Merge f31aae4 into fae5ca5

.github/workflows/build.yml

@@ -45,7 +45,7 @@ jobs:
           - os: ubuntu-latest
             python-version: 3.7
             OLDEST_SUPPORTED_VERSION: true
-            DEPENDENCIES: diffpy.structure==3.0.0 matplotlib==3.3 numpy==1.17 orix==0.9.0 scipy==1.1 tqdm==4.9
+            DEPENDENCIES: diffpy.structure==3.0.2 matplotlib==3.3 numpy==1.17 orix==0.11.0 scipy==1.2 tqdm==4.9
             LABEL: -oldest
     steps:
       - uses: actions/checkout@v3

.pre-commit-config.yaml

@@ -0,0 +1,8 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 23.1.0
+    hooks:
+      - id: black
+      - id: black-jupyter
+        files: \.ipynb
+        args: [--line-length=77]

CHANGELOG.rst

@@ -13,13 +13,26 @@ Unreleased
 Added
 -----
 - Explicit support for Python 3.11.
+- Added deprecation tools for deprecating functions and arguments.
+- Added new class :class:`diffsims.generators.simulation_generator.SimulationGenerator` for
+  generating kinemetic diffraction from a phase and a set of reflections.
+- Added new class :class:`diffsims.generators.simulations.Simulation` for storing results
+  from a :class:`diffsims.generators.simulation_generator.SimulationGenerator`.
+- Added new class :class:`diffsims.simulations.Simulation1D` for storing the results of a
+  1D simulation.
 
 Changed
 -------
 - Documentation theme from Furo to the PyData-Sphinx-Theme.
 
 Deprecated
 ----------
+- Deprecated :class:`diffsims.generators.diffraction_generator.DiffractionGenerator` in
+  favor of :class:`diffsims.generators.simulation_generator.SimulationGenerator`.
+- Deprecated :class:`diffsims.generators.library_generator.DiffractionLibraryGenerator` in
+  favor of :class:`diffsims.generators.simulation_generator.SimulationGenerator`.
+- Deprecated :class:`diffsims.diffraction_library.DiffractionLibrary` in favor of
+  :class:`diffsims.generators.simulations.Simulation`.
 
 Removed
 -------

CONTRIBUTING.rst

@@ -124,6 +124,27 @@ Useful hints on testing:
   error-prone. See `pytest documentation for more details
   <https://doc.pytest.org/en/latest/how-to/parametrize.html>`_.
 
+
+Deprecations
+------------
+'This project attempts to adhere to (pre 1.0.0) semantic versioning and ideally no functionality
+should be broken between minor releases. Deprecation warnings are raised to give user a full minor
+release cycle to adjust their code before a breaking change is implemented.'
+
+The decorator should be placed right above the object signature to be deprecated::
+
+.. code-block:: python
+    >>> from diffsims.utils._deprecated import deprecate
+    >>> @deprecate(since=0.8, removal=0.9, alternative="bar")
+    >>> def foo(self, n):
+    >>>     return n + 1
+
+    >>> @property
+    >>> @deprecate(since=0.9, removal=0.10, alternative="another", is_function=True)
+    >>> def this_property(self):
+    >>>     return 2
+
+
 Build and write documentation
 -----------------------------
 

diffsims/crystallography/reciprocal_lattice_point.py

@@ -29,7 +29,6 @@
     get_refraction_corrected_wavelength,
 )
 
-
 _FLOAT_EPS = np.finfo(float).eps  # Used to round values below 1e-16 to zero
 
 

diffsims/crystallography/reciprocal_lattice_vector.py

@@ -15,7 +15,7 @@
 #
 # You should have received a copy of the GNU General Public License
 # along with diffsims.  If not, see <http://www.gnu.org/licenses/>.
-
+from typing import Tuple
 from collections import defaultdict
 from copy import deepcopy
 
@@ -122,10 +122,11 @@ def __init__(self, phase, xyz=None, hkl=None, hkil=None):
 
         self._theta = np.full(self.shape, np.nan)
         self._structure_factor = np.full(self.shape, np.nan, dtype="complex128")
+        self._intensity = np.full(self.shape, np.nan)
 
     def __getitem__(self, key):
-        miller_new = self.to_miller().__getitem__(key)
-        rlv_new = self.from_miller(miller_new)
+        new_data = self.data[key]
+        rlv_new = self.__class__(self.phase, xyz=new_data)
 
         if np.isnan(self.structure_factor).all():
             rlv_new._structure_factor = np.full(
@@ -139,6 +140,18 @@ def __getitem__(self, key):
         else:
             rlv_new._theta = self.theta[key]
 
+        if np.isnan(self.intensity).all():
+            rlv_new._intensity = np.full(rlv_new.shape, np.nan)
+        else:
+            slic = self.intensity[key]
+            if not hasattr(slic, "__len__"):
+                slic = np.array(
+                    [
+                        slic,
+                    ]
+                )
+            rlv_new._intensity = slic
+
         return rlv_new
 
     def __repr__(self):
@@ -169,7 +182,6 @@ def hkl(self):
         >>> rlv.hkl
         array([[1., 1., 1.],
                [2., 0., 0.]])
-
         """
 
         return _transform_space(self.data, "c", "r", self.phase.structure.lattice)
@@ -502,6 +514,28 @@ def scattering_parameter(self):
 
         return 0.5 * self.gspacing
 
+    @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 rotate_from_matrix(self, rotation_matrix):
+        return ReciprocalLatticeVector(
+            phase=self.phase, xyz=np.matmul(rotation_matrix, self.data.T).T
+        )
+
     @property
     def structure_factor(self):
         r"""Kinematical structure factors :math:`F`.
@@ -1070,7 +1104,7 @@ def from_highest_hkl(cls, phase, hkl):
         return cls(phase, hkl=idx).unique()
 
     @classmethod
-    def from_min_dspacing(cls, phase, min_dspacing=0.7):
+    def from_min_dspacing(cls, phase, min_dspacing=0.7, include_zero_beam=False):
         """Create a set of unique reciprocal lattice vectors with a
         a direct space interplanar spacing greater than a lower
         threshold.
@@ -1128,6 +1162,8 @@ def from_min_dspacing(cls, phase, min_dspacing=0.7):
         dspacing = 1 / phase.structure.lattice.rnorm(hkl)
         idx = dspacing >= min_dspacing
         hkl = hkl[idx]
+        if include_zero_beam:
+            hkl = np.vstack((hkl, np.zeros(3, dtype=int)))
         return cls(phase, hkl=hkl).unique()
 
     @classmethod
@@ -1180,6 +1216,54 @@ def from_miller(cls, miller):
             )
         return cls(miller.phase, **{miller.coordinate_format: miller.coordinates})
 
+    def to_polar(
+        self, degrees: bool = False
+    ) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
+        """Convert the vectors to polar coordinates.
+
+        Parameters
+        ----------
+        degrees : bool, optional
+            Whether to return angles in degrees (default is False).
+
+        Returns
+        -------
+        r : numpy.ndarray
+            Length of the vectors.
+        theta : numpy.ndarray
+            Polar angle of the vectors.
+        phi : numpy.ndarray
+            Azimuthal angle of the vectors.
+
+        Examples
+        --------
+        See :class:`ReciprocalLatticeVector` for the creation of ``rlv``
+
+        >>> rlv
+        ReciprocalLatticeVector (2,), al (m-3m)
+        [[1. 1. 1.]
+         [2. 0. 0.]]
+        >>> r, theta, phi = rlv.to_polar()
+        >>> r
+        array([1.73205081, 2.        ])
+        >>> theta
+        array([0.95531662, 0.        ])
+        >>> phi
+        array([0., 0.])
+
+        """
+
+        x = self.data[:, 0]
+        y = self.data[:, 1]
+        z = self.data[:, 2]
+
+        r = np.sqrt(x**2 + y**2)
+        theta = np.arctan2(y, x)
+
+        if degrees:
+            theta = np.rad2deg(theta)
+        return r, theta, z
+
     def to_miller(self):
         """Return the vectors as a ``Miller`` instance.
 

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",
 ]

diffsims/generators/diffraction_generator.py

@@ -41,6 +41,7 @@
     lorentzian_precession,
 )
 
+from diffsims.utils._deprecated import deprecated
 
 __all__ = [
     "AtomicDiffractionGenerator",
@@ -153,6 +154,9 @@ class DiffractionGenerator(object):
     `custom shape_factor_model` is used.
     """
 
+    @deprecated(since="0.6.0",
+                removal="0.7.0",
+                alternative="diffsims.generators.simulation_generator.SimulationGenerator")
     def __init__(
         self,
         accelerating_voltage,

diffsims/generators/library_generator.py

@@ -27,7 +27,7 @@
 
 from diffsims.utils.sim_utils import get_points_in_sphere
 from diffsims.utils.vector_utils import get_angle_cartesian_vec
-
+from diffsims.utils._deprecated import deprecated
 
 __all__ = [
     "DiffractionLibraryGenerator",
@@ -39,7 +39,7 @@ class DiffractionLibraryGenerator:
     """Computes a library of electron diffraction patterns for specified atomic
     structures and orientations.
     """
-
+    @deprecated(since="0.6.0", alternative="Diffsims.generators.SimulationGenerator")
     def __init__(self, electron_diffraction_calculator):
         """Initialises the generator with a diffraction calculator.