コード例 #1
0
ファイル: legacy_writer.py プロジェクト: gdmcbain/meshio
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
コード例 #2
0
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
コード例 #3
0
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)
コード例 #4
0
ファイル: VToXLoop.py プロジェクト: aeslaughter/VTK
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)
コード例 #5
0
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")
コード例 #6
0
ファイル: vtk_io.py プロジェクト: nasseralkmim/meshio
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
コード例 #7
0
ファイル: VToXLoop.py プロジェクト: aeslaughter/VTK
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")