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Merge branch 'Poly_data_with_verts' into 'development' 

Poly data with verts

See merge request damask/DAMASK!262
This commit is contained in:
Philip Eisenlohr 2020-10-27 20:32:09 +01:00
parent 93a791abd1 a5a127b787
commit ea49044992
11 changed files with 100 additions and 149 deletions
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4
python/damask/_geom.py
View File

@ -473,7 +473,7 @@ class Geom:
Compress with zlib algorithm. Defaults to True.
"""
v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin)
v = VTK.from_rectilinear_grid(self.grid,self.size,self.origin)
v.add(self.material.flatten(order='F'),'material')
v.add_comments(self.comments)
@ -508,7 +508,7 @@ class Geom:
def show(self):
"""Show on screen."""
v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin)
v = VTK.from_rectilinear_grid(self.grid,self.size,self.origin)
v.show()

10
python/damask/_result.py
View File

@ -1212,14 +1212,14 @@ class Result:
if mode.lower()=='cell':
if self.structured:
v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin)
v = VTK.from_rectilinear_grid(self.grid,self.size,self.origin)
else:
with h5py.File(self.fname,'r') as f:
v = VTK.from_unstructuredGrid(f['/geometry/x_n'][()],
f['/geometry/T_c'][()]-1,
f['/geometry/T_c'].attrs['VTK_TYPE'].decode())
v = VTK.from_unstructured_grid(f['/geometry/x_n'][()],
f['/geometry/T_c'][()]-1,
f['/geometry/T_c'].attrs['VTK_TYPE'].decode())
elif mode.lower()=='point':
v = VTK.from_polyData(self.cell_coordinates())
v = VTK.from_poly_data(self.cell_coordinates)
N_digits = int(np.floor(np.log10(max(1,int(self.increments[-1][3:])))))+1

22
python/damask/_vtk.py
View File

@ -36,7 +36,7 @@ class VTK:
@staticmethod
def from_rectilinearGrid(grid,size,origin=np.zeros(3)):
def from_rectilinear_grid(grid,size,origin=np.zeros(3)):
"""
Create VTK of type vtk.vtkRectilinearGrid.
@ -64,7 +64,7 @@ class VTK:
@staticmethod
def from_unstructuredGrid(nodes,connectivity,cell_type):
def from_unstructured_grid(nodes,connectivity,cell_type):
"""
Create VTK of type vtk.vtkUnstructuredGrid.
@ -96,7 +96,7 @@ class VTK:
@staticmethod
def from_polyData(points):
def from_poly_data(points):
"""
Create VTK of type vtk.polyData.
@ -108,11 +108,18 @@ class VTK:
Spatial position of the points.
"""
N = points.shape[0]
vtk_points = vtk.vtkPoints()
vtk_points.SetData(np_to_vtk(points))
vtk_cells = vtk.vtkCellArray()
vtk_cells.SetNumberOfCells(N)
vtk_cells.SetCells(N,np_to_vtkIdTypeArray(np.stack((np.ones (N,dtype=np.int64),
np.arange(N,dtype=np.int64)),axis=1).ravel(),deep=True))
vtk_data = vtk.vtkPolyData()
vtk_data.SetPoints(vtk_points)
vtk_data.SetVerts(vtk_cells)
return VTK(vtk_data)
@ -164,6 +171,7 @@ class VTK:
return VTK(vtk_data)
@staticmethod
def _write(writer):
"""Wrapper for parallel writing."""
@ -192,7 +200,7 @@ class VTK:
default_ext = writer.GetDefaultFileExtension()
ext = Path(fname).suffix
if ext and ext != '.'+default_ext:
raise ValueError(f'Given extension {ext} does not match default .{default_ext}')
raise ValueError(f'Given extension "{ext}" does not match default ".{default_ext}"')
writer.SetFileName(str(Path(fname).with_suffix('.'+default_ext)))
if compress:
writer.SetCompressorTypeToZLib()
@ -238,10 +246,10 @@ class VTK:
else data).reshape(N_data,-1),deep=True) # avoid large files
d.SetName(label)
if N_data == N_cells:
self.vtk_data.GetCellData().AddArray(d)
elif N_data == N_points:
if N_data == N_points:
self.vtk_data.GetPointData().AddArray(d)
elif N_data == N_cells:
self.vtk_data.GetCellData().AddArray(d)
else:
raise ValueError(f'Cell / point count ({N_cells} / {N_points}) differs from data ({N_data}).')
elif isinstance(data,pd.DataFrame):

61
python/tests/reference/Result/12grains6x7x8.geom
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@ -1,61 +0,0 @@
4 header
grid a 6 b 7 c 8
size x 0.75 y 0.875 z 1.0
origin x 0.0 y 0.0 z 0.0
homogenization 1
9 3 3 10 9 9
9 1 1 1 9 9
9 11 1 1 7 9
7 11 11 7 7 7
7 11 11 7 7 7
12 3 3 10 7 12
12 3 3 10 10 12
12 3 3 1 9 9
9 1 1 1 9 9
9 1 1 1 7 7
7 1 1 7 7 7
12 12 3 7 7 7
12 3 3 3 12 12
12 3 3 3 12 12
12 3 3 1 1 12
9 1 1 1 1 9
6 1 1 1 8 8
7 6 8 8 8 8
12 12 8 8 8 12
12 3 3 3 12 12
12 3 3 3 12 12
5 6 6 6 1 12
6 6 6 6 8 8
6 6 6 8 8 8
8 6 8 8 8 8
12 5 8 8 8 8
12 5 5 8 8 12
5 5 5 3 12 12
5 5 6 6 6 5
6 6 6 6 6 6
6 6 6 6 8 8
4 4 6 8 8 8
4 4 2 2 2 8
5 5 5 2 2 2
5 5 5 5 2 5
5 5 5 10 10 5
6 6 6 6 10 4
4 4 11 11 2 4
4 4 11 2 2 4
4 4 2 2 2 2
5 5 5 2 2 2
5 5 5 10 10 5
5 5 10 10 10 9
4 11 11 11 10 9
4 4 11 11 11 4
4 4 11 11 2 4
4 4 2 2 2 2
5 5 2 2 2 2
5 5 10 10 10 10
9 10 10 10 10 9
9 11 11 10 9 9
4 11 11 11 9 9
4 11 11 11 7 7
4 4 11 2 7 7
12 10 10 10 10 7
9 10 10 10 10 9

30
python/tests/reference/Result/12grains6x7x8.vtr Normal file
View File

@ -0,0 +1,30 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 6 0 7 0 8">
<FieldData>
<Array type="String" Name="comments" NumberOfTuples="1" format="binary">
AQAAAACAAAARAAAAGQAAAA==eF7LyM/NT0/Ny6xKLMnMz1MwZAAAPsIGPQ==
</Array>
</FieldData>
<Piece Extent="0 6 0 7 0 8">
<PointData>
</PointData>
<CellData>
<DataArray type="Int64" Name="material" format="binary" RangeMin="0" RangeMax="11">
AQAAAACAAACACgAA2wAAAA==eF6tlssOgkAQBNcHiPj//2uM25eOZc8oc6kYagzdISzbeM/ZeJ/cgDTk7x/c16zm6fduXAOr/mOS8rqXfDH5mqP6pKHcVY9yJN/ziv5/R/k+8lI/GnnLV2uMm1G5tefXnZ6j6v3bD/nXyQWokU8e5a96tJc8z9H1aY88MfWZek3Xf6XnuBhTr+6fgPKpH9oj3/eS5+/bap/yPafo54buJ/mek3zqJeXu+tRP8vycp15E8tNe6rPaf7fPrk/9eO6q598/1GO1/67v53V6nul8T3n9Oy758p47Sgdl
</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.75">
AQAAAACAAAA4AAAAHAAAAA==eF5jYEAGB+wh9AUofQNKP4DST6D0C3sAisIGjw==
</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.875">
AQAAAACAAABAAAAAHwAAAA==eF5jYEAGB+wh9AUofQNKP4DST6D0Cyj9xh4AwVEHug==
</DataArray>
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="1">
AQAAAACAAABIAAAAIgAAAA==eF5jYEAGB+wh9AUofQNKP4DST6D0Cyj9Bkp/sAcAAU8I6Q==
</DataArray>
</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

61
python/tests/reference/Result/6grains6x7x8_single_phase.geom
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@ -1,61 +0,0 @@
4 header
grid a 6 b 7 c 8
size x 0.75 y 0.875 z 1.0
origin x 0.0 y 0.0 z 0.0
homogenization 1
3 3 3 4 3 3
3 1 1 1 3 3
3 5 1 1 1 3
1 5 5 1 1 1
1 5 5 1 1 1
6 3 3 4 1 6
6 3 3 4 4 6
6 3 3 1 3 3
3 1 1 1 3 3
3 1 1 1 1 1
1 1 1 1 1 1
6 6 3 1 1 1
6 3 3 3 6 6
6 3 3 3 6 6
6 3 3 1 1 6
3 1 1 1 1 3
6 1 1 1 2 2
1 6 2 2 2 2
6 6 2 2 2 6
6 3 3 3 6 6
6 3 3 3 6 6
5 6 6 6 1 6
6 6 6 6 2 2
6 6 6 2 2 2
2 6 2 2 2 2
6 5 2 2 2 2
6 5 5 2 2 6
5 5 5 3 6 6
5 5 6 6 6 5
6 6 6 6 6 6
6 6 6 6 2 2
4 4 6 2 2 2
4 4 2 2 2 2
5 5 5 2 2 2
5 5 5 5 2 5
5 5 5 4 4 5
6 6 6 6 4 4
4 4 5 5 2 4
4 4 5 2 2 4
4 4 2 2 2 2
5 5 5 2 2 2
5 5 5 4 4 5
5 5 4 4 4 3
4 5 5 5 4 3
4 4 5 5 5 4
4 4 5 5 2 4
4 4 2 2 2 2
5 5 2 2 2 2
5 5 4 4 4 4
3 4 4 4 4 3
3 5 5 4 3 3
4 5 5 5 3 3
4 5 5 5 1 1
4 4 5 2 1 1
6 4 4 4 4 1
3 4 4 4 4 3

30
python/tests/reference/Result/6grains6x7x8_single_phase.vtr Normal file
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@ -0,0 +1,30 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 6 0 7 0 8">
<FieldData>
<Array type="String" Name="comments" NumberOfTuples="1" format="binary">
AQAAAACAAAARAAAAGQAAAA==eF7LyM/NT0/Ny6xKLMnMz1MwZAAAPsIGPQ==
</Array>
</FieldData>
<Piece Extent="0 6 0 7 0 8">
<PointData>
</PointData>
<CellData>
<DataArray type="Int64" Name="material" format="binary" RangeMin="0" RangeMax="5">
AQAAAACAAACACgAAwAAAAA==eF69lcsOwjAQA6GU//9lDsUSGjHyBgq+WGpm09jqY7sc2uA3uR43Gb+/YV/FfXd405S/P93ykmt8vPHRWX3+SpbDZHnj3O8snpqeN+L9TFd4lDmu05ljyn3bj/F5P2yfyNZbnilnc1MuOVZ5mzMu3vpsvbb1T5057Ltk/ZBvfVo/qzznGsdzTvvknO3D8zS+9fjvPlsu4/ifn87bf7DNNf7sPlf59rxYbuPircdp/6s81Z5navoeRav9PACxsANv
</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.75">
AQAAAACAAAA4AAAAHAAAAA==eF5jYEAGB+wh9AUofQNKP4DST6D0C3sAisIGjw==
</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.875">
AQAAAACAAABAAAAAHwAAAA==eF5jYEAGB+wh9AUofQNKP4DST6D0Cyj9xh4AwVEHug==
</DataArray>
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="1">
AQAAAACAAABIAAAAIgAAAA==eF5jYEAGB+wh9AUofQNKP4DST6D0Cyj9Bkp/sAcAAU8I6Q==
</DataArray>
</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

10
python/tests/reference/VTK/polyData.vtp
View File

@ -1,7 +1,7 @@
<?xml version="1.0"?>
<VTKFile type="PolyData" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<PolyData>
<Piece NumberOfPoints="10" NumberOfVerts="0" NumberOfLines="0" NumberOfStrips="0" NumberOfPolys="0">
<Piece NumberOfPoints="10" NumberOfVerts="10" NumberOfLines="0" NumberOfStrips="0" NumberOfPolys="0">
<PointData>
<DataArray type="Float32" Name="coordinates" NumberOfComponents="3" format="binary" RangeMin="0.7453560147132696" RangeMax="2.449489742783178">
AQAAAACAAAB4AAAAVgAAAA==eF5jYICBhv2WfY9tLfuS7Ypk3PeDaCDf7okF3/7Vq1bZrV6lZQ+k94HEgHL2QHovUM7+iUUfiG0LlQdhkH77Ipnj9iB5qFp7kBjQDiBmcADRANsaLXM=
@ -31,11 +31,11 @@
</DataArray>
</Points>
<Verts>
<DataArray type="Int64" Name="connectivity" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
AAAAAACAAAAAAAAA
<DataArray type="Int64" Name="connectivity" format="binary" RangeMin="0" RangeMax="9">
AQAAAACAAABQAAAAIgAAAA==eF4txbcBACAIADAsiP7/sAPJkog2PL28nT4uXz9/BXgALg==
</DataArray>
<DataArray type="Int64" Name="offsets" format="binary" RangeMin="1e+299" RangeMax="-1e+299">
AAAAAACAAAAAAAAA
<DataArray type="Int64" Name="offsets" format="binary" RangeMin="1" RangeMax="10">
AQAAAACAAABQAAAAIgAAAA==eF4txbcBACAIADA76v8HM5As6a0MTy9vH4evn78TBzAAOA==
</DataArray>
</Verts>
<Lines>

2
python/tests/test_Geom.py
View File

@ -49,7 +49,7 @@ class TestGeom:
assert geom_equal(new,default)
def test_invalid_vtr(self,tmp_path):
v = VTK.from_rectilinearGrid(np.random.randint(5,10,3)*2,np.random.random(3) + 1.0)
v = VTK.from_rectilinear_grid(np.random.randint(5,10,3)*2,np.random.random(3) + 1.0)
v.save(tmp_path/'no_materialpoint.vtr')
with pytest.raises(ValueError):
Geom.load(tmp_path/'no_materialpoint.vtr')

5
python/tests/test_Result.py
View File

@ -341,6 +341,11 @@ class TestResult:
os.chdir(tmp_path)
default.save_vtk(output)
@pytest.mark.parametrize('mode',['point','cell'])
def test_vtk_mode(self,tmp_path,single_phase,mode):
os.chdir(tmp_path)
single_phase.save_vtk(mode=mode)
def test_XDMF(self,tmp_path,single_phase):
os.chdir(tmp_path)
single_phase.save_XDMF()

14
python/tests/test_VTK.py
View File

@ -18,7 +18,7 @@ def default():
"""Simple VTK."""
grid = np.array([5,6,7],int)
size = np.array([.6,1.,.5])
return VTK.from_rectilinearGrid(grid,size)
return VTK.from_rectilinear_grid(grid,size)
class TestVTK:
@ -30,7 +30,7 @@ class TestVTK:
grid = np.random.randint(5,10,3)*2
size = np.random.random(3) + 1.0
origin = np.random.random(3)
v = VTK.from_rectilinearGrid(grid,size,origin)
v = VTK.from_rectilinear_grid(grid,size,origin)
string = v.__repr__()
v.save(tmp_path/'rectilinearGrid',False)
vtr = VTK.load(tmp_path/'rectilinearGrid.vtr')
@ -41,7 +41,7 @@ class TestVTK:
def test_polyData(self,tmp_path):
points = np.random.rand(100,3)
v = VTK.from_polyData(points)
v = VTK.from_poly_data(points)
string = v.__repr__()
v.save(tmp_path/'polyData',False)
vtp = VTK.load(tmp_path/'polyData.vtp')
@ -60,7 +60,7 @@ class TestVTK:
def test_unstructuredGrid(self,tmp_path,cell_type,n):
nodes = np.random.rand(n,3)
connectivity = np.random.choice(np.arange(n),n,False).reshape(-1,n)
v = VTK.from_unstructuredGrid(nodes,connectivity,cell_type)
v = VTK.from_unstructured_grid(nodes,connectivity,cell_type)
string = v.__repr__()
v.save(tmp_path/'unstructuredGrid',False)
vtu = VTK.load(tmp_path/'unstructuredGrid.vtu')
@ -72,7 +72,7 @@ class TestVTK:
def test_parallel_out(self,tmp_path):
points = np.random.rand(102,3)
v = VTK.from_polyData(points)
v = VTK.from_poly_data(points)
fname_s = tmp_path/'single.vtp'
fname_p = tmp_path/'parallel.vtp'
v.save(fname_s,False)
@ -121,7 +121,7 @@ class TestVTK:
def test_compare_reference_polyData(self,update,reference_dir,tmp_path):
points=np.dstack((np.linspace(0.,1.,10),np.linspace(0.,2.,10),np.linspace(-1.,1.,10))).squeeze()
polyData = VTK.from_polyData(points)
polyData = VTK.from_poly_data(points)
polyData.add(points,'coordinates')
if update:
polyData.save(reference_dir/'polyData')
@ -133,7 +133,7 @@ class TestVTK:
def test_compare_reference_rectilinearGrid(self,update,reference_dir,tmp_path):
grid = np.array([5,6,7],int)
size = np.array([.6,1.,.5])
rectilinearGrid = VTK.from_rectilinearGrid(grid,size)
rectilinearGrid = VTK.from_rectilinear_grid(grid,size)
c = grid_filters.cell_coord0(grid,size).reshape(-1,3,order='F')
n = grid_filters.node_coord0(grid,size).reshape(-1,3,order='F')
rectilinearGrid.add(c,'cell')