DAMASK_EICMD/python/tests/test_Geom.py

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import os
import time
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import pytest
import numpy as np
from damask import VTK
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from damask import Geom
from damask import Rotation
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from damask import util
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def geom_equal(a,b):
return np.all(a.get_microstructure() == b.get_microstructure()) and \
np.all(a.get_grid() == b.get_grid()) and \
np.allclose(a.get_size(), b.get_size())
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@pytest.fixture
def default():
"""Simple geometry."""
x=np.concatenate((np.ones(40,dtype=int),
np.arange(2,42),
np.ones(40,dtype=int)*2,
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np.arange(1,41))).reshape(8,5,4,order='F')
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return Geom(x,[8e-6,5e-6,4e-6])
@pytest.fixture
def reference_dir(reference_dir_base):
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"""Directory containing reference results."""
return reference_dir_base/'Geom'
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class TestGeom:
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@pytest.mark.parametrize('flavor',['plain','explicit'])
def test_duplicate(self,default,flavor):
if flavor == 'plain':
modified = default.duplicate()
elif flavor == 'explicit':
modified = default.duplicate(
default.get_microstructure(),
default.get_size(),
default.get_origin()
)
print(modified)
assert geom_equal(default,modified)
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@pytest.mark.parametrize('masked',[True,False])
def test_set_microstructure(self,default,masked):
old = default.get_microstructure()
new = np.random.randint(200,size=default.grid)
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default.set_microstructure(np.ma.MaskedArray(new,np.full_like(new,masked)))
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assert np.all(default.microstructure==(old if masked else new))
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def test_write_read_str(self,default,tmpdir):
default.to_file(tmpdir/'default.geom')
new = Geom.from_file(tmpdir/'default.geom')
assert geom_equal(default,new)
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def test_write_read_file(self,default,tmpdir):
with open(tmpdir/'default.geom','w') as f:
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default.to_file(f)
with open(tmpdir/'default.geom') as f:
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new = Geom.from_file(f)
assert geom_equal(default,new)
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def test_write_as_ASCII(self,default,tmpdir):
with open(tmpdir/'str.geom','w') as f:
f.write(default.as_ASCII())
with open(tmpdir/'str.geom') as f:
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new = Geom.from_file(f)
assert geom_equal(default,new)
def test_export_import_vtk(self,default,tmpdir):
default.to_vtr(tmpdir/'default')
assert geom_equal(default,Geom.from_vtr(tmpdir/'default.vtr'))
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def test_read_write_vtr(self,default,tmpdir):
default.to_vtr(tmpdir/'default')
for _ in range(10):
time.sleep(.2)
if os.path.exists(tmpdir/'default.vtr'): break
new = Geom.from_vtr(tmpdir/'default.vtr')
assert geom_equal(new,default)
def test_invalid_vtr(self,tmpdir):
v = VTK.from_rectilinearGrid(np.random.randint(5,10,3)*2,np.random.random(3) + 1.0)
v.write(tmpdir/'no_materialpoint.vtr')
for _ in range(10):
time.sleep(.2)
if os.path.exists(tmpdir/'no_materialpoint.vtr'): break
with pytest.raises(ValueError):
Geom.from_vtr(tmpdir/'no_materialpoint.vtr')
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@pytest.mark.parametrize('pack',[True,False])
def test_pack(self,default,tmpdir,pack):
default.to_file(tmpdir/'default.geom',pack=pack)
new = Geom.from_file(tmpdir/'default.geom')
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assert geom_equal(new,default)
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def test_invalid_combination(self,default):
with pytest.raises(ValueError):
default.duplicate(default.microstructure[1:,1:,1:],size=np.ones(3), autosize=True)
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def test_invalid_size(self,default):
with pytest.raises(ValueError):
default.duplicate(default.microstructure[1:,1:,1:],size=np.ones(2))
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def test_invalid_origin(self,default):
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with pytest.raises(ValueError):
default.duplicate(default.microstructure[1:,1:,1:],origin=np.ones(4))
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def test_invalid_microstructure_size(self,default):
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microstructure = np.ones((3,3))
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with pytest.raises(ValueError):
default.duplicate(microstructure)
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def test_invalid_microstructure_type(self,default):
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microstructure = np.random.randint(1,300,(3,4,5))==1
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with pytest.raises(TypeError):
default.duplicate(microstructure)
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def test_invalid_homogenization(self,default):
with pytest.raises(TypeError):
default.set_homogenization(homogenization=0)
@pytest.mark.parametrize('directions,reflect',[
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(['x'], False),
(['x','y','z'],True),
(['z','x','y'],False),
(['y','z'], False)
]
)
def test_mirror(self,default,update,reference_dir,directions,reflect):
modified = default.mirror(directions,reflect)
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tag = f'directions={"-".join(directions)}_reflect={reflect}'
reference = reference_dir/f'mirror_{tag}.geom'
if update: modified.to_file(reference)
assert geom_equal(Geom.from_file(reference),
modified)
@pytest.mark.parametrize('directions',[
['x'],
['x','y','z'],
['z','x','y'],
['y','z'],
]
)
def test_flip(self,default,update,reference_dir,directions):
modified = default.flip(directions)
tag = f'directions={"-".join(directions)}'
reference = reference_dir/f'flip_{tag}.geom'
if update: modified.to_file(reference)
assert geom_equal(Geom.from_file(reference),
modified)
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@pytest.mark.parametrize('directions',[(1,2,'y'),('a','b','x'),[1]])
def test_mirror_invalid(self,default,directions):
with pytest.raises(ValueError):
default.mirror(directions)
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@pytest.mark.parametrize('stencil',[1,2,3,4])
@pytest.mark.parametrize('selection',[None,[1],[1,2,3]])
@pytest.mark.parametrize('periodic',[True,False])
def test_clean(self,default,update,reference_dir,stencil,selection,periodic):
current = default.clean(stencil,selection,periodic)
reference = reference_dir/f'clean_{stencil}_{"+".join(map(str,[None] if selection is None else selection))}_{periodic}'
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(Geom.from_vtr(reference) if stencil > 1 else default,
current
)
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@pytest.mark.parametrize('grid',[
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(10,11,10),
[10,13,10],
np.array((10,10,10)),
np.array((8, 10,12)),
np.array((5, 4, 20)),
np.array((10,20,2))
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]
)
def test_scale(self,default,update,reference_dir,grid):
modified = default.scale(grid)
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tag = f'grid={util.srepr(grid,"-")}'
reference = reference_dir/f'scale_{tag}.geom'
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if update: modified.to_file(reference)
assert geom_equal(Geom.from_file(reference),
modified)
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def test_renumber(self,default):
microstructure = default.get_microstructure()
for m in np.unique(microstructure):
microstructure[microstructure==m] = microstructure.max() + np.random.randint(1,30)
modified = default.duplicate(microstructure)
assert not geom_equal(modified,default)
assert geom_equal(default,
modified.renumber())
def test_substitute(self,default):
offset = np.random.randint(1,500)
modified = default.duplicate(default.get_microstructure() + offset)
assert not geom_equal(modified,default)
assert geom_equal(default,
modified.substitute(np.arange(default.microstructure.max())+1+offset,
np.arange(default.microstructure.max())+1))
@pytest.mark.parametrize('axis_angle',[np.array([1,0,0,86.7]), np.array([0,1,0,90.4]), np.array([0,0,1,90]),
np.array([1,0,0,175]),np.array([0,-1,0,178]),np.array([0,0,1,180])])
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def test_rotate360(self,default,axis_angle):
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modified = default.copy()
for i in range(np.rint(360/axis_angle[3]).astype(int)):
modified.rotate(Rotation.from_axis_angle(axis_angle,degrees=True))
assert geom_equal(default,modified)
@pytest.mark.parametrize('Eulers',[[32.0,68.0,21.0],
[0.0,32.0,240.0]])
def test_rotate(self,default,update,reference_dir,Eulers):
modified = default.rotate(Rotation.from_Eulers(Eulers,degrees=True))
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tag = f'Eulers={util.srepr(Eulers,"-")}'
reference = reference_dir/f'rotate_{tag}.geom'
if update: modified.to_file(reference)
assert geom_equal(Geom.from_file(reference),
modified)
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def test_canvas(self,default):
grid = default.grid
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grid_add = np.random.randint(0,30,(3))
modified = default.canvas(grid + grid_add)
assert np.all(modified.microstructure[:grid[0],:grid[1],:grid[2]] == default.microstructure)
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@pytest.mark.parametrize('center1,center2',[(np.random.random(3)*.5,np.random.random(3)),
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(np.random.randint(4,8,(3)),np.random.randint(9,12,(3)))])
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@pytest.mark.parametrize('diameter',[np.random.random(3)*.5,
np.random.randint(4,10,(3))])
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def test_add_primitive(self,diameter,center1,center2):
"""Same volume fraction for periodic microstructures and different center."""
o = np.random.random(3)-.5
g = np.random.randint(8,32,(3))
s = np.random.random(3)+.5
G_1 = Geom(np.ones(g,'i'),s,o).add_primitive(diameter,center1,1)
G_2 = Geom(np.ones(g,'i'),s,o).add_primitive(diameter,center2,1)
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assert np.count_nonzero(G_1.microstructure!=2) == np.count_nonzero(G_2.microstructure!=2)
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@pytest.mark.parametrize('trigger',[[1],[]])
def test_vicinity_offset(self,trigger):
offset = np.random.randint(2,4)
vicinity = np.random.randint(2,4)
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g = np.random.randint(28,40,(3))
m = np.ones(g,'i')
x = (g*np.random.permutation(np.array([.5,1,1]))).astype('i')
m[slice(0,x[0]),slice(0,x[1]),slice(0,x[2])] = 2
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m2 = m.copy()
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for i in [0,1,2]:
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m2[(np.roll(m,+vicinity,i)-m)!=0] += offset
m2[(np.roll(m,-vicinity,i)-m)!=0] += offset
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if len(trigger) > 0:
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m2[m==1] = 1
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geom = Geom(m,np.random.rand(3)).vicinity_offset(vicinity,offset,trigger=trigger)
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assert np.all(m2==geom.microstructure)
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@pytest.mark.parametrize('periodic',[True,False])
def test_vicinity_offset_invariant(self,default,periodic):
old = default.get_microstructure()
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default.vicinity_offset(trigger=[old.max()+1,old.min()-1])
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assert np.all(old==default.microstructure)
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@pytest.mark.parametrize('periodic',[True,False])
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def test_tessellation_approaches(self,periodic):
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grid = np.random.randint(10,20,3)
size = np.random.random(3) + 1.0
N_seeds= np.random.randint(10,30)
seeds = np.random.rand(N_seeds,3) * np.broadcast_to(size,(N_seeds,3))
Voronoi = Geom.from_Voronoi_tessellation( grid,size,seeds, periodic)
Laguerre = Geom.from_Laguerre_tessellation(grid,size,seeds,np.ones(N_seeds),periodic)
assert geom_equal(Laguerre,Voronoi)
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def test_Laguerre_weights(self):
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grid = np.random.randint(10,20,3)
size = np.random.random(3) + 1.0
N_seeds= np.random.randint(10,30)
seeds = np.random.rand(N_seeds,3) * np.broadcast_to(size,(N_seeds,3))
weights= np.full((N_seeds),-np.inf)
ms = np.random.randint(1, N_seeds+1)
weights[ms-1] = np.random.random()
Laguerre = Geom.from_Laguerre_tessellation(grid,size,seeds,weights,np.random.random()>0.5)
assert np.all(Laguerre.microstructure == ms)
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@pytest.mark.parametrize('approach',['Laguerre','Voronoi'])
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def test_tessellate_bicrystal(self,approach):
grid = np.random.randint(5,10,3)*2
size = grid.astype(np.float)
seeds = np.vstack((size*np.array([0.5,0.25,0.5]),size*np.array([0.5,0.75,0.5])))
microstructure = np.ones(grid)
microstructure[:,grid[1]//2:,:] = 2
if approach == 'Laguerre':
geom = Geom.from_Laguerre_tessellation(grid,size,seeds,np.ones(2),np.random.random()>0.5)
elif approach == 'Voronoi':
geom = Geom.from_Voronoi_tessellation(grid,size,seeds, np.random.random()>0.5)
assert np.all(geom.microstructure == microstructure)