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to_pole now blends; corrected help texts

This commit is contained in:
Philip Eisenlohr 2021-08-16 13:23:31 -04:00 committed by Martin Diehl
parent af6a99921f
commit b754617c76
2 changed files with 172 additions and 117 deletions
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27
python/damask/_orientation.py
View File

@ -517,15 +517,15 @@ class Orientation(Rotation,Crystal):
Notes
-----
Currently requires same crystal family for both orientations.
For extension to cases with differing symmetry see A. Heinz and P. Neumann 1991 and 10.1107/S0021889808016373.
For extension to cases with differing symmetry see A. Heinz and P. Neumann 1991 and 10.1107/S0021889808016373.
Examples
--------
Disorientation between two specific orientations of hexagonal symmetry:
>>> import damask
>>> a = damask.Orientation.from_Eulers(phi=[123,32,21],degrees=True,lattice='hexagonal')
>>> b = damask.Orientation.from_Eulers(phi=[104,11,87],degrees=True,lattice='hexagonal')
>>> a = damask.Orientation.from_Euler_angles(phi=[123,32,21],degrees=True,family='hexagonal')
>>> b = damask.Orientation.from_Euler_angles(phi=[104,11,87],degrees=True,family='hexagonal')
>>> a.disorientation(b)
Crystal family hexagonal
Quaternion: (real=0.976, imag=<+0.189, +0.018, +0.103>)
@ -616,7 +616,7 @@ class Orientation(Rotation,Crystal):
----------
vector : numpy.ndarray of shape (...,3)
Lab frame vector to align with crystal frame direction.
Shape of other blends with shape of own rotation array.
Shape of vector blends with shape of own rotation array.
For example, a rotation array of shape (3,2) and a (2,4) vector array result in (3,2,4) outputs.
proper : bool, optional
Consider only vectors with z >= 0, hence combine two neighboring SSTs.
@ -696,6 +696,8 @@ class Orientation(Rotation,Crystal):
----------
vector : numpy.ndarray of shape (...,3)
Vector to colorize.
Shape of vector blends with shape of own rotation array.
For example, a rotation array of shape (3,2) and a (2,4) vector array result in (3,2,4) outputs.
in_SST : bool, optional
Consider symmetrically equivalent orientations such that poles are located in SST.
Defaults to True.
@ -713,7 +715,7 @@ class Orientation(Rotation,Crystal):
Inverse pole figure color of the e_3 direction for a crystal in "Cube" orientation with cubic symmetry:
>>> import damask
>>> o = damask.Orientation(lattice='cubic')
>>> o = damask.Orientation(family='cubic')
>>> o.IPF_color([0,0,1])
array([1., 0., 0.])
@ -835,22 +837,27 @@ class Orientation(Rotation,Crystal):
----------
uvw|hkl : numpy.ndarray of shape (...,3)
Miller indices of crystallographic direction or plane normal.
Shape of vector blends with shape of own rotation array.
For example, a rotation array of shape (3,2) and a (2,4) vector array result in (3,2,4) outputs.
with_symmetry : bool, optional
Calculate all N symmetrically equivalent vectors.
Returns
-------
vector : numpy.ndarray of shape (...,3) or (N,...,3)
vector : numpy.ndarray of shape (...,3) or (...,N,3)
Lab frame vector (or vectors if with_symmetry) along [uvw] direction or (hkl) plane normal.
"""
v = self.to_frame(uvw=uvw,hkl=hkl)
blend = util.shapeblender(self.shape,v.shape[:-1])
if with_symmetry:
sym_ops = self.symmetry_operations
v = sym_ops.broadcast_to(sym_ops.shape+v.shape[:-1],mode='right') \
@ np.broadcast_to(v,sym_ops.shape+v.shape)
return ~(self if self.shape+v.shape[:-1] == () else self.broadcast_to(self.shape+v.shape[:-1],mode='right')) \
@ np.broadcast_to(v,self.shape+v.shape)
shape = v.shape[:-1]+sym_ops.shape
blend += sym_ops.shape
v = sym_ops.broadcast_to(shape) \
@ np.broadcast_to(v.reshape(util.shapeshifter(v.shape,shape+(3,))),shape+(3,))
return ~(self.broadcast_to(blend)) \
@ np.broadcast_to(v,blend+(3,))
def Schmid(self,*,N_slip=None,N_twin=None):

262
python/tests/test_Orientation.py
View File

@ -77,6 +77,16 @@ class TestOrientation:
with pytest.raises(ValueError):
Orientation(**kwargs)
@pytest.mark.parametrize('invalid_family',[None,'fcc','bcc','hello'])
def test_invalid_family_init(self,invalid_family):
with pytest.raises(KeyError):
Orientation(family=invalid_family)
@pytest.mark.parametrize('invalid_lattice',[None,'fcc','bcc','hello'])
def test_invalid_family_init(self,invalid_lattice):
with pytest.raises(KeyError):
Orientation(lattice=invalid_lattice)
@pytest.mark.parametrize('kwargs',[
dict(lattice='aP',a=1.0,b=1.1,c=1.2,alpha=np.pi/4,beta=np.pi/3,gamma=np.pi/2),
dict(lattice='mP',a=1.0,b=1.1,c=1.2, beta=np.pi/3 ),
@ -203,6 +213,15 @@ class TestOrientation:
FZ = np.argmin(abs(eq.misorientation(i.broadcast_to(len(eq))).as_axis_angle(pair=True)[1]))
assert o.reduced == eq[FZ]
@pytest.mark.parametrize('family',crystal_families)
def test_reduced_corner_cases(self,family):
# test whether there is always a sym-eq rotation that falls into the FZ
N = np.random.randint(10,40)
size = np.ones(3)*np.pi**(2./3.)
grid = grid_filters.coordinates0_node([N+1,N+1,N+1],size,-size*.5)
evenly_distributed = Orientation.from_cubochoric(x=grid[:-2,:-2,:-2],family=family)
assert evenly_distributed.shape == evenly_distributed.reduced.shape
@pytest.mark.parametrize('family',crystal_families)
@pytest.mark.parametrize('N',[1,8,32])
def test_disorientation(self,family,N):
@ -221,81 +240,12 @@ class TestOrientation:
.misorientation(p[n].equivalent[ops[n][1]])
.as_quaternion())
@pytest.mark.parametrize('family',crystal_families)
@pytest.mark.parametrize('a,b',[
((2,3,2),(2,3,2)),
((2,2),(4,4)),
((3,1),(1,3)),
(None,None),
])
def test_disorientation_blending(self,family,a,b):
o = Orientation.from_random(family=family,shape=a)
p = Orientation.from_random(family=family,shape=b)
blend = util.shapeblender(o.shape,p.shape)
for loc in np.random.randint(0,blend,(10,len(blend))):
assert o[tuple(loc[:len(o.shape)])].disorientation(p[tuple(loc[-len(p.shape):])]) \
.isclose(o.disorientation(p)[tuple(loc)])
@pytest.mark.parametrize('family',crystal_families)
def test_disorientation360(self,family):
o_1 = Orientation(Rotation(),family=family)
o_2 = Orientation.from_Euler_angles(family=family,phi=[360,0,0],degrees=True)
assert np.allclose((o_1.disorientation(o_2)).as_matrix(),np.eye(3))
@pytest.mark.parametrize('family',crystal_families)
@pytest.mark.parametrize('shape',[(1),(2,3),(4,3,2)])
def test_reduced_vectorization(self,family,shape):
o = Orientation.from_random(family=family,shape=shape)
for r, theO in zip(o.reduced.flatten(),o.flatten()):
assert r == theO.reduced
@pytest.mark.parametrize('family',crystal_families)
def test_reduced_corner_cases(self,family):
# test whether there is always a sym-eq rotation that falls into the FZ
N = np.random.randint(10,40)
size = np.ones(3)*np.pi**(2./3.)
grid = grid_filters.coordinates0_node([N+1,N+1,N+1],size,-size*.5)
evenly_distributed = Orientation.from_cubochoric(x=grid[:-2,:-2,:-2],family=family)
assert evenly_distributed.shape == evenly_distributed.reduced.shape
@pytest.mark.parametrize('family',crystal_families)
@pytest.mark.parametrize('shape',[(1),(2,3),(4,3,2)])
@pytest.mark.parametrize('vector',np.array([[1,0,0],[1,2,3],[-1,1,-1]]))
@pytest.mark.parametrize('proper',[True,False])
def test_to_SST_vectorization(self,family,shape,vector,proper):
o = Orientation.from_random(family=family,shape=shape)
for r, theO in zip(o.to_SST(vector=vector,proper=proper).reshape((-1,3)),o.flatten()):
assert np.allclose(r,theO.to_SST(vector=vector,proper=proper))
@pytest.mark.parametrize('family',crystal_families)
@pytest.mark.parametrize('shape',[(1),(2,3),(4,3,2)])
@pytest.mark.parametrize('vector',np.array([[1,0,0],[1,2,3],[-1,1,-1]]))
@pytest.mark.parametrize('proper',[True,False])
@pytest.mark.parametrize('in_SST',[True,False])
def test_IPF_color_vectorization(self,family,shape,vector,proper,in_SST):
o = Orientation.from_random(family=family,shape=shape)
for r, theO in zip(o.IPF_color(vector,in_SST=in_SST,proper=proper).reshape((-1,3)),o.flatten()):
assert np.allclose(r,theO.IPF_color(vector,in_SST=in_SST,proper=proper))
@pytest.mark.parametrize('family',crystal_families)
@pytest.mark.parametrize('a,b',[
((2,3,2),(2,3,2)),
((2,2),(4,4)),
((3,1),(1,3)),
(None,(3,)),
])
def test_to_SST_blending(self,family,a,b):
o = Orientation.from_random(family=family,shape=a)
v = np.random.random(b+(3,))
blend = util.shapeblender(o.shape,b)
for loc in np.random.randint(0,blend,(10,len(blend))):
print(f'{a}/{b} @ {loc}')
print(o[tuple(loc[:len(o.shape)])].to_SST(v[tuple(loc[-len(b):])]))
print(o.to_SST(v)[tuple(loc)])
assert np.allclose(o[tuple(loc[:len(o.shape)])].to_SST(v[tuple(loc[-len(b):])]),
o.to_SST(v)[tuple(loc)])
@pytest.mark.parametrize('color',[{'label':'red', 'RGB':[1,0,0],'direction':[0,0,1]},
{'label':'green','RGB':[0,1,0],'direction':[0,1,1]},
{'label':'blue', 'RGB':[0,0,1],'direction':[1,1,1]}])
@ -314,33 +264,6 @@ class TestOrientation:
color = o.IPF_color(vector=direction,proper=proper)
assert np.allclose(np.broadcast_to(color[0,...],color.shape),color)
@pytest.mark.parametrize('family',crystal_families)
def test_in_FZ_vectorization(self,set_of_rodrigues,family):
result = Orientation.from_Rodrigues_vector(rho=set_of_rodrigues.reshape((-1,4,4)),family=family).in_FZ.reshape(-1)
for r,rho in zip(result,set_of_rodrigues[:len(result)]):
assert r == Orientation.from_Rodrigues_vector(rho=rho,family=family).in_FZ
@pytest.mark.parametrize('family',crystal_families)
def test_in_disorientation_FZ_vectorization(self,set_of_rodrigues,family):
result = Orientation.from_Rodrigues_vector(rho=set_of_rodrigues.reshape((-1,4,4)),
family=family).in_disorientation_FZ.reshape(-1)
for r,rho in zip(result,set_of_rodrigues[:len(result)]):
assert r == Orientation.from_Rodrigues_vector(rho=rho,family=family).in_disorientation_FZ
@pytest.mark.parametrize('proper',[True,False])
@pytest.mark.parametrize('family',crystal_families)
def test_in_SST_vectorization(self,family,proper):
vecs = np.random.rand(20,4,3)
result = Orientation(family=family).in_SST(vecs,proper).flatten()
for r,v in zip(result,vecs.reshape((-1,3))):
assert np.all(r == Orientation(family=family).in_SST(v,proper))
@pytest.mark.parametrize('invalid_family',[None,'fcc','bcc','hello'])
def test_invalid_lattice_init(self,invalid_family):
with pytest.raises(KeyError):
Orientation(family=invalid_family)
@pytest.mark.parametrize('relation',[None,'Peter','Paul'])
def test_unknown_relation(self,relation):
with pytest.raises(KeyError):
@ -371,12 +294,6 @@ class TestOrientation:
o = Orientation(family='cubic') # noqa
with pytest.raises(ValueError):
eval(f'o.{function}(np.ones(4))')
@pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch'])
@pytest.mark.parametrize('lattice',['cF','cI'])
def test_relationship_vectorize(self,set_of_quaternions,lattice,model):
r = Orientation(rotation=set_of_quaternions[:200].reshape((50,4,4)),lattice=lattice).related(model)
for i in range(200):
assert (r.reshape((-1,200))[:,i] == Orientation(set_of_quaternions[i],lattice=lattice).related(model)).all()
@pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch'])
@pytest.mark.parametrize('lattice',['cF','cI'])
@ -411,7 +328,6 @@ class TestOrientation:
)
assert np.allclose(o.to_frame(uvw=np.eye(3)),basis), 'Lattice basis disagrees with initialization'
@pytest.mark.parametrize('lattice,a,b,c,alpha,beta,gamma',
[
('aP',0.5,2.0,3.0,0.8,0.5,1.2),
@ -421,7 +337,6 @@ class TestOrientation:
('hP',1.0,1.0,1.6,np.pi/2,np.pi/2,2*np.pi/3),
('cF',1.0,1.0,1.0,np.pi/2,np.pi/2,np.pi/2),
])
@pytest.mark.parametrize('kw',['uvw','hkl'])
@pytest.mark.parametrize('with_symmetry',[False,True])
@pytest.mark.parametrize('shape',[None,1,(12,24)])
@ -436,7 +351,7 @@ class TestOrientation:
a=a,b=b,c=c,
alpha=alpha,beta=beta,gamma=gamma)
assert o.to_pole(**{kw:vector,'with_symmetry':with_symmetry}).shape \
== o.shape + (o.symmetry_operations.shape if with_symmetry else ()) + vector.shape
== o.shape + vector.shape[:-1] + (o.symmetry_operations.shape if with_symmetry else ()) + vector.shape[-1:]
@pytest.mark.parametrize('lattice',['hP','cI','cF']) #tI not included yet
def test_Schmid(self,update,ref_path,lattice):
@ -448,12 +363,145 @@ class TestOrientation:
table = Table(P.reshape(-1,9),{'Schmid':(3,3,)})
table.save(reference)
assert np.allclose(P,Table.load(reference).get('Schmid'))
### vectorization tests ###
@pytest.mark.parametrize('lattice',['hP','cI','cF']) # tI not included yet
def test_Schmid_vectorize(self,lattice):
def test_Schmid_vectorization(self,lattice):
O = Orientation.from_random(shape=4,lattice=lattice) # noqa
for mode in ['slip','twin']:
Ps = O.Schmid(N_slip='*') if mode == 'slip' else O.Schmid(N_twin='*')
for i in range(4):
P = O[i].Schmid(N_slip='*') if mode == 'slip' else O[i].Schmid(N_twin='*')
assert np.allclose(P,Ps[:,i])
@pytest.mark.parametrize('family',crystal_families)
@pytest.mark.parametrize('shape',[(1),(2,3),(4,3,2)])
def test_reduced_vectorization(self,family,shape):
o = Orientation.from_random(family=family,shape=shape)
for r, theO in zip(o.reduced.flatten(),o.flatten()):
assert r == theO.reduced
@pytest.mark.parametrize('family',crystal_families)
@pytest.mark.parametrize('shape',[(1),(2,3),(4,3,2)])
@pytest.mark.parametrize('vector',np.array([[1,0,0],[1,2,3],[-1,1,-1]]))
@pytest.mark.parametrize('proper',[True,False])
def test_to_SST_vectorization(self,family,shape,vector,proper):
o = Orientation.from_random(family=family,shape=shape)
for r, theO in zip(o.to_SST(vector=vector,proper=proper).reshape((-1,3)),o.flatten()):
assert np.allclose(r,theO.to_SST(vector=vector,proper=proper))
@pytest.mark.parametrize('proper',[True,False])
@pytest.mark.parametrize('family',crystal_families)
def test_in_SST_vectorization(self,family,proper):
vecs = np.random.rand(20,4,3)
result = Orientation(family=family).in_SST(vecs,proper).flatten()
for r,v in zip(result,vecs.reshape((-1,3))):
assert np.all(r == Orientation(family=family).in_SST(v,proper))
@pytest.mark.parametrize('family',crystal_families)
@pytest.mark.parametrize('shape',[(1),(2,3),(4,3,2)])
@pytest.mark.parametrize('vector',np.array([[1,0,0],[1,2,3],[-1,1,-1]]))
@pytest.mark.parametrize('proper',[True,False])
@pytest.mark.parametrize('in_SST',[True,False])
def test_IPF_color_vectorization(self,family,shape,vector,proper,in_SST):
o = Orientation.from_random(family=family,shape=shape)
for r, theO in zip(o.IPF_color(vector,in_SST=in_SST,proper=proper).reshape((-1,3)),o.flatten()):
assert np.allclose(r,theO.IPF_color(vector,in_SST=in_SST,proper=proper))
@pytest.mark.parametrize('family',crystal_families)
def test_in_FZ_vectorization(self,set_of_rodrigues,family):
result = Orientation.from_Rodrigues_vector(rho=set_of_rodrigues.reshape((-1,4,4)),family=family).in_FZ.reshape(-1)
for r,rho in zip(result,set_of_rodrigues[:len(result)]):
assert r == Orientation.from_Rodrigues_vector(rho=rho,family=family).in_FZ
@pytest.mark.parametrize('family',crystal_families)
def test_in_disorientation_FZ_vectorization(self,set_of_rodrigues,family):
result = Orientation.from_Rodrigues_vector(rho=set_of_rodrigues.reshape((-1,4,4)),
family=family).in_disorientation_FZ.reshape(-1)
for r,rho in zip(result,set_of_rodrigues[:len(result)]):
assert r == Orientation.from_Rodrigues_vector(rho=rho,family=family).in_disorientation_FZ
@pytest.mark.parametrize('model',['Bain','KS','GT','GT_prime','NW','Pitsch'])
@pytest.mark.parametrize('lattice',['cF','cI'])
def test_relationship_vectorization(self,set_of_quaternions,lattice,model):
r = Orientation(rotation=set_of_quaternions[:200].reshape((50,4,4)),lattice=lattice).related(model)
for i in range(200):
assert (r.reshape((-1,200))[:,i] == Orientation(set_of_quaternions[i],lattice=lattice).related(model)).all()
### blending tests ###
@pytest.mark.parametrize('family',crystal_families)
@pytest.mark.parametrize('left,right',[
((2,3,2),(2,3,2)),
((2,2),(4,4)),
((3,1),(1,3)),
(None,None),
])
def test_disorientation_blending(self,family,left,right):
o = Orientation.from_random(family=family,shape=left)
p = Orientation.from_random(family=family,shape=right)
blend = util.shapeblender(o.shape,p.shape)
for loc in np.random.randint(0,blend,(10,len(blend))):
# print(f'{a}/{b} @ {loc}')
# print(o[tuple(loc[:len(o.shape)])].disorientation(p[tuple(loc[-len(p.shape):])]))
# print(o.disorientation(p)[tuple(loc)])
assert o[tuple(loc[:len(o.shape)])].disorientation(p[tuple(loc[-len(p.shape):])]) \
.isclose(o.disorientation(p)[tuple(loc)])
@pytest.mark.parametrize('family',crystal_families)
@pytest.mark.parametrize('left,right',[
((2,3,2),(2,3,2)),
((2,2),(4,4)),
((3,1),(1,3)),
(None,(3,)),
])
def test_IPF_color_blending(self,family,left,right):
o = Orientation.from_random(family=family,shape=left)
v = np.random.random(right+(3,))
blend = util.shapeblender(o.shape,v.shape[:-1])
for loc in np.random.randint(0,blend,(10,len(blend))):
assert np.allclose(o[tuple(loc[:len(o.shape)])].IPF_color(v[tuple(loc[-len(v.shape[:-1]):])]),
o.IPF_color(v)[tuple(loc)])
@pytest.mark.parametrize('family',crystal_families)
@pytest.mark.parametrize('left,right',[
((2,3,2),(2,3,2)),
((2,2),(4,4)),
((3,1),(1,3)),
(None,(3,)),
])
def test_to_SST_blending(self,family,left,right):
o = Orientation.from_random(family=family,shape=left)
v = np.random.random(right+(3,))
blend = util.shapeblender(o.shape,v.shape[:-1])
for loc in np.random.randint(0,blend,(10,len(blend))):
assert np.allclose(o[tuple(loc[:len(o.shape)])].to_SST(v[tuple(loc[-len(v.shape[:-1]):])]),
o.to_SST(v)[tuple(loc)])
@pytest.mark.parametrize('lattice,a,b,c,alpha,beta,gamma',
[
('aP',0.5,2.0,3.0,0.8,0.5,1.2),
('mP',1.0,2.0,3.0,np.pi/2,0.5,np.pi/2),
('oI',0.5,1.5,3.0,np.pi/2,np.pi/2,np.pi/2),
('tP',0.5,0.5,3.0,np.pi/2,np.pi/2,np.pi/2),
('hP',1.0,1.0,1.6,np.pi/2,np.pi/2,2*np.pi/3),
('cF',1.0,1.0,1.0,np.pi/2,np.pi/2,np.pi/2),
])
@pytest.mark.parametrize('left,right',[
((2,3,2),(2,3,2)),
((2,2),(4,4)),
((3,1),(1,3)),
(None,(3,)),
])
def test_to_pole_blending(self,lattice,a,b,c,alpha,beta,gamma,left,right):
o = Orientation.from_random(shape=left,
lattice=lattice,
a=a,b=b,c=c,
alpha=alpha,beta=beta,gamma=gamma)
v = np.random.random(right+(3,))
blend = util.shapeblender(o.shape,v.shape[:-1])
for loc in np.random.randint(0,blend,(10,len(blend))):
assert np.allclose(o[tuple(loc[:len(o.shape)])].to_pole(uvw=v[tuple(loc[-len(v.shape[:-1]):])]),
o.to_pole(uvw=v)[tuple(loc)])