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geom is written to vtr exlcusively, not to general vtk 

base tests on vtr
This commit is contained in:
Martin Diehl 2020-08-23 10:46:15 +02:00
parent 64e7582e8e
commit 07af7b2f98
19 changed files with 354 additions and 121 deletions
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20
python/damask/_geom.py
View File

@ -347,17 +347,18 @@ class Geom:
@staticmethod @staticmethod
def from_vtk(fname): def from_vtr(fname):
""" """
Read a geom from a VTK file. Read a VTK rectilinear grid.
Parameters Parameters
---------- ----------
fname : str or file handle fname : str or or pathlib.Path
Geometry file to read. Geometry file to read.
Valid extension is .vtr, it will be appended if not given.
""" """
g = VTK.from_file(fname).geom g = VTK.from_file(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr').geom
grid = np.array(g.GetDimensions())-1 grid = np.array(g.GetDimensions())-1
bbox = np.array(g.GetBounds()).reshape(3,2).T bbox = np.array(g.GetBounds()).reshape(3,2).T
size = bbox[1] - bbox[0] size = bbox[1] - bbox[0]
@ -513,21 +514,22 @@ class Geom:
f.write(f'{reps} of {former}\n') f.write(f'{reps} of {former}\n')
def to_vtk(self,fname=None): def to_vtr(self,fname=None):
""" """
Generates vtk file. Generates vtk rectilinear grid.
Parameters Parameters
---------- ----------
fname : str, optional fname : str, optional
Vtk file to write. If no file is given, a string is returned. Filename to write. If no file is given, a string is returned.
Valid extension is .vtr, it will be appended if not given.
""" """
v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin) v = VTK.from_rectilinearGrid(self.grid,self.size,self.origin)
v.add(self.microstructure.flatten(order='F'),'materialpoint') v.add(self.microstructure.flatten(order='F'),'materialpoint')
if fname: if fname:
v.write(fname) v.write(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
else: else:
sys.stdout.write(v.__repr__()) sys.stdout.write(v.__repr__())
@ -642,7 +644,7 @@ class Geom:
grid/self.get_grid(), grid/self.get_grid(),
output=self.microstructure.dtype, output=self.microstructure.dtype,
order=0, order=0,
mode=('wrap' if periodic else 'nearest'), mode=('wrap' if periodic else 'nearest'),
prefilter=False prefilter=False
) )
) )

25
python/tests/reference/Geom/clean.vtr Normal file
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@ -0,0 +1,25 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 20 0 18 0 8">
<Piece Extent="0 20 0 18 0 8">
<PointData>
</PointData>
<CellData>
<DataArray type="Int32" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
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</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="1">
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</RectilinearGrid>
</VTKFile>

25
python/tests/reference/Geom/clean_2_1_False.vtr Normal file
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@ -0,0 +1,25 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 20 0 18 0 8">
<Piece Extent="0 20 0 18 0 8">
<PointData>
</PointData>
<CellData>
<DataArray type="Int32" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
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</RectilinearGrid>
</VTKFile>

25
python/tests/reference/Geom/clean_2_1_True.vtr Normal file
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@ -0,0 +1,25 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 20 0 18 0 8">
<Piece Extent="0 20 0 18 0 8">
<PointData>
</PointData>
<CellData>
<DataArray type="Int32" Name="materialpoint" format="binary" RangeMin="1" RangeMax="2">
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25
python/tests/reference/Geom/clean_2_None_False.vtr Normal file
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@ -0,0 +1,25 @@
<?xml version="1.0"?>
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<RectilinearGrid WholeExtent="0 20 0 18 0 8">
<Piece Extent="0 20 0 18 0 8">
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<CellData>
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25
python/tests/reference/Geom/clean_2_None_True.vtr Normal file
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@ -0,0 +1,25 @@
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25
python/tests/reference/Geom/clean_3_1_False.vtr Normal file
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@ -0,0 +1,25 @@
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25
python/tests/reference/Geom/clean_3_1_True.vtr Normal file
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25
python/tests/reference/Geom/clean_3_None_False.vtr Normal file
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25
python/tests/reference/Geom/clean_3_None_True.vtr Normal file
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25
python/tests/reference/Geom/clean_4_1_False.vtr Normal file
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</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="1">
AQAAAACAAACYAAAAVgAAAA==eF5jYIAAmeOFQLTGHkLvsQ8Fg6NQ/hn7IjDjIlT8qr1F32MgugGVv2MPMeUBVN1D+8cQBVD1T+3BymSeQ/W9sF8FBq+g+t/Yg4Ut3kHN+WAPAAVdQE4=
</DataArray>
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="1">
AQAAAACAAABIAAAAIgAAAA==eF5jYEAGB+wh9AUofQNKP4DST6D0Cyj9Bkp/sAcAAU8I6Q==
</DataArray>
</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

25
python/tests/reference/Geom/clean_4_None_True.vtr Normal file
View File

@ -0,0 +1,25 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 20 0 18 0 8">
<Piece Extent="0 20 0 18 0 8">
<PointData>
</PointData>
<CellData>
<DataArray type="Int32" Name="materialpoint" format="binary" RangeMin="1" RangeMax="1">
AQAAAACAAAAALQAAJAAAAA==eF7twwEJAAAMBKH7/qWXY6DgqqmqqqqqqqqqqqqqPnhyUwtB
</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="1">
AQAAAACAAACoAAAAVQAAAA==eF5jYICAWTNBYKU9hN5pb2IMAoeh/JP2EFUXoOKX7dPTQOAaVP6m/dkzIHAHqu4BVPwhVP1jqPwTqL5nUHUvoOpeQtW9hqp7A1X3Dqrugz0ASSZF3Q==
</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="1">
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</DataArray>
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="1">
AQAAAACAAABIAAAAIgAAAA==eF5jYEAGB+wh9AUofQNKP4DST6D0Cyj9Bkp/sAcAAU8I6Q==
</DataArray>
</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

25
python/tests/reference/Geom/clean_stencil=1.geom
View File

@ -1,25 +0,0 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
2 3 4 5 6 7 8 9
10 11 12 13 14 15 16 17
18 19 20 21 22 23 24 25
26 27 28 29 30 31 32 33
34 35 36 37 38 39 40 41
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
1 2 3 4 5 6 7 8
9 10 11 12 13 14 15 16
17 18 19 20 21 22 23 24
25 26 27 28 29 30 31 32
33 34 35 36 37 38 39 40

25
python/tests/reference/Geom/clean_stencil=2.geom
View File

@ -1,25 +0,0 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
1 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2

25
python/tests/reference/Geom/clean_stencil=3.geom
View File

@ -1,25 +0,0 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
2 2 1 1 1 1 1 1
2 2 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2

25
python/tests/reference/Geom/clean_stencil=4.geom
View File

@ -1,25 +0,0 @@
4 header
grid a 8 b 5 c 4
size x 8e-06 y 5e-06 z 4e-06
origin x 0.0 y 0.0 z 0.0
homogenization 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
2 2 2 2 1 1 1 1
2 2 2 2 1 1 1 1
2 2 2 2 1 1 1 1
1 1 1 1 1 1 1 1
1 1 1 1 1 1 1 1
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2
2 2 2 2 2 2 2 2

30
python/tests/test_Geom.py
View File

@ -69,23 +69,23 @@ class TestGeom:
new = Geom.from_file(f) new = Geom.from_file(f)
assert geom_equal(new,default) assert geom_equal(new,default)
def test_read_write_vtk(self,default,tmpdir): def test_read_write_vtr(self,default,tmpdir):
default.to_vtk(tmpdir/'default') default.to_vtr(tmpdir/'default')
for _ in range(10): for _ in range(10):
time.sleep(.2) time.sleep(.2)
if os.path.exists(tmpdir/'default.vtr'): break if os.path.exists(tmpdir/'default.vtr'): break
new = Geom.from_vtk(tmpdir/'default.vtr') new = Geom.from_vtr(tmpdir/'default.vtr')
assert geom_equal(new,default) assert geom_equal(new,default)
def test_invalid_vtk(self,tmpdir): def test_invalid_vtr(self,tmpdir):
v = VTK.from_rectilinearGrid(np.random.randint(5,10,3)*2,np.random.random(3) + 1.0) v = VTK.from_rectilinearGrid(np.random.randint(5,10,3)*2,np.random.random(3) + 1.0)
v.write(tmpdir/'no_materialpoint.vtr') v.write(tmpdir/'no_materialpoint.vtr')
for _ in range(10): for _ in range(10):
time.sleep(.2) time.sleep(.2)
if os.path.exists(tmpdir/'no_materialpoint.vtr'): break if os.path.exists(tmpdir/'no_materialpoint.vtr'): break
with pytest.raises(ValueError): with pytest.raises(ValueError):
Geom.from_vtk(tmpdir/'no_materialpoint.vtr') Geom.from_vtr(tmpdir/'no_materialpoint.vtr')
@pytest.mark.parametrize('pack',[True,False]) @pytest.mark.parametrize('pack',[True,False])
@ -136,13 +136,19 @@ class TestGeom:
assert geom_equal(modified,Geom.from_file(reference)) assert geom_equal(modified,Geom.from_file(reference))
@pytest.mark.parametrize('stencil',[1,2,3,4]) @pytest.mark.parametrize('stencil',[1,2,3,4])
def test_clean(self,default,update,reference_dir,stencil): @pytest.mark.parametrize('selection',[None,1])
modified = default.copy() @pytest.mark.parametrize('periodic',[True,False])
modified.clean(stencil) def test_clean(self,update,reference_dir,stencil,selection,periodic):
tag = f'stencil={stencil}' current = Geom.from_vtr((reference_dir/'clean').with_suffix('.vtr'))
reference = reference_dir/f'clean_{tag}.geom' current.clean(stencil,None if selection is None else [selection],periodic)
if update: modified.to_file(reference) reference = reference_dir/f'clean_{stencil}_{selection}_{periodic}'
assert geom_equal(modified,Geom.from_file(reference)) altered = stencil !=1 and selection is not None
if update and stencil !=1:
current.to_vtr(reference)
for _ in range(10):
time.sleep(.2)
if os.path.exists(reference.with_suffix('.vtr')): break
assert geom_equal(current,Geom.from_vtr(reference if stencil !=1 else reference_dir/'clean'))
@pytest.mark.parametrize('grid',[ @pytest.mark.parametrize('grid',[
(10,11,10), (10,11,10),