예제 #1
0
def compare_files_vtu(first_file, second_file, file_type, tolerance=1e-12):
    import vtk

    # read files:
    if file_type == "vtu":
        reader1 = vtk.vtkXMLUnstructuredGridReader()
        reader2 = vtk.vtkXMLUnstructuredGridReader()
    else:
        reader1 = vtk.vtkXMLPUnstructuredGridReader()
        reader2 = vtk.vtkXMLPUnstructuredGridReader()

    reader1.SetFileName(first_file)
    reader1.Update()
    output1 = reader1.GetOutput()

    reader2.SetFileName(second_file)
    reader2.Update()
    output2 = reader2.GetOutput()

    # check fidelity
    point_data1 = output1.GetPointData()
    point_data2 = output2.GetPointData()

    # verify same number of PointData arrays in both files
    if point_data1.GetNumberOfArrays() != point_data2.GetNumberOfArrays():
        print("File 1:", point_data1.GetNumberOfArrays(), "\n", "File 2:",
              point_data2.GetNumberOfArrays())
        raise ValueError("Fidelity test failed: Mismatched data array count")

    for i in range(point_data1.GetNumberOfArrays()):
        arr1 = point_data1.GetArray(i)
        arr2 = point_data2.GetArray(i)

        # verify both files contain same arrays
        if point_data1.GetArrayName(i) != point_data2.GetArrayName(i):
            print("File 1:", point_data1.GetArrayName(i), "\n", "File 2:",
                  point_data2.GetArrayName(i))
            raise ValueError(
                "Fidelity test failed: Mismatched data array names")

        # verify arrays are same sizes in both files
        if arr1.GetSize() != arr2.GetSize():
            print("File 1, DataArray", i, ":", arr1.GetSize(), "\n",
                  "File 2, DataArray", i, ":", arr2.GetSize())
            raise ValueError(
                "Fidelity test failed: Mismatched data array sizes")

        # verify individual values w/in given tolerance
        for j in range(arr1.GetSize()):
            if abs(arr1.GetValue(j) - arr2.GetValue(j)) > tolerance:
                print("Tolerance:", tolerance)
                raise ValueError(
                    "Fidelity test failed: Mismatched data array values with given tolerance"
                )

    print("VTU Fidelity test completed successfully with tolerance", tolerance)
예제 #2
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    def scalar(self):
        pass
        '''
        '''
        #self.scalar= scalar

        # define reader for pvtu, set timestape
        xmlReader = vtk.vtkXMLPUnstructuredGridReader()
        xmlReader.SetFileName(self.fname)
        xmlReader.Update()

        # number of arrays
        narrays = xmlReader.GetOutput().GetPointData().GetNumberOfArrays()
        # number of partitions
        npartition = xmlReader.GetNumberOfPieces()
        output = xmlReader.GetOutput()
        xmlReader.Update()

        self.dict_scalars = {}

        for i in range(narrays):

            self.dict_scalars[i] = xmlReader.GetPointArrayName(i)

        print(self.dict_scalars)

        return self.dict_scalars

        def reader(self):
            pass

        xmlReader = vtk.vtkXMLPUnstructuredGridReader()
        xmlReader.SetFileName(self.path_timestep)
        xmlReader.Update()
        narrays = xmlReader.GetOutput().GetPointData().GetNumberOfArrays()
        output = xmlReader.GetOutput()
        xmlReader.Update()
        npartition = xmlReader.GetNumberOfPieces()

        dict_var = {}

        for i in range(narrays):

            dict_var[i] = xmlReader.GetPointArrayName(i)

        self.velocity = vtk_to_numpy(
            xmlReader.GetOutput().GetPointData().GetArray(19))

        print(dict_var)
        print(narrays)
        print(npartition)
예제 #3
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    def __init__(self,offset,get=1,file='data',type='vtu',mirrorPlane=None,silent=0):
        self.offset=offset
        self.filenameout = file
        self.type = type
        self.isLoaded = False
        self.mirrorPlane=mirrorPlane
        self.silent = silent

        if type == 'vtu':
            self.filename=''.join([self.filenameout,repr(offset).zfill(4),'.vtu'])
            self.datareader = v.vtkXMLUnstructuredGridReader()
        elif type == 'pvtu':
            self.filename=''.join([self.filenameout,repr(offset).zfill(4),'.pvtu'])
            self.datareader = v.vtkXMLPUnstructuredGridReader()
        elif type == 'vti':
            self.filename=''.join([self.filenameout,repr(offset).zfill(4),'.vti'])
            self.datareader = v.vtkXMLImageDataReader()
        else:
            print 'Unknown filetype'
            
        if (self.silent == 0): print '========================================'
        if (self.silent == 0): print  'loading file %s' % (self.filename)

        if get != None:
            self.getAll()
 def __init__(self, module_manager):
     SimpleVTKClassModuleBase.__init__(
         self, module_manager,
         vtk.vtkXMLPUnstructuredGridReader(), 'Reading vtkXMLPUnstructuredGrid.',
         (), ('vtkXMLPUnstructuredGrid',),
         replaceDoc=True,
         inputFunctions=None, outputFunctions=None)
예제 #5
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    def read_vertical_heatflux(self, n, verbose=False, **kwargs):
        if not (hasattr(self, 'snames')):
            self.get_solution_filenames(verbose=verbose)

        if self.mesh_file != self.mnames[n]:
            self.read_mesh(n, verbose=verbose)

        filename = self.directory + self.snames[n]
        if verbose:
            print("Reading vertical heat flux from", filename)

        if self.format == 'hdf5':
            f = h5py.File(filename, "r")
            Fz_data = f['vertical_heat_flux']
            Fz = Fz_data[:, 0]

        if self.format == 'vtu':
            reader = vtk.vtkXMLPUnstructuredGridReader()
            reader.SetFileName(filename)
            reader.Update()
            my_vtk_array = reader.GetOutput().GetPointData().GetArray(
                "vertical_heat_flux")
            Fz = vtk_to_numpy(my_vtk_array)
        #             print('loaded shape', np.shape(T))

        Fz = Fz[self.indices]
        Fz.shape = self.array_shape

        #         print('final shape', np.shape(Fz))
        return self.x, self.y, self.z, Fz
예제 #6
0
파일: vtkio.py 프로젝트: paralab/GRVis
def ReadPVTUFile(fname):

    reader = vtk.vtkXMLPUnstructuredGridReader()
    reader.SetFileName(fname)
    reader.Update()
    #print reader.GetNumberOfPieces()
    return reader
예제 #7
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 def __init__(self, filename=None):
     """Creates a vtu object by reading the specified file."""
     if filename is None:
         self.ugrid = vtk.vtkUnstructuredGrid()
     else:
         self.gridreader = None
         if filename[-4:] == ".vtu":
             self.gridreader = vtk.vtkXMLUnstructuredGridReader()
         elif filename[-5:] == ".pvtu":
             self.gridreader = vtk.vtkXMLPUnstructuredGridReader()
         else:
             raise Exception("ERROR: don't recognise file extension" +
                             filename)
         self.gridreader.SetFileName(filename)
         self.gridreader.Update()
         self.ugrid = self.gridreader.GetOutput()
         self.points = self.ugrid.GetPoints()
         self.pointdata = self.ugrid.GetPointData()
         self.cells = self.ugrid.GetCells()
         self.celldata = self.ugrid.GetCellData()
         if self.ugrid.GetNumberOfPoints() + self.ugrid.GetNumberOfCells(
         ) == 0:
             raise Exception(
                 "ERROR: No points or cells found after loading vtu " +
                 filename)
     self._coords = None
     self.filename = filename
     self._data_dict = {}
     self._rawdata_dict = {}
     self._rawcelldata_dict = {}
     self._raw_coords = None
예제 #8
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def load_vtk_mesh(fileName):
    """
    Loads surface/volume mesh to VTK
    """
    if (fileName == ''):
        return 0
    fn_dir, fn_ext = os.path.splitext(fileName)
    if (fn_ext == '.vtk'):
        print('Reading vtk with name: ', fileName)
        reader = vtk.vtkPolyDataReader()
    elif (fn_ext == '.vtp'):
        print('Reading vtp with name: ', fileName)
        reader = vtk.vtkXMLPolyDataReader()
    elif (fn_ext == '.stl'):
        print('Reading stl with name: ', fileName)
        reader = vtk.vtkSTLReader()
    elif (fn_ext == '.obj'):
        print('Reading obj with name: ', fileName)
        reader = vtk.vtkOBJReader()
    elif (fn_ext == '.vtu'):
        print('Reading vtu with name: ', fileName)
        reader = vtk.vtkXMLUnstructuredGridReader()
    elif (fn_ext == '.pvtu'):
        print('Reading pvtu with name: ', fileName)
        reader = vtk.vtkXMLPUnstructuredGridReader()
    else:
        print(fn_ext)
        raise ValueError('File extension not supported')

    reader.SetFileName(fileName)
    reader.Update()
    return reader.GetOutput()
예제 #9
0
def get_pointdata(offset,filenameout='data',type='pvtu',attribute_mode='cell'):

    if type == 'vtu':
        filename=''.join([filenameout,repr(offset).zfill(4),'.vtu'])
        datareader = v.vtkXMLUnstructuredGridReader()
    elif type == 'pvtu':
        filename=''.join([filenameout,repr(offset).zfill(4),'.pvtu'])
        datareader = v.vtkXMLPUnstructuredGridReader()
        
    print '=== Reading ',filename,' ==='
        
    datareader.SetFileName(filename)
    datareader.Update()
    data = datareader.GetOutput()

    if attribute_mode == 'cell':
        c2p = v.vtkCellDataToPointData()
        c2p.SetInput(data)
        pointdata=c2p.GetOutput()
        pointdata.Update()
    else:
        pointdata = data 


    vtk_points=data.GetPoints().GetData()
    points=ah.vtk2array(vtk_points)
 
    print '=== Done with reading data! ==='
    return {'pointdata': pointdata, 'points': points}
예제 #10
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 def ReadVTKXMLPMeshFile(self):
     if (self.InputFileName == ''):
         self.PrintError('Error: no InputFileName.')
     self.PrintLog('Reading VTK XML Parallel format mesh file.')
     reader = vtk.vtkXMLPUnstructuredGridReader()
     reader.SetFileName(self.InputFileName)
     reader.Update()
     self.Mesh = reader.GetOutput()
예제 #11
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    def read_mesh(self, n, verbose=False):
        if not (hasattr(self, 'snames')):
            self.get_solution_filenames(verbose=verbose)

        # if self.format=='hdf5':
        #    mesh_filename = self.directory+"mesh-00000.h5"
        # if self.format=='vtu':
        #    mesh_filename = self.directory+"solution-09999.pvtu"
        mesh_filename = self.directory + self.mnames[n]
        self.mesh_file = self.mnames[n]

        if verbose:
            print("Reading mesh from", mesh_filename)

        if self.format == 'hdf5':
            mesh_file = h5py.File(mesh_filename, "r")
            nodes_data = mesh_file['nodes']
            coords = nodes_data[:, :]

        if self.format == 'vtu':
            reader = vtk.vtkXMLPUnstructuredGridReader()
            reader.SetFileName(mesh_filename)
            reader.Update()
            my_vtk_array = reader.GetOutput().GetPointData().GetArray("T")
            nodes_vtk_array = reader.GetOutput().GetPoints().GetData()
            coords = vtk_to_numpy(nodes_vtk_array)

        # Just collect unique rows (duplication due to parallel files)
        coords = coords.round(decimals=14)
        # idx = unique_rows_indices(coords)
        u, idx = np.unique(coords, axis=0, return_index=True)

        ind = np.lexsort((coords[idx, 2], coords[idx, 1], coords[idx, 0]))
        self.indices = idx[ind]
        self.coords = coords[self.indices, :]

        xm = self.coords[:, 0]
        ym = self.coords[:, 1]
        zm = self.coords[:, 2]

        xu = np.unique(xm)
        yu = np.unique(ym)
        zu = np.unique(zm)

        self.x, self.y, self.z = xu, yu, zu

        nx, ny, nz = len(self.x), len(self.y), len(self.z)

        self.array_shape = (nx, ny, nz)
        xm.shape = self.array_shape
        ym.shape = self.array_shape
        zm.shape = self.array_shape

        self.xm = xm
        self.ym = ym
        self.zm = zm

        return self.x, self.y, self.z
 def __init__(self, module_manager):
     SimpleVTKClassModuleBase.__init__(self,
                                       module_manager,
                                       vtk.vtkXMLPUnstructuredGridReader(),
                                       'Reading vtkXMLPUnstructuredGrid.',
                                       (), ('vtkXMLPUnstructuredGrid', ),
                                       replaceDoc=True,
                                       inputFunctions=None,
                                       outputFunctions=None)
def get_numpy_arrays(t):

    # Load modules
    import vtk as vtk
    from vtk.util import numpy_support

    # Get pvtu number
    pvtu_number = get_pvtu_number(time_steps[t])

    # Load vtu data (pvtu directs to vtu files)
    reader = vtk.vtkXMLPUnstructuredGridReader()
    reader.SetFileName(vtk_directory + 'solution-' + pvtu_number + '.pvtu')
    reader.Update()

    # Get the coordinates of nodes in the mesh
    nodes_vtk_array = reader.GetOutput().GetPoints().GetData()

    # Convert nodal vtk data to a numpy array
    nodes_numpy_array = vtk.util.numpy_support.vtk_to_numpy(nodes_vtk_array)

    # Extract x, y and z coordinates from numpy array
    x, y, z = nodes_numpy_array[:,
                                0], nodes_numpy_array[:,
                                                      1], nodes_numpy_array[:,
                                                                            2]

    # Determine the number of scalar fields contained in the .pvtu file
    number_of_fields = reader.GetOutput().GetPointData().GetNumberOfArrays()

    # Determine the name of each field and place it in an array.
    field_names = []
    for i in range(number_of_fields):
        field_names.append(reader.GetOutput().GetPointData().GetArrayName(i))

    # Determine the index of the temperature field
    idx = field_names.index("T")

    # Extract values of temperature
    field_vtk_array = reader.GetOutput().GetPointData().GetArray(idx)
    temperature = numpy_support.vtk_to_numpy(field_vtk_array)

    # Determine the index of the pressure field
    idx = field_names.index("p")

    # Extract values of pressure
    field_vtk_array = reader.GetOutput().GetPointData().GetArray(idx)
    pressure = numpy_support.vtk_to_numpy(field_vtk_array)

    # Save unfiltered (raw vtk) arrays
    np.savez(results_directory + '/' + 'unfiltered_' + pvtu_number,
             x=x,
             y=y,
             z=z,
             temperature=temperature,
             pressure=pressure)

    return x, y, z, temperature, pressure
예제 #14
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 def __init__(self, bodypoints, geoname, AutomaticFile, AutomaticVTU_Number, 
              parallel, U0 = None, p0 = None, rho0 = None):
     """
     Read vtu/pvtu file and geo file, set basic information.
     
     """
     self.bodypoints = bodypoints
     self.geoname = geoname
     self.AutomaticFile = AutomaticFile
     self.AutomaticVTU_Number = AutomaticVTU_Number
     self.parallel = parallel
     self.U0 = U0
     self.p0 = p0
     self.rho0 = rho0
     
     # Reading *.vtu/*.pvtu file
     if (len(sys.argv)>1):
         filename   = sys.argv[1]
         vtu_number = int(sys.argv[2])
     else:
         filename = self.AutomaticFile
         vtu_number = int(self.AutomaticVTU_Number)
     if parallel == True:
         reader = vtk.vtkXMLPUnstructuredGridReader()
         reader.SetFileName(filename+'_'+str(vtu_number)+'.pvtu')
     elif parallel == False:
         reader = vtk.vtkXMLUnstructuredGridReader()
         reader.SetFileName(filename+'_'+str(vtu_number)+'.vtu')
     self.reader = reader
 
     # Read *.geo file
     info = []
     infile = open(self.geoname, "rb")
     for line in infile:
         if line.split()[0] != 'Point':
             break
         words = line.split('{')[1].split('}')[0].split(', ')
         
         nums = []
         for i in range(3):
             num = float(words[i])
             nums.append(num)
         info.append(nums)
     arrays = np.array(info)
     
     self.c0 = arrays[0]
     r = abs(arrays[1, 0] - self.c0[0])
     #r = sum(abs(arrays[1:self.bodypoints + 1, 0] - self.c0[0]))/self.bodypoints 
     self.D = 2 * r
     geolen = []
     for i in range(3):
         geolen.append(max(arrays[:,i]))
     self.geolen = np.array(geolen)
예제 #15
0
파일: read.py 프로젝트: OVGULIU/amrvac
    def __init__(self,
                 offset,
                 get=1,
                 file='data',
                 type='vtu',
                 mirrorPlane=None,
                 rotateX=0,
                 rotateY=0,
                 rotateZ=0,
                 scaleX=1,
                 scaleY=1,
                 scaleZ=1,
                 silent=0):
        self.offset = offset
        self.filenameout = file
        self.type = type
        self.isLoaded = False
        self.mirrorPlane = mirrorPlane
        self.silent = silent

        self.rotateX = rotateX
        self.rotateY = rotateY
        self.rotateZ = rotateZ

        self.scaleX = scaleX
        self.scaleY = scaleY
        self.scaleZ = scaleZ

        if type == 'vtu':
            self.filename = ''.join(
                [self.filenameout,
                 repr(offset).zfill(4), '.vtu'])
            self.datareader = v.vtkXMLUnstructuredGridReader()
        elif type == 'pvtu':
            self.filename = ''.join(
                [self.filenameout,
                 repr(offset).zfill(4), '.pvtu'])
            self.datareader = v.vtkXMLPUnstructuredGridReader()
        elif type == 'vti':
            self.filename = ''.join(
                [self.filenameout,
                 repr(offset).zfill(4), '.vti'])
            self.datareader = v.vtkXMLImageDataReader()
        else:
            print('Unknown filetype')

        if (self.silent == 0):
            print('========================================')
        if (self.silent == 0): print('loading file %s' % (self.filename))

        if get is not None:
            self.getAll()
예제 #16
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def vtu_values(offset,varname,filenameout='data',attribute_mode='cell',type='vtu'):

    if type == 'vtu':
        filename=''.join([filenameout,repr(offset).zfill(4),'.vtu'])
        datareader = v.vtkXMLUnstructuredGridReader()
    elif type == 'pvtu':
        filename=''.join([filenameout,repr(offset).zfill(4),'.pvtu'])
        datareader = v.vtkXMLPUnstructuredGridReader()
        
    datareader.SetFileName(filename)
    datareader.Update()
    data = datareader.GetOutput()
    
    return read.extract(data,varname,attribute_mode=attribute_mode)
예제 #17
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def read_ugrid(filename):
    if filename.endswith(".pvtu"):
        reader = vtk.vtkXMLPUnstructuredGridReader()
    elif filename.endswith(".vtk"):
        reader = vtk.vtkUnstructuredGridReader()
    elif filename.endswith(".vtu"):
        reader = vtk.vtkUnstructuredGridReader()
    else:
        raise BaseException("Illegal filename suffix %s" % filename)

    reader.SetFileName(filename)
    reader.Update()

    return reader.GetOutput()
def read_ugrid(filename):
    if filename.endswith(".pvtu"):
        reader = vtk.vtkXMLPUnstructuredGridReader()
    elif filename.endswith(".vtk"):
        reader = vtk.vtkUnstructuredGridReader()
    elif filename.endswith(".vtu"):
        reader = vtk.vtkUnstructuredGridReader()
    else:
        raise BaseException("Illegal filename suffix %s" % filename)

    reader.SetFileName(filename)
    reader.Update()

    return reader.GetOutput()
예제 #19
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def _read_single(filename, vtk_type=None):
    vtk_type = vtk_type or _get_vtk_type(filename)
    if vtk_type == 'UnstructuredGrid':
        reader = vtk.vtkXMLUnstructuredGridReader()
    elif vtk_type == 'PUnstructuredGrid':
        reader = vtk.vtkXMLPUnstructuredGridReader()
    else:
        raise NotImplementedError(
            f"VTK Files of type {vtk_type} can not yet be processed")
    reader.SetFileName(filename)
    reader.Update()
    geometryFilter = vtk.vtkGeometryFilter()
    geometryFilter.SetInputData(reader.GetOutput())
    geometryFilter.Update()
    return geometryFilter.GetOutput()
예제 #20
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def vtu_points(offset,filenameout='data',type='vtu'):

    if type == 'vtu':
        filename=''.join([filenameout,repr(offset).zfill(4),'.vtu'])
        datareader = v.vtkXMLUnstructuredGridReader()
    elif type == 'pvtu':
        filename=''.join([filenameout,repr(offset).zfill(4),'.pvtu'])
        datareader = v.vtkXMLPUnstructuredGridReader()

    datareader.SetFileName(filename)
    datareader.Update()
    data = datareader.GetOutput()
    
    vtk_points=data.GetPoints().GetData()
    points=ah.vtk2array(vtk_points)
    return points
예제 #21
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    def readData(self):
      
        if self.type == 'vtu':
            filename=''.join([self.filenameout,repr(self.offset).zfill(4),'.vtu'])
            datareader = v.vtkXMLUnstructuredGridReader()
        elif self.type == 'pvtu':
            filename=''.join([self.filenameout,repr(self.offset).zfill(4),'.pvtu'])
            datareader = v.vtkXMLPUnstructuredGridReader()

        print '=== Reading ',filename,' ==='

        datareader.SetFileName(filename)
        datareader.Update()
        self.data = datareader.GetOutput()
        vtk_points=self.data.GetPoints().GetData()
        self.points=ah.vtk2array(vtk_points)
예제 #22
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def readXMLPUGrid(mesh_file_name, verbose=True):
    if (verbose): print '*** readXMLPUGrid ***'

    mesh_reader = vtk.vtkXMLPUnstructuredGridReader()
    mesh_reader.SetFileName(mesh_file_name)
    mesh_reader.Update()
    mesh = mesh_reader.GetOutput()

    if (verbose):
        nb_points = mesh.GetNumberOfPoints()
        print 'nb_points =', nb_points

        nb_cells = mesh.GetNumberOfCells()
        print 'nb_cells =', nb_cells

    return mesh
예제 #23
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def vtu_points(offset, filenameout='data', type='vtu'):

    if type == 'vtu':
        filename = ''.join([filenameout, repr(offset).zfill(4), '.vtu'])
        datareader = v.vtkXMLUnstructuredGridReader()
    elif type == 'pvtu':
        filename = ''.join([filenameout, repr(offset).zfill(4), '.pvtu'])
        datareader = v.vtkXMLPUnstructuredGridReader()

    datareader.SetFileName(filename)
    datareader.Update()
    data = datareader.GetOutput()

    vtk_points = data.GetPoints().GetData()
    points = ah.vtk2array(vtk_points)
    return points
예제 #24
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 def __init__(self, filename = None):
   """Creates a vtu object by reading the specified file."""
   if filename is None:
     self.ugrid = vtk.vtkUnstructuredGrid()
   else:
     self.gridreader = None
     if filename[-4:] == ".vtu":
       self.gridreader=vtk.vtkXMLUnstructuredGridReader()
     elif filename[-5:] == ".pvtu":
       self.gridreader=vtk.vtkXMLPUnstructuredGridReader()
     else:
       raise Exception("ERROR: don't recognise file extension" + filename)
     self.gridreader.SetFileName(filename)
     self.gridreader.Update()
     self.ugrid=self.gridreader.GetOutput()
     if self.ugrid.GetNumberOfPoints() + self.ugrid.GetNumberOfCells() == 0:
       raise Exception("ERROR: No points or cells found after loading vtu " + filename)
   self.filename=filename
예제 #25
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def vtu_values(offset,
               varname,
               filenameout='data',
               attribute_mode='cell',
               type='vtu'):

    if type == 'vtu':
        filename = ''.join([filenameout, repr(offset).zfill(4), '.vtu'])
        datareader = v.vtkXMLUnstructuredGridReader()
    elif type == 'pvtu':
        filename = ''.join([filenameout, repr(offset).zfill(4), '.pvtu'])
        datareader = v.vtkXMLPUnstructuredGridReader()

    datareader.SetFileName(filename)
    datareader.Update()
    data = datareader.GetOutput()

    return read.extract(data, varname, attribute_mode=attribute_mode)
예제 #26
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    def Contour(self, val):
        parallel = False
        if self.vtuname.endswith(".pvtu"):
            parallel = True
        # NAME OF THE VARIABLE YOU WANT TO EXTRACT DATA FROM
        path = self.path
        data_name_field = self.field
        # Initial
        if (parallel == True):
            reader = vtk.vtkXMLPUnstructuredGridReader()
        else:
            reader = vtk.vtkXMLUnstructuredGridReader()
        reader.SetFileName(self.path + self.vtuname)
        reader.Update()

        field = []
        coords = []
        X = []
        Y = []
        ugrid = reader.GetOutput()
        ugrid.GetPointData().SetActiveScalars(data_name_field)

        Contour = vtk.vtkContourFilter()
        Contour.SetInputData(ugrid)
        Contour.SetNumberOfContours(1)
        Contour.SetValue(0, val)
        Contour.Update()
        # Fields=Contour.GetOutputDataObject(0)
        CContour = Contour.GetOutput()

        num = CContour.GetNumberOfPoints()
        print(num)
        for i in range(num):
            #field.append(CContour.GetPointData().GetScalars().GetTuple3(i))
            coords.append(CContour.GetPoints().GetData().GetTuple3(i))
            X.append(float(coords[i][0]))
            Y.append(float(coords[i][1]))
            # for i in range(0,4000):
        #      field.append(Contour.GetPointData().GetScalars().GetTuple3(i))

        # plt.plot(np.unique(Y), np.poly1d(np.polyfit(Y, X, 25))(np.unique(Y)))
        #

        return coords, X, Y
예제 #27
0
def load(offset, filenameout='data', type='pvtu'):
    if type == 'vtu':
        filename = ''.join([filenameout, repr(offset).zfill(4), '.vtu'])
        datareader = v.vtkXMLUnstructuredGridReader()
    elif type == 'pvtu':
        filename = ''.join([filenameout, repr(offset).zfill(4), '.pvtu'])
        datareader = v.vtkXMLPUnstructuredGridReader()

    print '=== loading and converting to pointdata, file:', filename, ' ==='

    datareader.SetFileName(filename)
    datareader.Update()
    c2p = v.vtkCellDataToPointData()
    c2p.SetInput(datareader.GetOutput())
    pointdata = c2p.GetOutput()
    pointdata.Update()

    print '=== Done with loading pointdata ==='
    return pointdata
예제 #28
0
파일: aniso.py 프로젝트: yangyha/mpi-AMRVAC
def load(offset, filenameout="data", type="pvtu"):
    if type == "vtu":
        filename = "".join([filenameout, repr(offset).zfill(4), ".vtu"])
        datareader = v.vtkXMLUnstructuredGridReader()
    elif type == "pvtu":
        filename = "".join([filenameout, repr(offset).zfill(4), ".pvtu"])
        datareader = v.vtkXMLPUnstructuredGridReader()

    print "=== loading and converting to pointdata, file:", filename, " ==="

    datareader.SetFileName(filename)
    datareader.Update()
    c2p = v.vtkCellDataToPointData()
    c2p.SetInput(datareader.GetOutput())
    pointdata = c2p.GetOutput()
    pointdata.Update()

    print "=== Done with loading pointdata ==="
    return pointdata
예제 #29
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    def __init__(self,
                 bodypoints,
                 geoname,
                 AutomaticFile,
                 AutomaticVTU_Number,
                 parallel,
                 c0,
                 D,
                 geolen,
                 U0=None,
                 p0=None,
                 rho0=None):
        """
        Read vtu/pvtu file and geo file, set basic information.
        
        """
        self.bodypoints = bodypoints
        self.geoname = geoname
        self.AutomaticFile = AutomaticFile
        self.AutomaticVTU_Number = AutomaticVTU_Number
        self.parallel = parallel
        self.U0 = U0
        self.p0 = p0
        self.rho0 = rho0
        self.c0 = c0
        self.D = D
        self.geolen = geolen

        # Reading *.vtu/*.pvtu file
        if (len(sys.argv) > 1):
            filename = sys.argv[1]
            vtu_number = int(sys.argv[2])
        else:
            filename = self.AutomaticFile
            vtu_number = int(self.AutomaticVTU_Number)
        if parallel == True:
            reader = vtk.vtkXMLPUnstructuredGridReader()
            reader.SetFileName(filename + '_' + str(vtu_number) + '.pvtu')
        elif parallel == False:
            reader = vtk.vtkXMLUnstructuredGridReader()
            reader.SetFileName(filename + '_' + str(vtu_number) + '.vtu')
        self.reader = reader
예제 #30
0
    def read_velocity(self, n, verbose=False, **kwargs):
        if not (hasattr(self, 'snames')):
            self.get_solution_filenames(verbose=verbose)

        if self.mesh_file != self.mnames[n]:
            self.read_mesh(n, verbose=verbose)

        filename = self.directory + self.snames[n]
        if verbose:
            print("Reading velocity from", filename)

        if self.format == 'hdf5':
            f = h5py.File(filename, "r")
            vel_data = f['velocity']
            u = vel_data[:, 0]
            v = vel_data[:, 1]
            w = vel_data[:, 2]

        if self.format == 'vtu':
            reader = vtk.vtkXMLPUnstructuredGridReader()
            reader.SetFileName(filename)
            reader.Update()
            my_vtk_array = reader.GetOutput().GetPointData().GetArray(
                "velocity")
            vel_data = vtk_to_numpy(my_vtk_array)
            u = vel_data[:, 0]
            v = vel_data[:, 1]
            w = vel_data[:, 2]

        u = u[self.indices]
        u.shape = self.array_shape

        v = v[self.indices]
        v.shape = self.array_shape

        w = w[self.indices]
        w.shape = self.array_shape

        mag = np.sqrt(u**2 + v**2 + w**2)

        return self.x, self.y, self.z, u, v, w, mag
예제 #31
0
def MergeVTKWorker(itime, args):

    appendF = vtk.vtkAppendFilter()

    for inpts in args.inputs:

        # g = vtkXMLUnstructuredGridReader() # VTU file
        g = vtk.vtkXMLPUnstructuredGridReader()  # PVTU file
        g.SetFileName(inpts)
        g.Update()
        appendF.AddInputData(g.GetOutput())

    # print appendF.GetMergePoints()
    appendF.MergePointsOn()
    # print appendF.GetMergePoints()
    appendF.Update()

    W = vtk.vtkXMLUnstructuredGridWriter()
    W.SetFileName(args.output)
    W.SetInputData(appendF.GetOutput())
    W.Update()
예제 #32
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def read_dataset(filename):
    import vtk
    extension = os.path.splitext(filename)[1]
    if (extension == ".vtk"): # VTK Legacy format
        reader = vtk.vtkDataSetReader()
    elif (extension == ".vtp"): # VTK XML Poly format
        reader = vtk.vtkXMLPolyDataReader()
    elif (extension == ".vtu"): # VTK XML Unstructured format
        reader = vtk.vtkXMLUnstructuredGridReader()
    elif (extension == ".stl"): # Stereolithography format
        reader = vtk.vtkSTLReader()
    elif (extension == ".ply"): # Stanford triangle format
        reader = vtk.vtkPLYReader()
    elif (extension == ".obj"): # Wavefront OBJ format
        reader = vtk.vtkOBJReader()
    elif (extension == ".pvtu"):
        reader = vtk.vtkXMLPUnstructuredGridReader() # Parallel XML format
    else:
        raise MeshFormatError()
    reader.SetFileName(filename)
    reader.Update()
    return reader.GetOutput()
예제 #33
0
def get_pointdata(offset,filenameout='data',type='pvtu'):

    if type == 'vtu':
        filename=''.join([filenameout,repr(offset).zfill(4),'.vtu'])
        datareader = v.vtkXMLUnstructuredGridReader()
    elif type == 'pvtu':
        filename=''.join([filenameout,repr(offset).zfill(4),'.pvtu'])
        datareader = v.vtkXMLPUnstructuredGridReader()
        
    print '=== Reading ',filename,' ==='
        
    datareader.SetFileName(filename)
    datareader.Update()
    data = datareader.GetOutput()
    c2p = v.vtkCellDataToPointData()
    c2p.SetInput(data)
    pointdata=c2p.GetOutput()
    pointdata.Update()
 
    vtk_points=data.GetPoints().GetData()
    points=ah.vtk2array(vtk_points)
 
    print '=== Done with reading data! ==='
    return {'pointdata': pointdata, 'points': points}
예제 #34
0
            if not useSubdir:
                os.remove(VTK_TEMP_DIR + "/%s_%d.%s" % (dataType, i, ext))
            else:
                os.remove(VTK_TEMP_DIR + "/%s/%s_%d.%s" %
                          (dataType, dataType, i, ext))

    assert da2.GetValue(0) == numTris


TestDataType('ImageData', vtk.vtkXMLPImageDataReader(),
             vtk.vtkXMLPImageDataWriter(), 'vti', 4924)
TestDataType('RectilinearGrid', vtk.vtkXMLPRectilinearGridReader(),
             vtk.vtkXMLPRectilinearGridWriter(), 'vtr', 4924)
TestDataType('StructuredGrid', vtk.vtkXMLPStructuredGridReader(),
             vtk.vtkXMLPStructuredGridWriter(), 'vts', 4924)
TestDataType('UnstructuredGrid', vtk.vtkXMLPUnstructuredGridReader(),
             vtk.vtkXMLPUnstructuredGridWriter(), 'vtu', 11856)

# Test writers with UseSubdirectory on
TestDataType('ImageData',
             vtk.vtkXMLPImageDataReader(),
             vtk.vtkXMLPImageDataWriter(),
             'vti',
             4924,
             useSubdir=True)
TestDataType('RectilinearGrid',
             vtk.vtkXMLPRectilinearGridReader(),
             vtk.vtkXMLPRectilinearGridWriter(),
             'vtr',
             4924,
             useSubdir=True)
예제 #35
0
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
예제 #36
0
    cf.SetValue(0, 130)
    cf.SetComputeNormals(0)
    cf.SetComputeGradients(0)
    cf.SetInputConnection(reader.GetOutputPort())
    cf.UpdateInformation()
    cf.GetOutputInformation(0).Set(vtk.vtkStreamingDemandDrivenPipeline.UPDATE_NUMBER_OF_PIECES(), nranks)
    cf.GetOutputInformation(0).Set(vtk.vtkStreamingDemandDrivenPipeline.UPDATE_PIECE_NUMBER(), rank)
    cf.Update()

    ntris = cf.GetOutput().GetNumberOfCells()
    da = vtk.vtkIntArray()
    da.InsertNextValue(ntris)

    da2 = vtk.vtkIntArray()
    da2.SetNumberOfTuples(1)
    contr.AllReduce(da, da2, vtk.vtkCommunicator.SUM_OP)

    if rank == 0:
        print(da2.GetValue(0))
        import os
        os.remove(filename)
        for i in range(npieces):
            os.remove(VTK_TEMP_DIR + "/%s_%d.%s" % (dataType, i, ext))

    assert da2.GetValue(0) == numTris

TestDataType('ImageData', vtk.vtkXMLPImageDataReader(), vtk.vtkXMLPImageDataWriter(), 'vti', 4924)
TestDataType('RectilinearGrid', vtk.vtkXMLPRectilinearGridReader(), vtk.vtkXMLPRectilinearGridWriter(), 'vtr', 4924)
TestDataType('StructuredGrid', vtk.vtkXMLPStructuredGridReader(), vtk.vtkXMLPStructuredGridWriter(), 'vts', 4924)
TestDataType('UnstructuredGrid', vtk.vtkXMLPUnstructuredGridReader(), vtk.vtkXMLPUnstructuredGridWriter(), 'vtu', 11856)
예제 #37
0
    def Line(self, X1, X2, Y1, Y2, Z1, Z2, res):
        parallel = False
        if self.vtuname.endswith(".pvtu"):
            parallel = True
        ############################ Plot from Numerical results
        #NAME OF THE VARIABLE YOU WANT TO EXTRACT DATA FROM
        path = self.path
        data_name_field = self.field
        ############ initial
        AutoVTU = 2
        AutoNumber = 0
        if AutoVTU == 1:
            for files in os.listdir(path):
                if files.endswith(".vtu"):
                    pos = files.rfind('_')
                    pos2 = files.rfind('.')
                    AutoFile = files[:pos]
                    AutoNumber = max(AutoNumber, int(files[pos + 1:pos2]))
            AutomaticFile = AutoFile
            AutomaticVTU_Number = AutoNumber
            if (len(sys.argv) > 1):
                filename = sys.argv[1]
                vtu_number = int(sys.argv[2])
            else:
                filename = AutomaticFile
                vtu_number = int(AutomaticVTU_Number)
            # serial
            if (parallel == True):
                reader = vtk.vtkXMLPUnstructuredGridReader()
                reader.SetFileName(filename + '_' + str(vtu_number) + '.pvtu')
            else:
                reader = vtk.vtkXMLUnstructuredGridReader()
                reader.SetFileName(filename + '_' + str(vtu_number) + '.vtu')
        else:
            if (parallel == True):
                reader = vtk.vtkXMLPUnstructuredGridReader()
            else:
                reader = vtk.vtkXMLUnstructuredGridReader()
            reader.SetFileName(self.path + self.vtuname)
        #reader.Update()
        ugrid = reader.GetOutputPort()
        #Initial and last coordinate of the probe
        x0 = X1
        x1 = X2
        y0 = Y1  # 1.0/float(NUMBER)
        y1 = Y2
        z0 = Z1
        z1 = Z2
        #Resolution of the probe
        resolution = res
        #ugrid.Update()
        ###########Create the probe line#############
        Field = []
        detector = []
        Dline = []
        hx = (x1 - x0) / resolution
        hy = (y1 - y0) / resolution
        hz = (z1 - z0) / resolution

        for i in range(resolution + 1):
            detector.append([hx * i + x0, hy * i + y0, hz * i + z0])

        #print 'using',len(detector),'detectors'
        points = vtk.vtkPoints()
        points.SetDataTypeToDouble()

        for i in range(len(detector)):
            points.InsertNextPoint(detector[i][0], detector[i][1],
                                   detector[i][2])

        detectors = vtk.vtkPolyData()
        detectors.SetPoints(points)
        ###########Create the probe line end#############
        probe = vtk.vtkProbeFilter()
        probe.SetInputConnection(ugrid)
        probe.SetSourceConnection(ugrid)
        probe.SetInputData(detectors)
        probe.Update()
        valid_ids = probe.GetOutput().GetPointData().GetArray(
            "vtkValidPointMask")

        data = probe.GetOutput()
        for j in range(points.GetNumberOfPoints()):
            ID = valid_ids.GetTuple(j)
            if ID[0] > 0:
                Dline.append(detector[j][:])
                Field.append(data.GetPointData().GetScalars(
                    data_name_field).GetTuple(j))
        return Dline, Field
def compute_vonMisesStress_for_MV(inputfilename, outputfilename):
	# ======================================================================
	# get system arguments -------------------------------------------------
	# Path to input file and name of the output file
	#inputfilename = sys.argv[1]
	#outputfilename = sys.argv[2]
	
	print " "
	print "=================================================================================================="
	print "=== Execute Python script to analyze MV geometry in order for the HiFlow3-based MVR-Simulation ==="
	print "=================================================================================================="
	print " "
	
	# ======================================================================
	# Read file
	if inputfilename[-4] == 'p':
		reader = vtk.vtkXMLPUnstructuredGridReader()
		reader.SetFileName(inputfilename)
		reader.Update()
	else:
		reader = vtk.vtkXMLUnstructuredGridReader()
		reader.SetFileName(inputfilename)
		reader.Update()
	
	print "Reading input files: DONE."
	
	# ======================================================================
	# Compute displacement vector
	calc = vtk.vtkArrayCalculator()
	calc.SetInput(reader.GetOutput())
	calc.SetAttributeModeToUsePointData()
	calc.AddScalarVariable('x', 'u0', 0)
	calc.AddScalarVariable('y', 'u1', 0)
	calc.AddScalarVariable('z', 'u2', 0)
	calc.SetFunction('x*iHat+y*jHat+z*kHat')
	calc.SetResultArrayName('DisplacementSolutionVector')
	calc.Update()
	
	# ======================================================================
	# Compute strain tensor
	derivative = vtk.vtkCellDerivatives()
	derivative.SetInput(calc.GetOutput())
	derivative.SetTensorModeToComputeStrain()
	derivative.Update()
	
	# ======================================================================
	# Compute von Mises stress
	calc = vtk.vtkArrayCalculator()
	calc.SetInput(derivative.GetOutput())
	calc.SetAttributeModeToUseCellData()
	calc.AddScalarVariable('Strain_0', 'Strain', 0)
	calc.AddScalarVariable('Strain_1', 'Strain', 1)
	calc.AddScalarVariable('Strain_2', 'Strain', 2)
	calc.AddScalarVariable('Strain_3', 'Strain', 3)
	calc.AddScalarVariable('Strain_4', 'Strain', 4)
	calc.AddScalarVariable('Strain_5', 'Strain', 5)
	calc.AddScalarVariable('Strain_6', 'Strain', 6)
	calc.AddScalarVariable('Strain_7', 'Strain', 7)
	calc.AddScalarVariable('Strain_8', 'Strain', 8)
	calc.SetFunction('sqrt( (2*700*Strain_0 + 28466*(Strain_0+Strain_4+Strain_8))^2 + (2*700*Strain_4 + 28466*(Strain_0+Strain_4+Strain_8))^2 + (2*700*Strain_8 + 28466*(Strain_0+Strain_4+Strain_8))^2 - ( (2*700*Strain_0 + 28466*(Strain_0+Strain_4+Strain_8))*(2*700*Strain_4 + 28466*(Strain_0+Strain_4+Strain_8)) ) - ( (2*700*Strain_0 + 28466*(Strain_0+Strain_4+Strain_8))*(2*700*Strain_8 + 28466*(Strain_0+Strain_4+Strain_8)) ) - ( (2*700*Strain_4 + 28466*(Strain_0+Strain_4+Strain_8))*(2*700*Strain_8 + 28466*(Strain_0+Strain_4+Strain_8)) ) + 3 * ((2*700*Strain_3)^2 + (2*700*Strain_6)^2 + (2*700*Strain_7)^2) )')
	calc.SetResultArrayName('vonMisesStress_forMV_mu700_lambda28466')
	calc.Update()
	
	print "Computation of displacement vectors, Cauchy strain and vom Mises stress: DONE."
	
	# ======================================================================
	# Define dummy variable; get output of calc filter
	dummy = calc.GetOutput()
	
	# Get point data arrays u0, u1 and u2
	pointData_u0 = dummy.GetPointData().GetArray('u0')
	pointData_u1 = dummy.GetPointData().GetArray('u1')
	pointData_u2 = dummy.GetPointData().GetArray('u2')
	
	# Set scalars
	dummy.GetPointData().SetScalars(pointData_u0)
	
	# ======================================================================
	# Warp by scalar u0
	warpScalar = vtk.vtkWarpScalar()
	warpScalar.SetInput(dummy)
	warpScalar.SetNormal(1.0,0.0,0.0)
	warpScalar.SetScaleFactor(1.0)
	warpScalar.SetUseNormal(1)
	warpScalar.Update()
	
	# Get output and set scalars
	dummy = warpScalar.GetOutput()
	dummy.GetPointData().SetScalars(pointData_u1)
	
	# ======================================================================
	# Warp by scalar u1
	warpScalar = vtk.vtkWarpScalar()
	warpScalar.SetInput(dummy)
	warpScalar.SetNormal(0.0,1.0,0.0)
	warpScalar.SetScaleFactor(1.0)
	warpScalar.SetUseNormal(1)
	warpScalar.Update()
	
	# Get output and set scalars
	dummy = warpScalar.GetOutput()
	dummy.GetPointData().SetScalars(pointData_u2)
	
	# ======================================================================
	# Warp by scalar u2
	warpScalar = vtk.vtkWarpScalar()
	warpScalar.SetInput(dummy)
	warpScalar.SetNormal(0.0,0.0,1.0)
	warpScalar.SetScaleFactor(1.0)
	warpScalar.SetUseNormal(1)
	warpScalar.Update()
	
	# Get ouput and add point data arrays that got deleted earlier
	dummy = warpScalar.GetOutput()
	dummy.GetPointData().AddArray(pointData_u0)
	dummy.GetPointData().AddArray(pointData_u1)
	
	# ======================================================================
	# Write output to vtu
	writer = vtk.vtkXMLUnstructuredGridWriter()
	writer.SetDataModeToAscii()
	writer.SetFileName(outputfilename)
	writer.SetInput(dummy)
	writer.Write()
	
	# ======================================================================
	print "Writing Extended VTU incl. von Mises Stress information: DONE."
	print "=============================================================="
	print " "
    da.InsertNextValue(ntris)

    da2 = vtk.vtkIntArray()
    da2.SetNumberOfTuples(1)
    contr.AllReduce(da, da2, vtk.vtkCommunicator.SUM_OP)

    if rank == 0:
        print(da2.GetValue(0))
        import os
        os.remove(filename)
        for i in range(npieces):
            if not useSubdir:
                os.remove(VTK_TEMP_DIR + "/%s_%d.%s" % (dataType, i, ext))
            else:
                os.remove(VTK_TEMP_DIR + "/%s/%s_%d.%s" %(dataType, dataType, i, ext))

    assert da2.GetValue(0) == numTris

TestDataType('ImageData', vtk.vtkXMLPImageDataReader(), vtk.vtkXMLPImageDataWriter(), 'vti', 4924)
TestDataType('RectilinearGrid', vtk.vtkXMLPRectilinearGridReader(), vtk.vtkXMLPRectilinearGridWriter(), 'vtr', 4924)
TestDataType('StructuredGrid', vtk.vtkXMLPStructuredGridReader(), vtk.vtkXMLPStructuredGridWriter(), 'vts', 4924)
TestDataType('UnstructuredGrid', vtk.vtkXMLPUnstructuredGridReader(), vtk.vtkXMLPUnstructuredGridWriter(), 'vtu', 11856)
TestDataType('Table', vtk.vtkXMLPTableReader(), vtk.vtkXMLPTableWriter(), 'vtt', 18522)

# Test writers with UseSubdirectory on
TestDataType('ImageData', vtk.vtkXMLPImageDataReader(), vtk.vtkXMLPImageDataWriter(), 'vti', 4924, useSubdir=True)
TestDataType('RectilinearGrid', vtk.vtkXMLPRectilinearGridReader(), vtk.vtkXMLPRectilinearGridWriter(), 'vtr', 4924, useSubdir=True)
TestDataType('StructuredGrid', vtk.vtkXMLPStructuredGridReader(), vtk.vtkXMLPStructuredGridWriter(), 'vts', 4924, useSubdir=True)
TestDataType('UnstructuredGrid', vtk.vtkXMLPUnstructuredGridReader(), vtk.vtkXMLPUnstructuredGridWriter(), 'vtu', 11856, useSubdir=True)
TestDataType('Table', vtk.vtkXMLPTableReader(), vtk.vtkXMLPTableWriter(), 'vtt', 18522, useSubdir=True)
        indexFile = 0
        if run == runs[0]:  #First data comes from previous Run
            path = '/home/users/merino4i/MISMIP+/' + caseFirst + '/' + run + '/'
            filesIce = glob.glob(path + '*.pvtu')
            filesIce.sort()
            for fileTest in filesIce:
                file1 = fileTest
        else:

            path = '/home/users/merino4i/MISMIP+/' + case + '/' + run + '/'
            filesIce = glob.glob(path + '*.pvtu')
            filesIce.sort()
            for fileTest in filesIce:
                file1 = fileTest

        reader = vtk.vtkXMLPUnstructuredGridReader()
        print file1
        reader.SetFileName(file1)
        reader.Update()
        output = reader.GetOutput()
        Coords = vtk_to_numpy(output.GetPoints().GetData())
        PointData = output.GetPointData()
        numArrays = PointData.GetNumberOfArrays()

        for i in np.arange(numArrays):
            if PointData.GetArrayName(i) == 'ssavelocity':
                VarIndex = i
                break
        Vel = vtk_to_numpy(PointData.GetArray(VarIndex))

        for i in np.arange(numArrays):