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)
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)
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)
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
def ReadPVTUFile(fname):
reader = vtk.vtkXMLPUnstructuredGridReader()
reader.SetFileName(fname)
reader.Update()
#print reader.GetNumberOfPieces()
return reader
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
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()
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}
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()
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
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)
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()
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)
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()
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()
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
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)
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
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
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
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)
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
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
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
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
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
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()
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()
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}
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)
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
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)
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):