Merge branch 'typehints_orientation_rotation' into 'development'
04 First typehints for rotation and orientation modules See merge request damask/DAMASK!479
This commit is contained in:
Martin Diehl
commit
fe0ff7cab2
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@ -2,10 +2,11 @@ from typing import Union, Dict, List, Tuple
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import numpy as np
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from ._typehints import FloatSequence, CrystalFamily, CrystalLattice, CrystalKinematics
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from . import util
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from . import Rotation
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lattice_symmetries = {
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lattice_symmetries: Dict[CrystalLattice, CrystalFamily] = {
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'aP': 'triclinic',
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'mP': 'monoclinic',
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@ -30,9 +31,9 @@ lattice_symmetries = {
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class Crystal():
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"""Crystal lattice."""
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def __init__(self,*,
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family = None,
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lattice = None,
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def __init__(self, *,
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family: CrystalFamily = None,
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lattice: CrystalLattice = None,
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a: float = None, b: float = None, c: float = None,
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alpha: float = None, beta: float = None, gamma: float = None,
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degrees: bool = False):
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@ -130,9 +131,8 @@ class Crystal():
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Crystal to check for equality.
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"""
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if not isinstance(other, Crystal):
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return NotImplemented
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return self.lattice == other.lattice and \
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return NotImplemented if not isinstance(other, Crystal) else \
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self.lattice == other.lattice and \
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self.parameters == other.parameters and \
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self.family == other.family
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@ -208,7 +208,7 @@ class Crystal():
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... }
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"""
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_basis = {
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_basis: Dict[CrystalFamily, Dict[str, np.ndarray]] = {
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'cubic': {'improper':np.array([ [-1. , 0. , 1. ],
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[ np.sqrt(2.) , -np.sqrt(2.) , 0. ],
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[ 0. , np.sqrt(3.) , 0. ] ]),
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@ -315,19 +315,19 @@ class Crystal():
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self.lattice[-1],None),dtype=float)
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def to_lattice(self, *,
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direction: np.ndarray = None,
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plane: np.ndarray = None) -> np.ndarray:
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direction: FloatSequence = None,
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plane: FloatSequence = None) -> np.ndarray:
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"""
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Calculate lattice vector corresponding to crystal frame direction or plane normal.
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Parameters
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----------
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direction|plane : numpy.ndarray of shape (...,3)
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direction|plane : numpy.ndarray, shape (...,3)
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Vector along direction or plane normal.
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Returns
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-------
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Miller : numpy.ndarray of shape (...,3)
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Miller : numpy.ndarray, shape (...,3)
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Lattice vector of direction or plane.
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Use util.scale_to_coprime to convert to (integer) Miller indices.
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@ -341,19 +341,19 @@ class Crystal():
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def to_frame(self, *,
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uvw: np.ndarray = None,
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hkl: np.ndarray = None) -> np.ndarray:
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uvw: FloatSequence = None,
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hkl: FloatSequence = None) -> np.ndarray:
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"""
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Calculate crystal frame vector along lattice direction [uvw] or plane normal (hkl).
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Parameters
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----------
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uvw|hkl : numpy.ndarray of shape (...,3)
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uvw|hkl : numpy.ndarray, shape (...,3)
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Miller indices of crystallographic direction or plane normal.
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Returns
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-------
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vector : numpy.ndarray of shape (...,3)
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vector : numpy.ndarray, shape (...,3)
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Crystal frame vector along [uvw] direction or (hkl) plane normal.
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"""
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@ -366,7 +366,7 @@ class Crystal():
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def kinematics(self,
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mode: str) -> Dict[str, List[np.ndarray]]:
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mode: CrystalKinematics) -> Dict[str, List[np.ndarray]]:
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"""
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Return crystal kinematics systems.
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@ -381,7 +381,7 @@ class Crystal():
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Directions and planes of deformation mode families.
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"""
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_kinematics = {
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_kinematics: Dict[CrystalLattice, Dict[CrystalKinematics, List[np.ndarray]]] = {
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'cF': {
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'slip': [np.array([
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[+0,+1,-1, +1,+1,+1],
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@ -626,7 +626,7 @@ class Crystal():
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def relation_operations(self,
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model: str) -> Tuple[str, Rotation]:
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model: str) -> Tuple[CrystalLattice, Rotation]:
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"""
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Crystallographic orientation relationships for phase transformations.
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@ -658,7 +658,7 @@ class Crystal():
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https://doi.org/10.1016/j.actamat.2004.11.021
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"""
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_orientation_relationships = {
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_orientation_relationships: Dict[str, Dict[CrystalLattice,np.ndarray]] = {
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'KS': {
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'cF' : np.array([
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[[-1, 0, 1],[ 1, 1, 1]],
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@ -1,8 +1,10 @@
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import inspect
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import copy
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from typing import Union, Callable, List, Dict, Any, Tuple, TypeVar
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import numpy as np
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from ._typehints import FloatSequence, IntSequence, CrystalFamily, CrystalLattice
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from . import Rotation
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from . import Crystal
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from . import util
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@ -33,6 +35,7 @@ _parameter_doc = \
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"""
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MyType = TypeVar('MyType', bound='Orientation')
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class Orientation(Rotation,Crystal):
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"""
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@ -93,12 +96,13 @@ class Orientation(Rotation,Crystal):
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@util.extend_docstring(_parameter_doc)
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def __init__(self,
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rotation = np.array([1.0,0.0,0.0,0.0]), *,
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family = None,
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lattice = None,
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a = None,b = None,c = None,
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alpha = None,beta = None,gamma = None,
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degrees = False):
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rotation: Union[FloatSequence, Rotation] = np.array([1.,0.,0.,0.]),
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*,
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family: CrystalFamily = None,
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lattice: CrystalLattice = None,
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a: float = None, b: float = None, c: float = None,
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alpha: float = None, beta: float = None, gamma: float = None,
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degrees: bool = False):
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"""
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New orientation.
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@ -115,13 +119,13 @@ class Orientation(Rotation,Crystal):
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a=a,b=b,c=c, alpha=alpha,beta=beta,gamma=gamma, degrees=degrees)
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def __repr__(self):
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def __repr__(self) -> str:
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"""Represent."""
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return '\n'.join([Crystal.__repr__(self),
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Rotation.__repr__(self)])
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def __copy__(self,rotation=None):
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def __copy__(self: MyType,
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rotation: Union[FloatSequence, Rotation] = None) -> MyType:
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"""Create deep copy."""
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dup = copy.deepcopy(self)
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if rotation is not None:
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@ -131,7 +135,9 @@ class Orientation(Rotation,Crystal):
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copy = __copy__
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def __eq__(self,other):
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def __eq__(self,
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other: object) -> bool:
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"""
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Equal to other.
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@ -141,12 +147,15 @@ class Orientation(Rotation,Crystal):
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Orientation to check for equality.
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"""
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if not isinstance(other, Orientation):
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return NotImplemented
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matching_type = self.family == other.family and \
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self.lattice == other.lattice and \
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self.parameters == other.parameters
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return np.logical_and(matching_type,super(self.__class__,self.reduced).__eq__(other.reduced))
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def __ne__(self,other):
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def __ne__(self,
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other: object) -> bool:
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"""
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Not equal to other.
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@ -156,10 +165,14 @@ class Orientation(Rotation,Crystal):
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Orientation to check for equality.
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"""
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return np.logical_not(self==other)
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return np.logical_not(self==other) if isinstance(other, Orientation) else NotImplemented
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def isclose(self,other,rtol=1e-5,atol=1e-8,equal_nan=True):
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def isclose(self: MyType,
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other: MyType,
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rtol: float = 1e-5,
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atol: float = 1e-8,
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equal_nan: bool = True) -> bool:
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"""
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Report where values are approximately equal to corresponding ones of other Orientation.
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@ -176,7 +189,7 @@ class Orientation(Rotation,Crystal):
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Returns
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-------
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mask : numpy.ndarray bool
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mask : numpy.ndarray of bool, shape (self.shape)
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Mask indicating where corresponding orientations are close.
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"""
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@ -187,7 +200,11 @@ class Orientation(Rotation,Crystal):
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def allclose(self,other,rtol=1e-5,atol=1e-8,equal_nan=True):
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def allclose(self: MyType,
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other: MyType,
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rtol: float = 1e-5,
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atol: float = 1e-8,
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equal_nan: bool = True) -> bool:
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"""
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Test whether all values are approximately equal to corresponding ones of other Orientation.
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@ -208,10 +225,11 @@ class Orientation(Rotation,Crystal):
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Whether all values are close between both orientations.
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"""
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return np.all(self.isclose(other,rtol,atol,equal_nan))
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return bool(np.all(self.isclose(other,rtol,atol,equal_nan)))
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def __mul__(self,other):
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def __mul__(self: MyType,
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other: Union[Rotation, 'Orientation']) -> MyType:
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"""
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Compose this orientation with other.
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@ -226,14 +244,15 @@ class Orientation(Rotation,Crystal):
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Compound rotation self*other, i.e. first other then self rotation.
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"""
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if isinstance(other,Orientation) or isinstance(other,Rotation):
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return self.copy(rotation=Rotation.__mul__(self,Rotation(other.quaternion)))
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if isinstance(other, (Orientation,Rotation)):
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return self.copy(Rotation(self.quaternion)*Rotation(other.quaternion))
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else:
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raise TypeError('use "O@b", i.e. matmul, to apply Orientation "O" to object "b"')
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@staticmethod
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def _split_kwargs(kwargs,target):
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def _split_kwargs(kwargs: Dict[str, Any],
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target: Callable) -> Tuple[Dict[str, Any], ...]:
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"""
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Separate keyword arguments in 'kwargs' targeted at 'target' from general keyword arguments of Orientation objects.
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@ -252,7 +271,7 @@ class Orientation(Rotation,Crystal):
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Valid keyword arguments of Orientation object.
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"""
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kws = ()
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kws: Tuple[Dict[str, Any], ...] = ()
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for t in (target,Orientation.__init__):
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kws += ({key: kwargs[key] for key in set(inspect.signature(t).parameters) & set(kwargs)},)
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@ -264,105 +283,108 @@ class Orientation(Rotation,Crystal):
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@classmethod
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@util.extended_docstring(Rotation.from_random,_parameter_doc)
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def from_random(cls,**kwargs):
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@util.extended_docstring(Rotation.from_random, _parameter_doc)
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def from_random(cls, **kwargs) -> 'Orientation':
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kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_random)
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return cls(rotation=Rotation.from_random(**kwargs_rot),**kwargs_ori)
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@classmethod
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@util.extended_docstring(Rotation.from_quaternion,_parameter_doc)
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def from_quaternion(cls,**kwargs):
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def from_quaternion(cls, **kwargs) -> 'Orientation':
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kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_quaternion)
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return cls(rotation=Rotation.from_quaternion(**kwargs_rot),**kwargs_ori)
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@classmethod
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@util.extended_docstring(Rotation.from_Euler_angles,_parameter_doc)
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def from_Euler_angles(cls,**kwargs):
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def from_Euler_angles(cls, **kwargs) -> 'Orientation':
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kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_Euler_angles)
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return cls(rotation=Rotation.from_Euler_angles(**kwargs_rot),**kwargs_ori)
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@classmethod
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@util.extended_docstring(Rotation.from_axis_angle,_parameter_doc)
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def from_axis_angle(cls,**kwargs):
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def from_axis_angle(cls, **kwargs) -> 'Orientation':
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kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_axis_angle)
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return cls(rotation=Rotation.from_axis_angle(**kwargs_rot),**kwargs_ori)
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@classmethod
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@util.extended_docstring(Rotation.from_basis,_parameter_doc)
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def from_basis(cls,**kwargs):
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def from_basis(cls, **kwargs) -> 'Orientation':
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kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_basis)
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return cls(rotation=Rotation.from_basis(**kwargs_rot),**kwargs_ori)
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@classmethod
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@util.extended_docstring(Rotation.from_matrix,_parameter_doc)
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def from_matrix(cls,**kwargs):
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def from_matrix(cls, **kwargs) -> 'Orientation':
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kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_matrix)
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return cls(rotation=Rotation.from_matrix(**kwargs_rot),**kwargs_ori)
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@classmethod
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@util.extended_docstring(Rotation.from_Rodrigues_vector,_parameter_doc)
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def from_Rodrigues_vector(cls,**kwargs):
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def from_Rodrigues_vector(cls, **kwargs) -> 'Orientation':
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kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_Rodrigues_vector)
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return cls(rotation=Rotation.from_Rodrigues_vector(**kwargs_rot),**kwargs_ori)
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@classmethod
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@util.extended_docstring(Rotation.from_homochoric,_parameter_doc)
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def from_homochoric(cls,**kwargs):
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def from_homochoric(cls, **kwargs) -> 'Orientation':
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kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_homochoric)
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return cls(rotation=Rotation.from_homochoric(**kwargs_rot),**kwargs_ori)
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|
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@classmethod
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@util.extended_docstring(Rotation.from_cubochoric,_parameter_doc)
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def from_cubochoric(cls,**kwargs):
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def from_cubochoric(cls, **kwargs) -> 'Orientation':
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kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_cubochoric)
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return cls(rotation=Rotation.from_cubochoric(**kwargs_rot),**kwargs_ori)
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|
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@classmethod
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@util.extended_docstring(Rotation.from_spherical_component,_parameter_doc)
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def from_spherical_component(cls,**kwargs):
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def from_spherical_component(cls, **kwargs) -> 'Orientation':
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kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_spherical_component)
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return cls(rotation=Rotation.from_spherical_component(**kwargs_rot),**kwargs_ori)
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|
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@classmethod
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@util.extended_docstring(Rotation.from_fiber_component,_parameter_doc)
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def from_fiber_component(cls,**kwargs):
|
||||
def from_fiber_component(cls, **kwargs) -> 'Orientation':
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kwargs_rot,kwargs_ori = Orientation._split_kwargs(kwargs,Rotation.from_fiber_component)
|
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return cls(rotation=Rotation.from_fiber_component(**kwargs_rot),**kwargs_ori)
|
||||
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||||
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@classmethod
|
||||
@util.extend_docstring(_parameter_doc)
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def from_directions(cls,uvw,hkl,**kwargs):
|
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def from_directions(cls,
|
||||
uvw: FloatSequence,
|
||||
hkl: FloatSequence,
|
||||
**kwargs) -> 'Orientation':
|
||||
"""
|
||||
Initialize orientation object from two crystallographic directions.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
uvw : list, numpy.ndarray of shape (...,3)
|
||||
lattice direction aligned with lab frame x-direction.
|
||||
hkl : list, numpy.ndarray of shape (...,3)
|
||||
lattice plane normal aligned with lab frame z-direction.
|
||||
uvw : numpy.ndarray, shape (...,3)
|
||||
Lattice direction aligned with lab frame x-direction.
|
||||
hkl : numpy.ndarray, shape (...,3)
|
||||
Lattice plane normal aligned with lab frame z-direction.
|
||||
|
||||
"""
|
||||
o = cls(**kwargs)
|
||||
x = o.to_frame(uvw=uvw)
|
||||
z = o.to_frame(hkl=hkl)
|
||||
om = np.stack([x,np.cross(z,x),z],axis=-2)
|
||||
return o.copy(rotation=Rotation.from_matrix(tensor.transpose(om/np.linalg.norm(om,axis=-1,keepdims=True))))
|
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return o.copy(Rotation.from_matrix(tensor.transpose(om/np.linalg.norm(om,axis=-1,keepdims=True))))
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@property
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def equivalent(self):
|
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def equivalent(self: MyType) -> MyType:
|
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"""
|
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Orientations that are symmetrically equivalent.
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||||
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||||
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|
@ -372,11 +394,11 @@ class Orientation(Rotation,Crystal):
|
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"""
|
||||
sym_ops = self.symmetry_operations
|
||||
o = sym_ops.broadcast_to(sym_ops.shape+self.shape,mode='right')
|
||||
return self.copy(rotation=o*Rotation(self.quaternion).broadcast_to(o.shape,mode='left'))
|
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return self.copy(o*Rotation(self.quaternion).broadcast_to(o.shape,mode='left'))
|
||||
|
||||
|
||||
@property
|
||||
def reduced(self):
|
||||
def reduced(self: MyType) -> MyType:
|
||||
"""Select symmetrically equivalent orientation that falls into fundamental zone according to symmetry."""
|
||||
eq = self.equivalent
|
||||
ok = eq.in_FZ
|
||||
|
|
@ -387,13 +409,13 @@ class Orientation(Rotation,Crystal):
|
|||
|
||||
|
||||
@property
|
||||
def in_FZ(self):
|
||||
def in_FZ(self) -> Union[np.bool_, np.ndarray]:
|
||||
"""
|
||||
Check whether orientation falls into fundamental zone of own symmetry.
|
||||
|
||||
Returns
|
||||
-------
|
||||
in : numpy.ndarray of bool, quaternion.shape
|
||||
in : numpy.ndarray of bool, shape (self.shape)
|
||||
Whether Rodrigues-Frank vector falls into fundamental zone.
|
||||
|
||||
Notes
|
||||
|
|
@ -431,13 +453,13 @@ class Orientation(Rotation,Crystal):
|
|||
|
||||
|
||||
@property
|
||||
def in_disorientation_FZ(self):
|
||||
def in_disorientation_FZ(self) -> np.ndarray:
|
||||
"""
|
||||
Check whether orientation falls into fundamental zone of disorientations.
|
||||
|
||||
Returns
|
||||
-------
|
||||
in : numpy.ndarray of bool, quaternion.shape
|
||||
in : numpy.ndarray of bool, shape (self.shape)
|
||||
Whether Rodrigues-Frank vector falls into disorientation FZ.
|
||||
|
||||
References
|
||||
|
|
@ -471,8 +493,9 @@ class Orientation(Rotation,Crystal):
|
|||
else:
|
||||
return np.ones_like(rho[...,0],dtype=bool)
|
||||
|
||||
|
||||
def disorientation(self,other,return_operators=False):
|
||||
def disorientation(self,
|
||||
other: 'Orientation',
|
||||
return_operators: bool = False) -> object:
|
||||
"""
|
||||
Calculate disorientation between myself and given other orientation.
|
||||
|
||||
|
|
@ -490,7 +513,7 @@ class Orientation(Rotation,Crystal):
|
|||
-------
|
||||
disorientation : Orientation
|
||||
Disorientation between self and other.
|
||||
operators : numpy.ndarray int of shape (...,2), conditional
|
||||
operators : numpy.ndarray of int, shape (...,2), conditional
|
||||
Index of symmetrically equivalent orientation that rotated vector to the SST.
|
||||
|
||||
Notes
|
||||
|
|
@ -530,7 +553,7 @@ class Orientation(Rotation,Crystal):
|
|||
raise NotImplementedError('disorientation between different crystal families')
|
||||
|
||||
blend = util.shapeblender(self.shape,other.shape)
|
||||
s = self.equivalent
|
||||
s = self.equivalent
|
||||
o = other.equivalent
|
||||
|
||||
s_ = s.reshape((s.shape[0],1)+ self.shape).broadcast_to((s.shape[0],o.shape[0])+blend,mode='right')
|
||||
|
|
@ -557,13 +580,15 @@ class Orientation(Rotation,Crystal):
|
|||
)
|
||||
|
||||
|
||||
def average(self,weights=None,return_cloud=False):
|
||||
def average(self,
|
||||
weights: FloatSequence = None,
|
||||
return_cloud: bool = False):
|
||||
"""
|
||||
Return orientation average over last dimension.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
weights : numpy.ndarray, optional
|
||||
weights : numpy.ndarray, shape (self.shape), optional
|
||||
Relative weights of orientations.
|
||||
return_cloud : bool, optional
|
||||
Return the set of symmetrically equivalent orientations that was used in averaging.
|
||||
|
|
@ -583,31 +608,30 @@ class Orientation(Rotation,Crystal):
|
|||
|
||||
"""
|
||||
eq = self.equivalent
|
||||
m = eq.misorientation(self[...,0].reshape((1,)+self.shape[:-1]+(1,))
|
||||
.broadcast_to(eq.shape))\
|
||||
.as_axis_angle()[...,3]
|
||||
m = eq.misorientation(self[...,0].reshape((1,)+self.shape[:-1]+(1,)) # type: ignore
|
||||
.broadcast_to(eq.shape)).as_axis_angle()[...,3] # type: ignore
|
||||
r = Rotation(np.squeeze(np.take_along_axis(eq.quaternion,
|
||||
np.argmin(m,axis=0)[np.newaxis,...,np.newaxis],
|
||||
axis=0),
|
||||
axis=0))
|
||||
return (
|
||||
(self.copy(rotation=Rotation(r).average(weights)),
|
||||
self.copy(rotation=Rotation(r)))
|
||||
if return_cloud else
|
||||
self.copy(rotation=Rotation(r).average(weights))
|
||||
return ((self.copy(Rotation(r).average(weights)),self.copy(Rotation(r))) if return_cloud else
|
||||
self.copy(Rotation(r).average(weights))
|
||||
)
|
||||
|
||||
|
||||
def to_SST(self,vector,proper=False,return_operators=False):
|
||||
def to_SST(self,
|
||||
vector: FloatSequence,
|
||||
proper: bool = False,
|
||||
return_operators: bool = False) -> np.ndarray:
|
||||
"""
|
||||
Rotate vector to ensure it falls into (improper or proper) standard stereographic triangle of crystal symmetry.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
vector : numpy.ndarray of shape (...,3)
|
||||
vector : numpy.ndarray, shape (...,3)
|
||||
Lab frame vector to align with crystal frame direction.
|
||||
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.
|
||||
For example, a rotation array of shape (3,2) and a vector array of shape (2,4) result in (3,2,4) outputs.
|
||||
proper : bool, optional
|
||||
Consider only vectors with z >= 0, hence combine two neighboring SSTs.
|
||||
Defaults to False.
|
||||
|
|
@ -617,15 +641,18 @@ class Orientation(Rotation,Crystal):
|
|||
|
||||
Returns
|
||||
-------
|
||||
vector_SST : numpy.ndarray of shape (...,3)
|
||||
vector_SST : numpy.ndarray, shape (...,3)
|
||||
Rotated vector falling into SST.
|
||||
operators : numpy.ndarray int of shape (...), conditional
|
||||
operators : numpy.ndarray of int, shape (...), conditional
|
||||
Index of symmetrically equivalent orientation that rotated vector to SST.
|
||||
|
||||
"""
|
||||
vector_ = np.array(vector,float)
|
||||
if vector_.shape[-1] != 3:
|
||||
raise ValueError('input is not a field of three-dimensional vectors')
|
||||
eq = self.equivalent
|
||||
blend = util.shapeblender(eq.shape,np.array(vector).shape[:-1])
|
||||
poles = eq.broadcast_to(blend,mode='right') @ np.broadcast_to(np.array(vector),blend+(3,))
|
||||
blend = util.shapeblender(eq.shape,vector_.shape[:-1])
|
||||
poles = eq.broadcast_to(blend,mode='right') @ np.broadcast_to(vector_,blend+(3,))
|
||||
ok = self.in_SST(poles,proper=proper)
|
||||
ok &= np.cumsum(ok,axis=0) == 1
|
||||
loc = np.where(ok)
|
||||
|
|
@ -637,13 +664,15 @@ class Orientation(Rotation,Crystal):
|
|||
)
|
||||
|
||||
|
||||
def in_SST(self,vector,proper=False):
|
||||
def in_SST(self,
|
||||
vector: FloatSequence,
|
||||
proper: bool = False) -> Union[np.bool_, np.ndarray]:
|
||||
"""
|
||||
Check whether given crystal frame vector falls into standard stereographic triangle of own symmetry.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
vector : numpy.ndarray of shape (...,3)
|
||||
vector : numpy.ndarray, shape (...,3)
|
||||
Vector to check.
|
||||
proper : bool, optional
|
||||
Consider only vectors with z >= 0, hence combine two neighboring SSTs.
|
||||
|
|
@ -655,39 +684,43 @@ class Orientation(Rotation,Crystal):
|
|||
Whether vector falls into SST.
|
||||
|
||||
"""
|
||||
if not isinstance(vector,np.ndarray) or vector.shape[-1] != 3:
|
||||
vector_ = np.array(vector,float)
|
||||
if vector_.shape[-1] != 3:
|
||||
raise ValueError('input is not a field of three-dimensional vectors')
|
||||
|
||||
if self.standard_triangle is None: # direct exit for no symmetry
|
||||
return np.ones_like(vector[...,0],bool)
|
||||
return np.ones_like(vector_[...,0],bool)
|
||||
|
||||
if proper:
|
||||
components_proper = np.around(np.einsum('...ji,...i',
|
||||
np.broadcast_to(self.standard_triangle['proper'], vector.shape+(3,)),
|
||||
vector), 12)
|
||||
np.broadcast_to(self.standard_triangle['proper'], vector_.shape+(3,)),
|
||||
vector_), 12)
|
||||
components_improper = np.around(np.einsum('...ji,...i',
|
||||
np.broadcast_to(self.standard_triangle['improper'], vector.shape+(3,)),
|
||||
vector), 12)
|
||||
np.broadcast_to(self.standard_triangle['improper'], vector_.shape+(3,)),
|
||||
vector_), 12)
|
||||
return np.all(components_proper >= 0.0,axis=-1) \
|
||||
| np.all(components_improper >= 0.0,axis=-1)
|
||||
else:
|
||||
components = np.around(np.einsum('...ji,...i',
|
||||
np.broadcast_to(self.standard_triangle['improper'], vector.shape+(3,)),
|
||||
np.block([vector[...,:2],np.abs(vector[...,2:3])])), 12)
|
||||
np.broadcast_to(self.standard_triangle['improper'], vector_.shape+(3,)),
|
||||
np.block([vector_[...,:2],np.abs(vector_[...,2:3])])), 12)
|
||||
|
||||
return np.all(components >= 0.0,axis=-1)
|
||||
|
||||
|
||||
def IPF_color(self,vector,in_SST=True,proper=False):
|
||||
def IPF_color(self,
|
||||
vector: FloatSequence,
|
||||
in_SST: bool = True,
|
||||
proper: bool = False) -> np.ndarray:
|
||||
"""
|
||||
Map vector to RGB color within standard stereographic triangle of own symmetry.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
vector : numpy.ndarray of shape (...,3)
|
||||
vector : numpy.ndarray, 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.
|
||||
For example, a rotation array of shape (3,2) and a vector array of shape (2,4) result in (3,2,4) outputs.
|
||||
in_SST : bool, optional
|
||||
Consider symmetrically equivalent orientations such that poles are located in SST.
|
||||
Defaults to True.
|
||||
|
|
@ -697,7 +730,7 @@ class Orientation(Rotation,Crystal):
|
|||
|
||||
Returns
|
||||
-------
|
||||
rgb : numpy.ndarray of shape (...,3)
|
||||
rgb : numpy.ndarray, shape (...,3)
|
||||
RGB array of IPF colors.
|
||||
|
||||
Examples
|
||||
|
|
@ -721,35 +754,35 @@ class Orientation(Rotation,Crystal):
|
|||
|
||||
if proper:
|
||||
components_proper = np.around(np.einsum('...ji,...i',
|
||||
np.broadcast_to(self.standard_triangle['proper'], vector_.shape+(3,)),
|
||||
np.broadcast_to(self.standard_triangle['proper'], vector_.shape+(3,)),
|
||||
vector_), 12)
|
||||
components_improper = np.around(np.einsum('...ji,...i',
|
||||
np.broadcast_to(self.standard_triangle['improper'], vector_.shape+(3,)),
|
||||
vector_), 12)
|
||||
in_SST = np.all(components_proper >= 0.0,axis=-1) \
|
||||
| np.all(components_improper >= 0.0,axis=-1)
|
||||
components = np.where((in_SST & np.all(components_proper >= 0.0,axis=-1))[...,np.newaxis],
|
||||
in_SST_ = np.all(components_proper >= 0.0,axis=-1) \
|
||||
| np.all(components_improper >= 0.0,axis=-1)
|
||||
components = np.where((in_SST_ & np.all(components_proper >= 0.0,axis=-1))[...,np.newaxis],
|
||||
components_proper,components_improper)
|
||||
else:
|
||||
components = np.around(np.einsum('...ji,...i',
|
||||
np.broadcast_to(self .standard_triangle['improper'], vector_.shape+(3,)),
|
||||
np.block([vector_[...,:2],np.abs(vector_[...,2:3])])), 12)
|
||||
|
||||
in_SST = np.all(components >= 0.0,axis=-1)
|
||||
in_SST_ = np.all(components >= 0.0,axis=-1)
|
||||
|
||||
with np.errstate(invalid='ignore',divide='ignore'):
|
||||
rgb = (components/np.linalg.norm(components,axis=-1,keepdims=True))**0.5 # smoothen color ramps
|
||||
rgb = np.clip(rgb,0.,1.) # clip intensity
|
||||
rgb /= np.max(rgb,axis=-1,keepdims=True) # normalize to (HS)V = 1
|
||||
rgb[np.broadcast_to(~in_SST[...,np.newaxis],rgb.shape)] = 0.0
|
||||
rgb[np.broadcast_to(~in_SST_[...,np.newaxis],rgb.shape)] = 0.0
|
||||
|
||||
return rgb
|
||||
|
||||
|
||||
@property
|
||||
def symmetry_operations(self):
|
||||
def symmetry_operations(self) -> Rotation:
|
||||
"""Symmetry operations as Rotations."""
|
||||
_symmetry_operations = {
|
||||
_symmetry_operations: Dict[CrystalFamily, List] = {
|
||||
'cubic': [
|
||||
[ 1.0, 0.0, 0.0, 0.0 ],
|
||||
[ 0.0, 1.0, 0.0, 0.0 ],
|
||||
|
|
@ -819,22 +852,25 @@ class Orientation(Rotation,Crystal):
|
|||
####################################################################################################
|
||||
# functions that require lattice, not just family
|
||||
|
||||
def to_pole(self,*,uvw=None,hkl=None,with_symmetry=False):
|
||||
def to_pole(self, *,
|
||||
uvw: FloatSequence = None,
|
||||
hkl: FloatSequence = None,
|
||||
with_symmetry: bool = False) -> np.ndarray:
|
||||
"""
|
||||
Calculate lab frame vector along lattice direction [uvw] or plane normal (hkl).
|
||||
|
||||
Parameters
|
||||
----------
|
||||
uvw|hkl : numpy.ndarray of shape (...,3)
|
||||
uvw|hkl : numpy.ndarray, 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.
|
||||
For example, a rotation array, shape (3,2) and a vector array of shape (2,4) 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, shape (...,3) or (...,N,3)
|
||||
Lab frame vector (or vectors if with_symmetry) along [uvw] direction or (hkl) plane normal.
|
||||
|
||||
"""
|
||||
|
|
@ -846,23 +882,24 @@ class Orientation(Rotation,Crystal):
|
|||
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,))
|
||||
return ~(self.broadcast_to(blend))@ np.broadcast_to(v,blend+(3,))
|
||||
|
||||
|
||||
def Schmid(self,*,N_slip=None,N_twin=None):
|
||||
def Schmid(self, *,
|
||||
N_slip: IntSequence = None,
|
||||
N_twin: IntSequence = None) -> np.ndarray:
|
||||
u"""
|
||||
Calculate Schmid matrix P = d ⨂ n in the lab frame for selected deformation systems.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
N_slip|N_twin : iterable of int
|
||||
N_slip|N_twin : '*' or iterable of int
|
||||
Number of deformation systems per family of the deformation system.
|
||||
Use '*' to select all.
|
||||
|
||||
Returns
|
||||
-------
|
||||
P : numpy.ndarray of shape (N,...,3,3)
|
||||
P : numpy.ndarray, shape (N,...,3,3)
|
||||
Schmid matrix for each of the N deformation systems.
|
||||
|
||||
Examples
|
||||
|
|
@ -887,6 +924,8 @@ class Orientation(Rotation,Crystal):
|
|||
(self.kinematics('twin'),N_twin)
|
||||
if active == '*': active = [len(a) for a in kinematics['direction']]
|
||||
|
||||
if not active:
|
||||
raise ValueError('Schmid matrix not defined')
|
||||
d = self.to_frame(uvw=np.vstack([kinematics['direction'][i][:n] for i,n in enumerate(active)]))
|
||||
p = self.to_frame(hkl=np.vstack([kinematics['plane'][i][:n] for i,n in enumerate(active)]))
|
||||
P = np.einsum('...i,...j',d/np.linalg.norm(d,axis=1,keepdims=True),
|
||||
|
|
@ -897,7 +936,8 @@ class Orientation(Rotation,Crystal):
|
|||
@ np.broadcast_to(P.reshape(util.shapeshifter(P.shape,shape)),shape)
|
||||
|
||||
|
||||
def related(self,model):
|
||||
def related(self: MyType,
|
||||
model: str) -> MyType:
|
||||
"""
|
||||
Orientations derived from the given relationship.
|
||||
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
|
|
@ -194,7 +194,7 @@ class Table:
|
|||
|
||||
Returns
|
||||
-------
|
||||
mask : numpy.ndarray bool
|
||||
mask : numpy.ndarray of bool
|
||||
Mask indicating where corresponding table values are close.
|
||||
|
||||
"""
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
"""Functionality for typehints."""
|
||||
|
||||
from typing import Sequence, Union, TextIO
|
||||
from typing import Sequence, Union, Literal, TextIO
|
||||
from pathlib import Path
|
||||
|
||||
import numpy as np
|
||||
|
|
@ -9,6 +9,9 @@ import numpy as np
|
|||
FloatSequence = Union[np.ndarray,Sequence[float]]
|
||||
IntSequence = Union[np.ndarray,Sequence[int]]
|
||||
FileHandle = Union[TextIO, str, Path]
|
||||
CrystalFamily = Union[None,Literal['triclinic', 'monoclinic', 'orthorhombic', 'tetragonal', 'hexagonal', 'cubic']]
|
||||
CrystalLattice = Union[None,Literal['aP', 'mP', 'mS', 'oP', 'oS', 'oI', 'oF', 'tP', 'tI', 'hP', 'cP', 'cI', 'cF']]
|
||||
CrystalKinematics = Literal['slip', 'twin']
|
||||
NumpyRngSeed = Union[int, IntSequence, np.random.SeedSequence, np.random.Generator]
|
||||
# BitGenerator does not exists in older numpy versions
|
||||
#NumpyRngSeed = Union[int, IntSequence, np.random.SeedSequence, np.random.BitGenerator, np.random.Generator]
|
||||
|
|
|
|||
|
|
@ -9,7 +9,7 @@ import re
|
|||
import fractions
|
||||
from collections import abc
|
||||
from functools import reduce
|
||||
from typing import Union, Tuple, Iterable, Callable, Dict, List, Any, Literal, SupportsIndex, Sequence
|
||||
from typing import Union, Tuple, Iterable, Callable, Dict, List, Any, Literal
|
||||
from pathlib import Path
|
||||
|
||||
import numpy as np
|
||||
|
|
@ -427,7 +427,7 @@ def hybrid_IA(dist: np.ndarray,
|
|||
def shapeshifter(fro: Tuple[int, ...],
|
||||
to: Tuple[int, ...],
|
||||
mode: Literal['left','right'] = 'left',
|
||||
keep_ones: bool = False) -> Sequence[SupportsIndex]:
|
||||
keep_ones: bool = False) -> Tuple[int, ...]:
|
||||
"""
|
||||
Return dimensions that reshape 'fro' to become broadcastable to 'to'.
|
||||
|
||||
|
|
@ -490,7 +490,7 @@ def shapeshifter(fro: Tuple[int, ...],
|
|||
|
||||
|
||||
def shapeblender(a: Tuple[int, ...],
|
||||
b: Tuple[int, ...]) -> Sequence[SupportsIndex]:
|
||||
b: Tuple[int, ...]) -> Tuple[int, ...]:
|
||||
"""
|
||||
Return a shape that overlaps the rightmost entries of 'a' with the leftmost of 'b'.
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue