Merge pull request #205 from CSSFrancis/use_phase_class2

Use phase class2

Author: hakonanes

.github/workflows/build.yml

@@ -46,7 +46,7 @@ jobs:
           - os: ubuntu-latest
             python-version: 3.8
             OLDEST_SUPPORTED_VERSION: true
-            DEPENDENCIES: diffpy.structure==3.0.2 matplotlib==3.5 numpy==1.17.3 orix==0.9.0 scipy==1.8 tqdm==4.9
+            DEPENDENCIES: diffpy.structure==3.0.2 matplotlib==3.5 numpy==1.17.3 orix==0.12.1 scipy==1.8 tqdm==4.9
             LABEL: -oldest
     steps:
       - uses: actions/checkout@v4

diffsims/crystallography/_diffracting_vector.py

@@ -0,0 +1,194 @@
+# -*- coding: utf-8 -*-
+# Copyright 2017-2024 The diffsims developers
+#
+# This file is part of diffsims.
+#
+# diffsims is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# diffsims is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with diffsims.  If not, see <http://www.gnu.org/licenses/>.
+
+from diffsims.crystallography import ReciprocalLatticeVector
+import numpy as np
+from orix.vector.miller import _transform_space
+from orix.quaternion import Rotation
+
+
+class DiffractingVector(ReciprocalLatticeVector):
+    r"""Reciprocal lattice vectors :math:`(hkl)` for use in electron
+    diffraction analysis and simulation.
+
+    All lengths are assumed to be given in Å or inverse Å.
+
+    This extends the :class:`ReciprocalLatticeVector` class.  `DiffractingVector`
+    focus on the subset of reciprocal lattice vectors that are relevant for
+    electron diffraction based on the intersection of the Ewald sphere with the
+    reciprocal lattice.
+
+    This class is only used internally to store the DiffractionVectors generated from the
+    :class:`~diffsims.simulations.DiffractionSimulation` class. It is not (currently)
+    intended to be used directly by the user.
+
+    Parameters
+    ----------
+    phase : orix.crystal_map.Phase
+        A phase with a crystal lattice and symmetry.
+    xyz : numpy.ndarray, list, or tuple, optional
+        Cartesian coordinates of indices of reciprocal lattice vector(s)
+        ``hkl``. Default is ``None``. This, ``hkl``, or ``hkil`` is
+        required.
+    hkl : numpy.ndarray, list, or tuple, optional
+        Indices of reciprocal lattice vector(s). Default is ``None``.
+        This, ``xyz``, or ``hkil`` is required.
+    hkil : numpy.ndarray, list, or tuple, optional
+        Indices of reciprocal lattice vector(s), often preferred over
+        ``hkl`` in trigonal and hexagonal lattices. Default is ``None``.
+        This, ``xyz``, or ``hkl`` is required.
+    intensity : numpy.ndarray, list, or tuple, optional
+        Intensity of the diffraction vector(s). Default is ``None``.
+    rotation : orix.quaternion.Rotation, optional
+        Rotation matrix previously applied to the reciprocal lattice vector(s) and the
+        lattice of the phase. Default is ``None`` which corresponds to the
+        identity matrix.
+
+
+    Examples
+    --------
+    >>> from diffpy.structure import Atom, Lattice, Structure
+    >>> from orix.crystal_map import Phase
+    >>> from diffsims.crystallography import DiffractingVector
+    >>> phase = Phase(
+    ...     "al",
+    ...     space_group=225,
+    ...     structure=Structure(
+    ...         lattice=Lattice(4.04, 4.04, 4.04, 90, 90, 90),
+    ...         atoms=[Atom("Al", [0, 0, 1])],
+    ...     ),
+    ... )
+    >>> rlv = DiffractingVector(phase, hkl=[[1, 1, 1], [2, 0, 0]])
+    >>> rlv
+    ReciprocalLatticeVector (2,), al (m-3m)
+    [[1. 1. 1.]
+     [2. 0. 0.]]
+
+    """
+
+    def __init__(self, phase, xyz=None, hkl=None, hkil=None, intensity=None):
+        super().__init__(phase, xyz=xyz, hkl=hkl, hkil=hkil)
+        if intensity is None:
+            self._intensity = np.full(self.shape, np.nan)
+        elif len(intensity) != self.size:
+            raise ValueError("Length of intensity array must match number of vectors")
+        else:
+            self._intensity = np.array(intensity)
+
+    def __getitem__(self, key):
+        new_data = self.data[key]
+        dv_new = self.__class__(self.phase, xyz=new_data)
+
+        if np.isnan(self.structure_factor).all():
+            dv_new._structure_factor = np.full(dv_new.shape, np.nan, dtype="complex128")
+
+        else:
+            dv_new._structure_factor = self.structure_factor[key]
+        if np.isnan(self.theta).all():
+            dv_new._theta = np.full(dv_new.shape, np.nan)
+        else:
+            dv_new._theta = self.theta[key]
+        if np.isnan(self.intensity).all():
+            dv_new._intensity = np.full(dv_new.shape, np.nan)
+        else:
+            slic = self.intensity[key]
+            if not hasattr(slic, "__len__"):
+                slic = np.array(
+                    [
+                        slic,
+                    ]
+                )
+            dv_new._intensity = slic
+
+        return dv_new
+
+    @property
+    def basis_rotation(self):
+        """
+        Returns the lattice basis rotation.
+        """
+        return Rotation.from_matrix(self.phase.structure.lattice.baserot)
+
+    def rotate_with_basis(self, rotation):
+        """Rotate both vectors and the basis with a given `Rotation`.
+        This differs from simply multiplying with a `Rotation`,
+        as that would NOT update the basis.
+
+        Parameters
+        ----------
+        rot : orix.quaternion.Rotation
+            A rotation to apply to vectors and the basis.
+
+        Returns
+        -------
+        DiffractingVector
+            A new DiffractingVector with the rotated vectors and basis. This maintains
+            the hkl indices of the vectors, but the underlying vector xyz coordinates
+            are rotated by the given rotation.
+
+        Notes
+        -----
+        Rotating the lattice basis may lead to undefined behavior in orix as it violates
+        the assumption that the basis is aligned with the crystal axes. Particularly,
+        applying symmetry operations to the phase may lead to unexpected results.
+        """
+
+        if rotation.size != 1:
+            raise ValueError("Rotation must be a single rotation")
+        # rotate basis
+        new_phase = self.phase.deepcopy()
+        br = new_phase.structure.lattice.baserot
+        # In case the base rotation is set already
+        new_br = br @ rotation.to_matrix().squeeze()
+        new_phase.structure.lattice.setLatPar(baserot=new_br)
+        # rotate vectors
+        vecs = ~rotation * self.to_miller()
+        return ReciprocalLatticeVector(new_phase, xyz=vecs.data)
+
+    @property
+    def intensity(self):
+        return self._intensity
+
+    @intensity.setter
+    def intensity(self, value):
+        if not hasattr(value, "__len__"):
+            value = np.array(
+                [
+                    value,
+                ]
+                * self.size
+            )
+        if len(value) != self.size:
+            raise ValueError("Length of intensity array must match number of vectors")
+        self._intensity = np.array(value)
+
+    def calculate_structure_factor(self):
+        raise NotImplementedError(
+            "Structure factor calculation not implemented for DiffractionVector. "
+            "Use ReciprocalLatticeVector instead."
+        )
+
+    def to_flat_polar(self):
+        """Return the vectors in polar coordinates as projected onto the x,y plane"""
+        flat_self = self.flatten()
+        r = np.linalg.norm(flat_self.data[:, :2], axis=1)
+        theta = np.arctan2(
+            flat_self.data[:, 1],
+            flat_self.data[:, 0],
+        )
+        return r, theta

diffsims/crystallography/reciprocal_lattice_vector.py

@@ -119,7 +119,6 @@ def __init__(self, phase, xyz=None, hkl=None, hkil=None):
             self._coordinate_format = "hkl"
             xyz = _transform_space(hkl, "r", "c", phase.structure.lattice)
         super().__init__(xyz)
-
         self._theta = np.full(self.shape, np.nan)
         self._structure_factor = np.full(self.shape, np.nan, dtype="complex128")
 
@@ -1023,7 +1022,7 @@ def symmetrise(self, return_multiplicity=False, return_index=False):
             return new_out
 
     @classmethod
-    def from_highest_hkl(cls, phase, hkl):
+    def from_highest_hkl(cls, phase, hkl, include_zero_vector=False):
         """Create a set of unique reciprocal lattice vectors from three
         highest indices.
 
@@ -1033,6 +1032,8 @@ def from_highest_hkl(cls, phase, hkl):
             A phase with a crystal lattice and symmetry.
         hkl : numpy.ndarray, list, or tuple
             Three highest reciprocal lattice vector indices.
+        include_zero_vector : bool
+            If ``True``, include the zero vector (000) in the set of vectors.
 
         Examples
         --------
@@ -1067,10 +1068,14 @@ def from_highest_hkl(cls, phase, hkl):
         """
 
         idx = _get_indices_from_highest(highest_indices=hkl)
-        return cls(phase, hkl=idx).unique()
+        new = cls(phase, hkl=idx).unique()
+        if include_zero_vector:
+            new_data = np.vstack((new.hkl, np.zeros(3, dtype=int)))
+            new = ReciprocalLatticeVector(phase, hkl=new_data)
+        return new
 
     @classmethod
-    def from_min_dspacing(cls, phase, min_dspacing=0.7):
+    def from_min_dspacing(cls, phase, min_dspacing=0.7, include_zero_vector=False):
         """Create a set of unique reciprocal lattice vectors with a
         a direct space interplanar spacing greater than a lower
         threshold.
@@ -1083,6 +1088,8 @@ def from_min_dspacing(cls, phase, min_dspacing=0.7):
             Smallest interplanar spacing to consider. Default is 0.7,
             in the unit used to define the lattice parameters in
             ``phase``, which is assumed to be Ångström.
+        include_zero_vector: bool
+            If ``True``, include the zero vector (000) in the set of vectors.
 
         Examples
         --------
@@ -1128,7 +1135,11 @@ def from_min_dspacing(cls, phase, min_dspacing=0.7):
         dspacing = 1 / phase.structure.lattice.rnorm(hkl)
         idx = dspacing >= min_dspacing
         hkl = hkl[idx]
-        return cls(phase, hkl=hkl).unique()
+        new = cls(phase, hkl=hkl).unique()
+        if include_zero_vector:
+            new_data = np.vstack((new.hkl, np.zeros(3, dtype=int)))
+            new = cls(phase, hkl=new_data)
+        return new
 
     @classmethod
     def from_miller(cls, miller):

diffsims/generators/__init__.py

@@ -26,12 +26,14 @@
     rotation_list_generators,
     sphere_mesh_generators,
     zap_map_generator,
+    simulation_generator,
 )
 
 __all__ = [
     "diffraction_generator",
     "library_generator",
     "rotation_list_generators",
     "sphere_mesh_generators",
+    "simulation_generator",
     "zap_map_generator",
 ]