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Point based vtk file in DADF5 class

This commit is contained in:
Vitesh Shah 2019-12-13 14:20:18 +01:00
parent b14c15fd9e
commit 7d849b639b
1 changed files with 75 additions and 40 deletions
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115
python/damask/dadf5.py
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@ -846,41 +846,58 @@ class DADF5():
pool.wait_completion()
def to_vtk(self,labels):
def to_vtk(self,labels,mode='Cell'):
"""
Export to vtk cell data.
Export to vtk cell/point data.
Parameters
----------
labels : list of str
Labels of the datasets to be exported.
mode : str
Export in cell format or point format.
Default value is 'Cell'
"""
if self.structured:
if mode=='Cell':
coordArray = [vtk.vtkDoubleArray(),vtk.vtkDoubleArray(),vtk.vtkDoubleArray()]
for dim in [0,1,2]:
for c in np.linspace(0,self.size[dim],1+self.grid[dim]):
coordArray[dim].InsertNextValue(c)
grid = vtk.vtkRectilinearGrid()
grid.SetDimensions(*(self.grid+1))
grid.SetXCoordinates(coordArray[0])
grid.SetYCoordinates(coordArray[1])
grid.SetZCoordinates(coordArray[2])
else:
nodes = vtk.vtkPoints()
with h5py.File(self.fname) as f:
nodes.SetData(numpy_support.numpy_to_vtk(f['/geometry/x_n'][()],deep=True))
if self.structured:
coordArray = [vtk.vtkDoubleArray(),vtk.vtkDoubleArray(),vtk.vtkDoubleArray()]
for dim in [0,1,2]:
for c in np.linspace(0,self.size[dim],1+self.grid[dim]):
coordArray[dim].InsertNextValue(c)
grid = vtk.vtkRectilinearGrid()
grid.SetDimensions(*(self.grid+1))
grid.SetXCoordinates(coordArray[0])
grid.SetYCoordinates(coordArray[1])
grid.SetZCoordinates(coordArray[2])
else:
grid = vtk.vtkUnstructuredGrid()
grid.SetPoints(nodes)
grid.Allocate(f['/geometry/T_c'].shape[0])
for i in f['/geometry/T_c']:
grid.InsertNextCell(vtk.VTK_HEXAHEDRON,8,i-1) # not for all elements!
nodes = vtk.vtkPoints()
with h5py.File(self.fname) as f:
nodes.SetData(numpy_support.numpy_to_vtk(f['/geometry/x_n'][()],deep=True))
grid = vtk.vtkUnstructuredGrid()
grid.SetPoints(nodes)
grid.Allocate(f['/geometry/T_c'].shape[0])
for i in f['/geometry/T_c']:
grid.InsertNextCell(vtk.VTK_HEXAHEDRON,8,i-1) # not for all elements!
else:
Points = vtk.vtkPoints()
Vertices = vtk.vtkCellArray()
for c in self.cell_coordinates():
pointID = Points.InsertNextPoint(c)
Vertices.InsertNextCell(1)
Vertices.InsertCellPoint(pointID)
Polydata = vtk.vtkPolyData()
Polydata.SetPoints(Points)
Polydata.SetVerts(Vertices)
Polydata.Modified()
N_digits = int(np.floor(np.log10(int(self.increments[-1][3:]))))+1
for i,inc in enumerate(self.iter_visible('increments')):
@ -900,7 +917,10 @@ class DADF5():
vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),
deep=True,array_type= vtk.VTK_DOUBLE))
vtk_data[-1].SetName('1_'+x[0].split('/',1)[1]) #ToDo: hard coded 1!
grid.GetCellData().AddArray(vtk_data[-1])
if mode=='Cell':
grid.GetCellData().AddArray(vtk_data[-1])
else:
Polydata.GetCellData().AddArray(vtk_data[-1])
else:
x = self.get_dataset_location(label)
if len(x) == 0:
@ -912,9 +932,12 @@ class DADF5():
ph_name = re.compile(r'(\/[1-9])_([A-Z][a-z]*)_(([a-z]*)|([A-Z]*))') #looking for phase name in dataset name
dset_name = '1_' + re.sub(ph_name,r'',x[0].split('/',1)[1]) #removing phase name from generic dataset
vtk_data[-1].SetName(dset_name)
grid.GetCellData().AddArray(vtk_data[-1])
if mode=='Cell':
grid.GetCellData().AddArray(vtk_data[-1])
else:
Polydata.GetCellData().AddArray(vtk_data[-1])
self.set_visible('materialpoints',materialpoints_backup)
constituents_backup = self.visible['constituents'].copy()
self.set_visible('constituents',False)
for label in labels:
@ -929,7 +952,10 @@ class DADF5():
vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),
deep=True,array_type= vtk.VTK_DOUBLE))
vtk_data[-1].SetName('1_'+x[0].split('/',1)[1]) #ToDo: why 1_?
grid.GetCellData().AddArray(vtk_data[-1])
if mode=='Cell':
grid.GetCellData().AddArray(vtk_data[-1])
else:
Polydata.GetCellData().AddArray(vtk_data[-1])
else:
x = self.get_dataset_location(label)
if len(x) == 0:
@ -939,17 +965,23 @@ class DADF5():
vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),
deep=True,array_type= vtk.VTK_DOUBLE))
vtk_data[-1].SetName('1_'+x[0].split('/',1)[1])
grid.GetCellData().AddArray(vtk_data[-1])
if mode=='Cell':
grid.GetCellData().AddArray(vtk_data[-1])
else:
Polydata.GetCellData().AddArray(vtk_data[-1])
self.set_visible('constituents',constituents_backup)
writer = vtk.vtkXMLRectilinearGridWriter() if self.structured else \
vtk.vtkXMLUnstructuredGridWriter()
if mode=='Cell':
writer = vtk.vtkXMLRectilinearGridWriter() if self.structured else \
vtk.vtkXMLUnstructuredGridWriter()
x = self.get_dataset_location('u_n')
vtk_data.append(numpy_support.numpy_to_vtk(num_array=self.read_dataset(x,0),
deep=True,array_type=vtk.VTK_DOUBLE))
vtk_data[-1].SetName('u')
grid.GetPointData().AddArray(vtk_data[-1])
else:
writer = vtk.vtkXMLPolyDataWriter()
x = self.get_dataset_location('u_n')
vtk_data.append(numpy_support.numpy_to_vtk(num_array=self.read_dataset(x,0),
deep=True,array_type=vtk.VTK_DOUBLE))
vtk_data[-1].SetName('u')
grid.GetPointData().AddArray(vtk_data[-1])
file_out = '{}_inc{}.{}'.format(os.path.splitext(os.path.basename(self.fname))[0],
inc[3:].zfill(N_digits),
@ -958,6 +990,9 @@ class DADF5():
writer.SetCompressorTypeToZLib()
writer.SetDataModeToBinary()
writer.SetFileName(file_out)
writer.SetInputData(grid)
if mode=='Cell':
writer.SetInputData(grid)
else:
writer.SetInputData(Polydata)
writer.Write()