def _load_file(self, filename):
"""Load a vtkMultiBlockDataSet from a file.
The supported extensions are: ``.vtm`` or ``.vtmb``.
"""
filename = os.path.abspath(os.path.expanduser(filename))
# test if file exists
if not os.path.isfile(filename):
raise Exception('File %s does not exist' % filename)
# Get extension
ext = pyvista.get_ext(filename)
# Extensions: .vtm and .vtmb
# Select reader
if ext in ['.vtm', '.vtmb']:
reader = vtk.vtkXMLMultiBlockDataReader()
else:
raise IOError('File extension must be either "vtm" or "vtmb"')
# Load file
reader.SetFileName(filename)
reader.Update()
self.shallow_copy(reader.GetOutput())
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtkXMLMultiBlockDataReader(), 'Reading vtkXMLMultiBlockData.',
(), ('vtkXMLMultiBlockData',),
replaceDoc=True,
inputFunctions=None, outputFunctions=None)
def ReadMultiBlockFile(self):
if (self.InputFileName == ''):
self.PrintError('Error: no InputFileName.')
self.PrintLog('Reading MultiBlockData File.')
reader = vtk.vtkXMLMultiBlockDataReader()
reader.SetFileName(self.InputFileName)
reader.Update()
self.Surface = reader.GetOutput()
def readDataSet(fileName, **kwargs):
"""Read the dataset from a file. The reader type used is determined from the file extension.
Returns:
+------------+----------------------+
| File ext. | Return type |
+============+======================+
| .vtp | vtkPolyData |
+------------+----------------------+
| .vtu | vtkUnstructuredGrid |
+------------+----------------------+
| .vti | vtkImageData |
+------------+----------------------+
| .stl | vtkPolyData |
+------------+----------------------+
| .case | vtkMultiBlockDataSet |
+------------+----------------------+
"""
if not os.path.isfile(fileName):
raise RuntimeError('The file', fileName, 'did not exist')
filePrefix, fileExtension = os.path.splitext(fileName)
if fileExtension == '.vtp':
reader = vtk.vtkXMLPolyDataReader()
elif fileExtension == '.vtu':
reader = vtk.vtkXMLUnstructuredGridReader()
elif fileExtension == '.vti':
reader = vtk.vtkXMLImageDataReader()
elif fileExtension == '.vtm':
reader = vtk.vtkXMLMultiBlockDataReader()
elif fileExtension == '.stl':
reader = vtk.vtkSTLReader()
elif fileExtension == '.vtk':
#reader = _createVTKReader(fileName)
reader = vtk.vtkDataSetReader()
elif fileExtension == '.case':
reader = vtk.vtkEnSightGoldBinaryReader()
for k, v in kwargs.items():
if k == 'disableCellArrays':
for arrName in v:
reader.GetCellDataArraySelection().DisableArray(arrName)
elif k == 'disablePointArrays':
for arrName in v:
reader.GetPointDataArraySelection().DisableArray(arrName)
else:
raise RuntimeError('Unknown keyword argument' + str(k))
else:
raise RuntimeError('Unknown file extension', fileExtension)
if fileExtension == '.case':
reader.SetCaseFileName(fileName)
else:
reader.SetFileName(fileName)
reader.Update()
return reader.GetOutput()
def __init__(self, fileName):
Reader.__init__(self, fileName)
self._vtkReader = vtk.vtkXMLMultiBlockDataReader()
self._fileName = fileName
self._vtkReader.SetFileName(self._fileName)
self._vtkReader.Update()
self._data = self._vtkReader.GetOutput()
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(self,
module_manager,
vtk.vtkXMLMultiBlockDataReader(),
'Reading vtkXMLMultiBlockData.', (),
('vtkXMLMultiBlockData', ),
replaceDoc=True,
inputFunctions=None,
outputFunctions=None)
def __init__(self, fileName):
Reader.__init__(self, fileName)
self._vtkReader = vtk.vtkXMLMultiBlockDataReader()
self._fileName = fileName
self._vtkReader.SetFileName(self._fileName)
self._vtkReader.Update()
self._data = self._vtkReader.GetOutput()
for i in range(self._data.GetNumberOfBlocks()):
points = dsa.WrapDataObject(self._data.GetBlock(i)).Points
points[:, 2] = 0
def vtk_geom_to_np(geom_vtm): reader = vtk.vtkXMLMultiBlockDataReader() reader.SetFileName(Path(geom_vtm).absolute().as_posix()) reader.Update() data = reader.GetOutput() data_iterator = data.NewIterator() img_data = data_iterator.GetCurrentDataObject() point_data = img_data.GetPointData() array_data = point_data.GetArray(0) np_array = vtk_to_numpy(array_data) img_shape = img_data.GetExtent()#.GetWholeExtent() np_shape = [img_shape[3] - img_shape[2] + 1, img_shape[1] - img_shape[0] + 1, 1] geometry_array = np_array.reshape(np_shape) return geometry_array # vtm = VTK_data() # vtm.load_data() # print(vtm.results)
def load_vtk_structured(self, file_name):
self.fname = file_name
#reader = vtk.vtkUnstructuredGridReader()
reader = vtk.vtkXMLMultiBlockDataReader()
reader.SetFileName(file_name)
reader.Update()
Merge = vtk.vtkMultiBlockMergeFilter()
Merge.AddInput(reader.GetOutput())
Merge.Update()
Mb = vtk.vtkStructuredGridOutlineFilter()
if vtk.VTK_MAJOR_VERSION <= 5:
Mb.SetInput(Merge.GetOutput())
else:
Mb.SetInputData(Merge.GetOutput())
Geom01 = vtk.vtkCompositeDataGeometryFilter()
Geom01.SetInputConnection(Merge.GetOutputPort())
self.output = Geom01.GetOutput()
self.vtk_pts = self.output.GetPointData()
self.vtk_n_pts = self.output.GetNumberOfPoints()
self.vtk_n_cells = self.output.GetNumberOfCells()
self.vtk_n_props = self.vtk_pts.GetNumberOfArrays()
self.reader = reader
#get_range = self.output.GetScalarRange()
#print get_range
print " [Vtk_unstructured_reader]:"
print " Cells: %d" % (self.vtk_n_cells)
print " Point: %d" % (self.vtk_n_pts)
print " Props: ",
for i in range(self.vtk_n_props):
print "\'%s\'" % (self.vtk_pts.GetArrayName(i)),
print
print "\n+[Vtk_multiblock_reader]: \'%s\'" % file_name
def vtk_results_to_np(results_vtm): # read file for steady state flow reader = vtk.vtkXMLMultiBlockDataReader() reader.SetFileName(Path(results_vtm).absolute().as_posix()) reader.Update() data = reader.GetOutput() data_iterator = data.NewIterator() img_data = data_iterator.GetCurrentDataObject() point_data = img_data.GetPointData() velocity_array_data = point_data.GetArray(0) pressure_array_data = point_data.GetArray(1) velocity_np_array = vtk_to_numpy(velocity_array_data) pressure_np_array = vtk_to_numpy(pressure_array_data) img_shape = img_data.GetExtent()#.GetWholeExtent() velocity_np_shape = [img_shape[3] - img_shape[2] + 1, img_shape[1] - img_shape[0] + 1, 2] pressure_np_shape = [img_shape[3] - img_shape[2] + 1, img_shape[1] - img_shape[0] + 1, 1] velocity_np_array = velocity_np_array.reshape(velocity_np_shape) pressure_np_array = pressure_np_array.reshape(pressure_np_shape) steady_flow_array = np.concatenate([velocity_np_array, pressure_np_array], axis=2) return steady_flow_array
def read_vtm_data(in_file):
reader = vtk.vtkXMLMultiBlockDataReader()
reader.SetFileName(in_file)
reader.Update()
return reader.GetOutput().GetBlock(0)
def load_data(self):
# reads in all xml data into lists
# get list of all xml file in dataset
xml_files = glob.glob(self.base_dir + "/xml_runs/*.xml")
for f in xml_files:
# parse xml file
tree = ET.parse(f)
root = tree.getroot()
dir_name = root.find('save_path').find('dirname').text
# get needed filenames
geometry_file = dir_name + "vtkData/geometry_iT0000000.vtm"
steady_flow_file = glob.glob(dir_name + "/vtkData/data/*.vtm")
if len(steady_flow_file) == 0:
continue
else:
steady_flow_file = steady_flow_file[0]
drag_vector_file = dir_name + "gnuplotData/data/drag.dat"
# read file for geometry
reader = vtk.vtkXMLMultiBlockDataReader()
reader.SetFileName(geometry_file)
reader.Update()
data = reader.GetOutput()
data_iterator = data.NewIterator()
img_data = data_iterator.GetCurrentDataObject()
img_data.Update()
point_data = img_data.GetPointData()
array_data = point_data.GetArray(0)
np_array = vtk_to_numpy(array_data)
img_shape = img_data.GetWholeExtent()
np_shape = [
img_shape[3] - img_shape[2] + 1,
img_shape[1] - img_shape[0] + 1, 1
]
geometry_array = np_array.reshape(np_shape)
if np.isnan(geometry_array).any():
continue
# read file for steady state flow
reader = vtk.vtkXMLMultiBlockDataReader()
reader.SetFileName(steady_flow_file)
reader.Update()
data = reader.GetOutput()
data_iterator = data.NewIterator()
img_data = data_iterator.GetCurrentDataObject()
img_data.Update()
point_data = img_data.GetPointData()
velocity_array_data = point_data.GetArray(0)
pressure_array_data = point_data.GetArray(1)
velocity_np_array = vtk_to_numpy(velocity_array_data)
pressure_np_array = vtk_to_numpy(pressure_array_data)
img_shape = img_data.GetWholeExtent()
velocity_np_shape = [
img_shape[3] - img_shape[2] + 1,
img_shape[1] - img_shape[0] + 1, 2
]
pressure_np_shape = [
img_shape[3] - img_shape[2] + 1,
img_shape[1] - img_shape[0] + 1, 1
]
velocity_np_array = velocity_np_array.reshape(velocity_np_shape)
pressure_np_array = pressure_np_array.reshape(pressure_np_shape)
steady_flow_array = np.concatenate(
[velocity_np_array, pressure_np_array], axis=2)
if np.isnan(steady_flow_array).any():
continue
# read file for drag vector
reader = open(drag_vector_file, "r")
drag_values = reader.readlines()
drag_array = np.zeros((len(drag_values)))
for i in range(len(drag_values)):
values = drag_values[i].split(' ')
drag_array[i] = float(values[1])
if np.isnan(drag_array).any():
continue
# if no nans then store
self.geometries.append(geometry_array)
self.steady_flows.append(steady_flow_array)
self.drag_vectors.append(drag_array)
self.split_line = int(self.train_test_split * len(self.geometries))
g.Update()
mb = g.GetOutputDataObject(0)
a = vtk.vtkFloatArray()
a.SetName("foo")
a.SetNumberOfTuples(1)
a.SetValue(0, 10)
mb.GetFieldData().AddArray(a)
file_root = VTK_TEMP_DIR + '/testxml'
file0 = file_root + ".vtm"
wri = vtk.vtkXMLMultiBlockDataWriter()
wri.SetInputData(mb)
wri.SetFileName(file0)
wri.Write()
read = vtk.vtkXMLMultiBlockDataReader()
read.SetFileName(file0)
read.Update()
output = read.GetOutputDataObject(0)
assert(output.GetFieldData().GetArray("foo"))
assert(output.GetFieldData().GetArray("foo").GetValue(0) == 10)
os.remove(file0)
os.remove(file_root + "/testxml_0.vti")
os.rmdir(file_root)
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
def __init__(self):
self.reader = vtk.vtkXMLMultiBlockDataReader()
def load_data(self, dim, size):
# reads in all xml data into lists
# get list of all xml file in dataset
tree = etree.parse(self.base_dir + "experiment_runs_master.xml")
root = tree.getroot()
run_roots = root.findall("run")
print("loading dataset")
reader = vtk.vtkXMLMultiBlockDataReader()
#stopper = 0
for run_root in tqdm(run_roots):
#stopper += 1
#if stopper > 10000:
# break
# check if right size
xml_size = int(run_root.find("size").text)
if xml_size != size:
continue
# check if right dim
xml_dim = int(run_root.find("dim").text)
if xml_dim != dim:
continue
# parse xml file
xml_file = run_root.find("xml_filename").text
tree = etree.parse(xml_file)
root = tree.getroot()
# check if flow data is availible
is_availible = root.find("flow_data").find("availible").text
if is_availible == "False":
continue
# get needed filenames
geometry_file = root.find("flow_data").find("geometry_file").text
steady_flow_file = root.find("flow_data").find("flow_file").text
drag_vector_file = root.find("flow_data").find("drag_file").text
# read file for geometry
reader.SetFileName(geometry_file)
try:
reader.Update()
except:
continue
data = reader.GetOutput()
data_iterator = data.NewIterator()
img_data = data_iterator.GetCurrentDataObject()
try:
img_data.Update()
except:
continue
point_data = img_data.GetPointData()
array_data = point_data.GetArray(0)
np_array = vtk_to_numpy(array_data)
img_shape = img_data.GetWholeExtent()
if img_shape[-1] == 0:
np_shape = [
img_shape[3] - img_shape[2] + 1,
img_shape[1] - img_shape[0] + 1, 1
]
else:
np_shape = [
img_shape[5] - img_shape[4] + 1,
img_shape[3] - img_shape[2] + 1,
img_shape[1] - img_shape[0] + 1, 1
]
if len(np_array.shape) == 2:
continue
geometry_array = np_array.reshape(np_shape)
geometry_array = geometry_array[..., 0:np_shape[0], :]
geometry_array = np.abs(geometry_array - 1.0)
geometry_array = np.minimum(geometry_array, 1.0)
geometry_array = np.abs(np.abs(geometry_array - 1.0) - 1.0)
if img_shape[-1] == 0:
geometry_array = fill_gaps(geometry_array,
[size / 2, size / 2], size)
geometry_array = 2.0 * geometry_array - 1.0
if np.isnan(geometry_array).any():
continue
# read file for steady state flow
#reader = vtk.vtkXMLMultiBlockDataReader()
reader.SetFileName(steady_flow_file)
try:
reader.Update()
except:
continue
data = reader.GetOutput()
data_iterator = data.NewIterator()
img_data = data_iterator.GetCurrentDataObject()
try:
img_data.Update()
except:
continue
point_data = img_data.GetPointData()
velocity_array_data = point_data.GetArray(0)
pressure_array_data = point_data.GetArray(1)
velocity_np_array = vtk_to_numpy(velocity_array_data)
pressure_np_array = vtk_to_numpy(pressure_array_data)
img_shape = img_data.GetWholeExtent()
if img_shape[-1] == 0:
np_shape = [
img_shape[3] - img_shape[2] + 1,
img_shape[1] - img_shape[0] + 1
]
velocity_np_shape = np_shape + [2]
pressure_np_shape = np_shape + [1]
else:
np_shape = [
img_shape[5] - img_shape[4] + 1,
img_shape[3] - img_shape[2] + 1,
img_shape[1] - img_shape[0] + 1
]
velocity_np_shape = np_shape + [3]
pressure_np_shape = np_shape + [1]
velocity_np_array = velocity_np_array.reshape(velocity_np_shape)
pressure_np_array = pressure_np_array.reshape(pressure_np_shape)
steady_flow_array = np.concatenate(
[velocity_np_array, pressure_np_array], axis=-1)
steady_flow_array = steady_flow_array[..., 0:np_shape[0], :]
if np.isnan(steady_flow_array).any():
continue
# read file for drag vector
csv_reader = open(drag_vector_file, "r")
drag_values = csv_reader.readlines()
drag_array = np.zeros((len(drag_values)))
for i in xrange(len(drag_values)):
values = drag_values[i].split(' ')
drag_array[i] = float(values[1])
if np.isnan(drag_array).any():
continue
csv_reader.close()
# if no nans then store
self.geometries.append(geometry_array)
self.steady_flows.append(steady_flow_array)
self.drag_vectors.append(drag_array)
self.split_line = int(self.train_test_split * len(self.geometries))
def compute(whole, split):
# prepare
controller = vtk.vtkMPIController()
vtk.vtkMultiProcessController.SetGlobalController(controller)
rank = controller.GetLocalProcessId()
nprocs = controller.GetNumberOfProcesses()
# print('rank={0}'.format(rank))
# print('nprocs={0}'.format(nprocs))
# whole
(wholeDataset, bounds, dimension) = readDataset(whole)
if pow(2,dimension) != nprocs:
print 'the number of procs must be 2^dimension'
sys.exit()
# coarse
coarseData = vtk.vtkImageData()
coarseData.CopyStructure(wholeDataset)
coarseData.SetSpacing(0.1,0.1,0.1)
if dimension == 2:
coarseData.SetDimensions(11,11,1)
else:
coarseData.SetDimensions(11,11,11)
# print data
# print coarseData
# compute moments
momentsFilter = vtk.vtkComputeMoments()
momentsFilter.SetFieldData(wholeDataset)
momentsFilter.SetGridData(coarseData)
momentsFilter.SetNameOfPointData(nameOfPointData)
momentsFilter.SetUseFFT(0)
momentsFilter.SetNumberOfIntegrationSteps(numberOfIntegrationSteps)
momentsFilter.SetOrder(order)
momentsFilter.SetRadiiArray([radius,0,0,0,0,0,0,0,0,0])
momentsFilter.Update()
# if rank ==0: print momentsFilter
# this is to make sure each proc only loads their piece
ids_to_read = [rank]
reqs = vtk.vtkInformation()
reqs.Set(vtk.vtkCompositeDataPipeline.UPDATE_COMPOSITE_INDICES(), ids_to_read, 1)
reader = vtk.vtkXMLMultiBlockDataReader()
reader.SetFileName(split)
reader.Update(reqs)
# print('reader={0}'.format(reader.GetOutput()))
multiblock = vtk.vtkMultiBlockDataSet.SafeDownCast(reader.GetOutput())
# print('multiblock={0}'.format(multiblock))
multipiece = vtk.vtkMultiPieceDataSet.SafeDownCast(multiblock.GetBlock(0))
# print('multipiece={0}'.format(multipiece))
data = vtk.vtkImageData.SafeDownCast(multipiece.GetPiece(rank))
# print('data={0}'.format(data))
# coarse
coarseData = vtk.vtkImageData()
coarseData.CopyStructure(data)
coarseData.SetSpacing(0.1,0.1,0.1)
if dimension == 2:
coarseData.SetDimensions(6,6,1)
else:
coarseData.SetDimensions(6,6,6)
# print data
# coarseData
# parallel
pMomentsFilter = vtk.vtkPComputeMoments()
pMomentsFilter.SetFieldData(data)
pMomentsFilter.SetGridData(coarseData)
pMomentsFilter.SetNameOfPointData(nameOfPointData)
pMomentsFilter.SetNumberOfIntegrationSteps(numberOfIntegrationSteps)
pMomentsFilter.SetRadiiArray([radius, 0, 0, 0, 0, 0, 0, 0, 0, 0 ])
pMomentsFilter.Update(reqs)
# if rank ==0: print pMomentsFilter
# check for difference except for the global boundary (the probe and parallel probe filters behave differently there. So, there is a difference if numberOfIntegrationSteps > 0 )
diff = 0
for i in xrange(pMomentsFilter.GetOutput().GetPointData().GetNumberOfArrays()):
diffArray = vtk.vtkDoubleArray()
diffArray.SetName( pMomentsFilter.GetOutput().GetPointData().GetArrayName(i) )
diffArray.SetNumberOfComponents( 1 )
diffArray.SetNumberOfTuples( pMomentsFilter.GetOutput().GetNumberOfPoints() )
diffArray.Fill( 0.0 )
momentsArray = momentsFilter.GetOutput().GetPointData().GetArray(i)
pMomentsArray = pMomentsFilter.GetOutput().GetPointData().GetArray(i)
for j in xrange(pMomentsFilter.GetOutput().GetNumberOfPoints()):
diffArray.SetTuple1(j, abs(momentsArray.GetTuple1(momentsFilter.GetOutput().FindPoint(pMomentsFilter.GetOutput().GetPoint(j))) - pMomentsArray.GetTuple1(j)))
if (dimension == 2 and pMomentsFilter.GetOutput().GetPoint(j)[0] > 0 and pMomentsFilter.GetOutput().GetPoint(j)[0] < 1 and pMomentsFilter.GetOutput().GetPoint(j)[1] > 0 and pMomentsFilter.GetOutput().GetPoint(j)[1] < 1) or (dimension == 3 and pMomentsFilter.GetOutput().GetPoint(j)[0] > 0 and pMomentsFilter.GetOutput().GetPoint(j)[0] < 1 and pMomentsFilter.GetOutput().GetPoint(j)[1] > 0 and pMomentsFilter.GetOutput().GetPoint(j)[1] < 1 and pMomentsFilter.GetOutput().GetPoint(j)[2] > 0 and pMomentsFilter.GetOutput().GetPoint(j)[2] < 1):
# if diffArray.GetTuple1(j) > 1e-10:
# print rank, i, j, pMomentsFilter.GetOutput().GetPoint(j), diffArray.GetTuple(j)
diff = max(diff, diffArray.GetTuple1(j))
if diff > 1e-10:
print "test failed, maxdiff =", diff
else:
print "test successful"
if rank == 0:
print 'all done!'
try:
shutil.rmtree(prefix)
except OSError:
pass
print("Output: %s" % fname)
# put a barrier here to make sure that the files are deleted by process 0
# before going further with the test
if contr:
contr.Barrier()
writer.SetFileName(fname)
writer.SetInputDataObject(createMB(rank, nranks))
writer.Write()
if contr:
contr.Barrier()
if rank == 0:
reader = vtk.vtkXMLMultiBlockDataReader()
reader.SetFileName(fname)
reader.Update()
# since verifying the md structure won't reveal if we have written the write
# set of files, let's just look at the files we wrote out.
files = os.listdir(prefix)
expected_file_count = nranks + nranks + 2 * (nranks * nranks)
print("Expecting %d files for the leaf nodes" % expected_file_count)
assert (len(files) == expected_file_count)
def getOutputVTKwithPointDataFromFile(fileName):
"""
Uses the correct VTK reader to obtain a VTK output object so that one can
work with the data in *fileName*.
NOTE : the cell data are transfered to the nodes.
Parameters
----------
fileName : string
The .vt* file to open
Returns
-------
data_outVTK : VTK output object from a VTK reader
VTK output object associated to the file type of *fileName*
"""
# function display
print '\n---- DAEPy::getOutputVTKwithPointDataFromFile ----'
# test if the file exists
print '\n--> Reading', fileName
if not os.path.isfile(fileName):
raise ValueError("Error : file does not exists")
extension = os.path.splitext(fileName)[-1]
if extension == '.vtu':
reader = vtk.vtkXMLUnstructuredGridReader()
elif extension == '.vtk':
reader = vtk.vtkStructuredGridReader()
elif extension == '.pvtu':
reader = vtk.vtkXMLPUnstructuredGridReader()
elif extension == '.vtp':
reader = vtk.vtkXMLPolyDataReader()
elif extension == '.vtm':
# TODO : To check
reader = vtk.vtkXMLMultiBlockDataReader()
reader = vtk.MergeBlocks(reader)
else:
raise ValueError("Error: unknown extension of file " + fileName)
reader.SetFileName(fileName)
reader.ReadAllScalarsOn()
reader.ReadAllVectorsOn()
reader.Update()
data_outVTK = reader.GetOutput()
# # All the data are transfered to the nodes
# c2p = vtk.vtkCellDataToPointData()
# c2p.SetInputData(data_outVTK)
# c2p.Update()
# data_outVTK = c2p.GetOutput()
# list the fields available
n_fields = data_outVTK.GetPointData().GetNumberOfArrays()
print '\n--> Available:', n_fields, 'fields\n'
for i in range(n_fields):
print ' -', data_outVTK.GetPointData().GetArrayName(i)
print ''
return data_outVTK
