}'.".format(filename)
writer = vtk.vtkExodusIIWriter()
# if the mesh contains vtkmodeldata information, make use of it
# and write out all time steps.
writer.WriteAllTimeStepsOn()
return writer
def _get_writer(filetype, filename):
import vtk
if filetype in "vtk-ascii":
logging.warning("VTK ASCII files are only meant for debugging.")
writer = vtk.vtkUnstructuredGridWriter()
writer.SetFileTypeToASCII()
elif filetype == "vtk-binary":
writer = vtk.vtkUnstructuredGridWriter()
writer.SetFileTypeToBinary()
elif filetype == "vtu-ascii":
logging.warning("VTU ASCII files are only meant for debugging.")
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetDataModeToAscii()
elif filetype == "vtu-binary":
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetDataModeToBinary()
elif filetype == "xdmf2":
writer = vtk.vtkXdmfWriter()
elif filetype == "xdmf3":
writer = vtk.vtkXdmf3Writer()
else:
assert filetype == "exodus", "Unknown file type '{}'.".format(filename)
writer = vtk.vtkExodusIIWriter()
# if the mesh contains vtkmodeldata information, make use of it
# and write out all time steps.
writer.WriteAllTimeStepsOn()
return writer
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)
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 write(filetype,
filename,
points,
cells,
point_data=None,
cell_data=None,
field_data=None
):
# pylint: disable=import-error
import vtk
def _create_vtkarray(X, name):
array = vtk.util.numpy_support.numpy_to_vtk(X, deep=1)
array.SetName(name)
return array
point_data = {} if point_data is None else point_data
cell_data = {} if cell_data is None else cell_data
field_data = {} if field_data is None else field_data
# assert data integrity
for key in point_data:
assert len(point_data[key]) == len(points), \
'Point data mismatch.'
for key in cell_data:
assert key in cells, 'Cell data without cell'
for key2 in cell_data[key]:
assert len(cell_data[key][key2]) == len(cells[key]), \
'Cell data mismatch.'
vtk_mesh = _generate_vtk_mesh(points, cells)
# add point data
pd = vtk_mesh.GetPointData()
for name, X in point_data.items():
# There is a naming inconsistency in VTK when it comes to multivectors
# in Exodus files:
# If a vector 'v' has two components, they are called 'v_x', 'v_y'
# (note the underscore), if it has three, then they are called 'vx',
# 'vy', 'vz'. See bug <http://www.vtk.org/Bug/view.php?id=15894>.
# For VT{K,U} files, no underscore is ever added.
pd.AddArray(_create_vtkarray(X, name))
# Add cell data.
# The cell_data is structured like
#
# cell_type ->
# key -> array
# key -> array
# [...]
# cell_type ->
# key -> array
# key -> array
# [...]
# [...]
#
# VTK expects one array for each `key`, so assemble the keys across all
# mesh_types. This requires each key to be present for each mesh_type, of
# course.
all_keys = []
for cell_type in cell_data:
all_keys += cell_data[cell_type].keys()
# create unified cell data
for key in all_keys:
for cell_type in cell_data:
assert key in cell_data[cell_type]
unified_cell_data = {
key: numpy.concatenate([
cell_data[cell_type][key]
for cell_type in cell_data
])
for key in all_keys
}
# add the array data to the mesh
cd = vtk_mesh.GetCellData()
for name, array in unified_cell_data.items():
cd.AddArray(_create_vtkarray(array, name))
# add field data
fd = vtk_mesh.GetFieldData()
for key, value in field_data.items():
fd.AddArray(_create_vtkarray(value, key))
if filetype in 'vtk-ascii':
logging.warning('ASCII files are only meant for debugging.')
writer = vtk.vtkUnstructuredGridWriter()
writer.SetFileTypeToASCII()
elif filetype == 'vtk-binary':
writer = vtk.vtkUnstructuredGridWriter()
writer.SetFileTypeToBinary()
elif filetype == 'vtu-ascii':
logging.warning('ASCII files are only meant for debugging.')
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetDataModeToAscii()
elif filetype == 'vtu-binary':
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetDataModeToBinary()
elif filetype == 'xdmf':
writer = vtk.vtkXdmfWriter()
elif filetype == 'xdmf3':
writer = vtk.vtkXdmf3Writer()
else:
assert filetype == 'exodus', \
'Unknown file type \'{}\'.'.format(filename)
writer = vtk.vtkExodusIIWriter()
# if the mesh contains vtkmodeldata information, make use of it
# and write out all time steps.
writer.WriteAllTimeStepsOn()
writer.SetFileName(filename)
try:
writer.SetInput(vtk_mesh)
except AttributeError:
writer.SetInputData(vtk_mesh)
writer.Write()
return
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")