encapsulating all lattice(-family) related data
This commit is contained in:
Martin Diehl
parent
4701eea10f
commit
3c8d06b6f1
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@ -1,4 +1,5 @@
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import inspect
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import copy
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import numpy as np
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@ -135,37 +136,11 @@ class Orientation(Rotation):
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if family in set(lattice_symmetries.values()) and lattice is None:
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self.family = family
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self.lattice = None
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self.structure = l = LatticeFamily(self.family) # noqa
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self.immutable = l.immutable
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self.basis = l.basis
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self.a = self.b = self.c = None
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self.alpha = self.beta = self.gamma = None
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self.structure = LatticeFamily(self.family)
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elif lattice in lattice_symmetries:
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self.family = lattice_symmetries[lattice]
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self.lattice = lattice
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self.structure = l = Lattice(self.lattice, a,b,c, alpha,beta,gamma, degrees) # noqa
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self.immutable = l.immutable
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self.basis = l.basis
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self.a = l.a
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self.b = l.b
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self.c = l.c
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self.alpha = l.alpha
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self.beta = l.beta
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self.gamma = l.gamma
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self.ratio = l.ratio
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self.to_frame = l.to_frame
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self.kinematics = l.kinematics
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self.relation_operations = l.relation_operations
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self.structure = l = Lattice(self.lattice, a,b,c, alpha,beta,gamma, degrees)
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else:
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raise KeyError(f'no valid family or lattice')
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@ -177,18 +152,12 @@ class Orientation(Rotation):
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+ [super().__repr__()])
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def __copy__(self,**kwargs):
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def __copy__(self,rotation=None):
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"""Create deep copy."""
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return self.__class__(rotation= kwargs['rotation'] if 'rotation' in kwargs else self.quaternion,
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family = kwargs['family'] if 'family' in kwargs else self.family,
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lattice = kwargs['lattice'] if 'lattice' in kwargs else self.lattice,
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a = kwargs['a'] if 'a' in kwargs else self.a,
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b = kwargs['b'] if 'b' in kwargs else self.b,
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c = kwargs['c'] if 'c' in kwargs else self.c,
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alpha = kwargs['alpha'] if 'alpha' in kwargs else self.alpha,
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beta = kwargs['beta'] if 'beta' in kwargs else self.beta,
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gamma = kwargs['gamma'] if 'gamma' in kwargs else self.gamma,
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)
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dup = copy.deepcopy(self)
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if rotation is not None:
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dup.quaternion = Orientation(rotation,family='cubic').quaternion
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return dup
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copy = __copy__
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@ -415,8 +384,8 @@ class Orientation(Rotation):
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"""
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o = cls(**kwargs)
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x = o.to_frame(uvw=uvw)
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z = o.to_frame(hkl=hkl)
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x = o.structure.to_frame(uvw=uvw)
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z = o.structure.to_frame(hkl=hkl)
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om = np.stack([x,np.cross(z,x),z],axis=-2)
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return o.copy(rotation=Rotation.from_matrix(tensor.transpose(om/np.linalg.norm(om,axis=-1,keepdims=True))))
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@ -707,21 +676,21 @@ class Orientation(Rotation):
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if not isinstance(vector,np.ndarray) or vector.shape[-1] != 3:
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raise ValueError('input is not a field of three-dimensional vectors')
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if self.basis is None: # direct exit for no symmetry
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if self.structure.basis is None: # direct exit for no symmetry
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return np.ones_like(vector[...,0],bool)
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if proper:
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components_proper = np.around(np.einsum('...ji,...i',
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np.broadcast_to(self.basis['proper'], vector.shape+(3,)),
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np.broadcast_to(self.structure.basis['proper'], vector.shape+(3,)),
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vector), 12)
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components_improper = np.around(np.einsum('...ji,...i',
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np.broadcast_to(self.basis['improper'], vector.shape+(3,)),
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np.broadcast_to(self.structure.basis['improper'], vector.shape+(3,)),
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vector), 12)
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return np.all(components_proper >= 0.0,axis=-1) \
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| np.all(components_improper >= 0.0,axis=-1)
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else:
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components = np.around(np.einsum('...ji,...i',
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np.broadcast_to(self.basis['improper'], vector.shape+(3,)),
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np.broadcast_to(self.structure.basis['improper'], vector.shape+(3,)),
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np.block([vector[...,:2],np.abs(vector[...,2:3])])), 12)
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return np.all(components >= 0.0,axis=-1)
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@ -762,15 +731,15 @@ class Orientation(Rotation):
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vector_ = self.to_SST(vector,proper) if in_SST else \
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self @ np.broadcast_to(vector,self.shape+(3,))
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if self.basis is None: # direct exit for no symmetry
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if self.structure.basis is None: # direct exit for no symmetry
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return np.zeros_like(vector_)
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if proper:
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components_proper = np.around(np.einsum('...ji,...i',
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np.broadcast_to(self.basis['proper'], vector_.shape+(3,)),
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np.broadcast_to(self.structure.basis['proper'], vector_.shape+(3,)),
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vector_), 12)
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components_improper = np.around(np.einsum('...ji,...i',
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np.broadcast_to(self.basis['improper'], vector_.shape+(3,)),
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np.broadcast_to(self.structure.basis['improper'], vector_.shape+(3,)),
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vector_), 12)
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in_SST = np.all(components_proper >= 0.0,axis=-1) \
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| np.all(components_improper >= 0.0,axis=-1)
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@ -778,7 +747,7 @@ class Orientation(Rotation):
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components_proper,components_improper)
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else:
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components = np.around(np.einsum('...ji,...i',
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np.broadcast_to(self.basis['improper'], vector_.shape+(3,)),
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np.broadcast_to(self.structure.basis['improper'], vector_.shape+(3,)),
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np.block([vector_[...,:2],np.abs(vector_[...,2:3])])), 12)
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in_SST = np.all(components >= 0.0,axis=-1)
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@ -813,7 +782,7 @@ class Orientation(Rotation):
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"""
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sym_ops = self.structure.symmetry_operations
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# ToDo: simplify 'with_symmetry'
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v = self.to_frame(uvw=uvw,hkl=hkl)
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v = self.structure.to_frame(uvw=uvw,hkl=hkl)
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if with_symmetry:
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v = sym_ops.broadcast_to(sym_ops.shape+v.shape[:-1],mode='right') \
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@ np.broadcast_to(v,sym_ops.shape+v.shape)
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@ -850,8 +819,8 @@ class Orientation(Rotation):
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"""
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try:
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d = self.to_frame(uvw=self.kinematics(mode)['direction'])
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p = self.to_frame(hkl=self.kinematics(mode)['plane'])
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d = self.structure.to_frame(uvw=self.structure.kinematics(mode)['direction'])
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p = self.structure.to_frame(hkl=self.structure.kinematics(mode)['plane'])
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except KeyError:
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raise (f'"{mode}" not defined for lattice "{self.lattice}"')
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P = np.einsum('...i,...j',d/np.linalg.norm(d,axis=-1,keepdims=True),
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@ -869,14 +838,15 @@ class Orientation(Rotation):
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is added to the left of the Rotation array.
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"""
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lattice,o = self.relation_operations(model)
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target = Orientation(lattice=lattice)
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lattice,o = self.structure.relation_operations(model)
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target = Lattice(lattice=lattice)
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struct = self.structure
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o = o.broadcast_to(o.shape+self.shape,mode='right')
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return self.copy(rotation=o*Rotation(self.quaternion).broadcast_to(o.shape,mode='left'),
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lattice=lattice,
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b = self.b if target.ratio['b'] is None else self.a*target.ratio['b'],
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c = self.c if target.ratio['c'] is None else self.a*target.ratio['c'],
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alpha = None if 'alpha' in target.immutable else self.alpha,
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beta = None if 'beta' in target.immutable else self.beta,
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gamma = None if 'gamma' in target.immutable else self.gamma,
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)
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return Orientation(rotation=o*Rotation(self.quaternion).broadcast_to(o.shape,mode='left'),
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lattice=lattice,
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b = struct.b if target.ratio['b'] is None else struct.a*target.ratio['b'],
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c = struct.c if target.ratio['c'] is None else struct.a*target.ratio['c'],
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alpha = None if 'alpha' in target.immutable else struct.alpha,
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beta = None if 'beta' in target.immutable else struct.beta,
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gamma = None if 'gamma' in target.immutable else struct.gamma,
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)
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@ -409,7 +409,7 @@ class TestOrientation:
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**dict(zip(['a','b','c'],lengths)),
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**dict(zip(['alpha','beta','gamma'],np.arccos(cosines))),
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)
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assert np.allclose(o.to_frame(uvw=np.eye(3)),basis), 'Lattice basis disagrees with initialization'
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assert np.allclose(o.structure.to_frame(uvw=np.eye(3)),basis), 'Lattice basis disagrees with initialization'
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@pytest.mark.parametrize('lattice,a,b,c,alpha,beta,gamma',
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