Merge f4e4003 into d7c1b9a

.github/workflows/build.yml

@@ -10,9 +10,6 @@ on:
   workflow_dispatch:
     workflow: '*'
 
-env:
-  MPLBACKEND: agg
-
 jobs:
   code:
     name: code style
@@ -59,15 +56,16 @@ jobs:
     name: ${{ matrix.os }}-py${{ matrix.python-version }}${{ matrix.LABEL }}
     runs-on: ${{ matrix.os }}
     timeout-minutes: 15
+    env:
+      MPLBACKEND: agg
     strategy:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.10", "3.11"]
+        python-version: ['3.10', '3.11']
         include:
           - os: ubuntu-latest
             python-version: 3.7
-            OLDEST_SUPPORTED_VERSION: true
             DEPENDENCIES: diffpy.structure==3  matplotlib==3.5
             LABEL: -oldest
     steps:
@@ -84,7 +82,7 @@ jobs:
           pip install -U -e .'[doc, tests]'
 
       - name: Install oldest supported version
-        if: ${{ matrix.OLDEST_SUPPORTED_VERSION }}
+        if: ${{ contains(matrix.LABEL, 'oldest') }}
         run: |
           pip install ${{ matrix.DEPENDENCIES }}
 
@@ -102,7 +100,7 @@ jobs:
 
       - name: Run tests
         run: |
-          pytest -n 2 --cov=orix --pyargs orix
+          pytest --pyargs orix --reruns 2 -n 2 --cov=orix
 
       - name: Generate line coverage
         if: ${{ matrix.os == 'ubuntu-latest' }}

.gitignore

@@ -67,6 +67,7 @@ doc/build/
 doc/examples/
 doc/reference/generated/
 doc/source/_autosummary/
+doc/sg_execution_times.rst
 
 # PyBuilder
 target/

CHANGELOG.rst

@@ -31,8 +31,9 @@ Added
 - The ``random()`` methods of ``Orientation`` and ``Misorientation`` now accept
   ``symmetry``. A ``random()`` method is also added to ``Vector3d`` and ``Miller``, the
   latter accepting a ``phase``.
-- ``Added orix.sampling.get_sample_zone_axis`` for getting zone axes for some point group.
-- ``Added orix.sampling.get_sample_reduced_fundamental`` for getting reduced
+- Added ``orix.sampling.get_sample_zone_axis()`` for getting zone axes for some point
+  group.
+- Added ``orix.sampling.get_sample_reduced_fundamental()`` for getting reduced
   fundamental zone for some point group.
 
 Changed
@@ -50,14 +51,13 @@ Deprecated
   and will be removed in v0.13. Use the existing ``from_axes_angles()`` and the new
   ``from_rodrigues()`` and ``from_homochoric()`` instead.
 
-Removed
--------
-
 Fixed
 -----
 - Transparency of polar stereographic grid lines can now be controlled by Matplotlib's
   ``grid.alpha``, just like the azimuth grid lines.
-- Previously ``Phase`` was failing to adjust atom position to accomodate for the change of basis. This is now fixed.
+- Previously, ``Phase`` did not adjust atom positions when forcing
+  ``Phase.structure.lattice.base`` to use the crystal axes alignment ``e1 || a``,
+  ``e3 || c*``. This is now fixed.
 
 2023-03-14 - version 0.11.1
 ===========================

doc/dev/building_writing_documentation.rst

@@ -10,7 +10,7 @@ New documents should fit into one of these categories.
 We use :doc:`Sphinx <sphinx:index>` for documenting functionality.
 Install necessary dependencies to build the documentation::
 
-    pip install --editable .[doc]
+    pip install --editable ".[doc]"
 
 .. note::
 
@@ -19,9 +19,6 @@ Install necessary dependencies to build the documentation::
     See the section on the :ref:`data module <adding-data-to-data-module>` for more
     details.
 
-If you get an error message running the above in a ``zsh`` shell, try wrapping the last
-part in a string, like ``'.[doc]'``.
-
 Then, build the documentation from the ``doc`` directory::
 
     cd doc

doc/dev/running_writing_tests.rst

@@ -6,10 +6,7 @@ The tests reside in a ``tests`` module.
 Tests are short methods that call functions in ``orix`` and compare resulting output
 values with known answers. Install necessary dependencies to run the tests::
 
-   pip install --editable .[tests]
-
-If you get an error message running the above in a ``zsh`` shell, try wrapping the last
-part in a string, like ``'.[tests]'``.
+   pip install --editable ".[tests]"
 
 Some useful :doc:`fixtures <pytest:explanation/fixtures>` are available in the
 ``conftest.py`` file.
@@ -39,7 +36,7 @@ Docstring examples are tested :doc:`with pytest <pytest:how-to/doctest>` as well
 already available in the namespace as ``np`` and ``plt``, respectively.
 The docstring tests can be run from the top directory::
 
-    pytest --doctest-modules --ignore-glob=orix/tests orix/*.py
+    pytest orix --doctest-modules --ignore-glob=orix/tests
 
 Tips for writing tests of Numba decorated functions:
 

doc/dev/setting_up_development_installation.rst

@@ -26,7 +26,7 @@ with the `Miniconda distribution <https://docs.conda.io/en/latest/miniconda.html
 Then, install the required dependencies while making the development version available
 globally (in the ``conda`` environment)::
 
-    pip install --editable .[dev]
+    pip install --editable ".[dev]"
 
 This installs all necessary development dependencies, including those for running tests
 and building documentation.

doc/tutorials/crystal_reference_frame.ipynb

@@ -220,7 +220,7 @@
    "source": [
     "## Alignment of symmetry operations\n",
     "\n",
-    "To see where the crystallographic axes about which the point group symmetry operations rotate, we can add symmetry operations to the figure, like is done in the [Visualizing point groups](point_groups.ipynb) tutorial for all point groups supported in orix"
+    "To see which crystallographic axes the point group symmetry operations rotate about, we can add symmetry operations to the figure, like is done in the [Visualizing point groups](point_groups.ipynb) tutorial for all point groups supported in orix"
    ]
   },
   {
@@ -238,7 +238,7 @@
    "outputs": [],
    "source": [
     "R = Rotation.from_axes_angles([0, 1, 0], -65, degrees=True)\n",
-    "phase.point_group.plot(figure=fig, orientation=R, fc=\"none\", ec=\"C0\", s=150)\n",
+    "phase.point_group.plot(figure=fig, orientation=R)\n",
     "fig"
    ]
   },
@@ -299,7 +299,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,

doc/tutorials/point_groups.ipynb

@@ -127,10 +127,10 @@
     "    # respectively, for Symmetry.plot()\n",
     "\n",
     "    # vectors on the upper hemisphere are shown as open circles\n",
-    "    ax[i].scatter(v, marker=\"o\", fc=\"None\", ec=\"k\", s=150)\n",
+    "    ax[i].scatter(v, marker=\"o\", c=\"None\", ec=\"C0\", s=150)\n",
     "    # vectors on the lower hemisphere are reprojected onto the upper\n",
     "    # hemisphere and shown as crosses\n",
-    "    ax[i].scatter(v_reproject, marker=\"+\", ec=\"C0\", s=150)\n",
+    "    ax[i].scatter(v_reproject, marker=\"+\", c=\"C0\", s=150)\n",
     "\n",
     "    ax[i].set_title(f\"${S}$ $({Si.name})$\")\n",
     "    ax[i].set_labels(\"$e_1$\", \"$e_2$\", None)"
@@ -156,7 +156,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.6"
+   "version": "3.11.8"
   }
  },
  "nbformat": 4,

doc/user/applications.rst

@@ -12,6 +12,14 @@ If you think your work should be listed here, please raise an issue `on GitHub
 <https://github.com/pyxem/orix>`__ or `contact the developers
 <pyxem.team@gmail.com>`__.
 
+2024
+====
+- I. MacLaren, E. Frutos-Myro, S. Zeltmann, C. Ophus, "A method for crystallographic
+  mapping of an alpha-beta titanium alloy with nanometre resolution using scanning
+  precession electron diffraction and open-source software libraries," *Journal of
+  Microscopy*, 1-9 (2024).
+  https://doi/10.1111/jmi.13275.
+
 2022
 ====
 

doc/user/related_projects.rst

@@ -24,6 +24,8 @@ find useful:
   orix depends on numpy-quaternion for quaternion multiplication.
 - `texture <https://github.com/usnistgov/texture>`_: Python scripts for analysis of
   crystallographic texture.
-- pymicro: Python package to work with material microstructures and 3D data sets.
-- Dream3D: C++ library to reconstruct, instatiate, quantify, mesh, handle and visualize
-  multidimensional (3D), multimodal data (mainly EBSD orientation data).
+- `pymicro <https://pymicro.readthedocs.io>`_`: Python package to work with material
+  microstructures and 3D data sets.
+- `DREAM.3D <https://dream3d.io/>`_`: C++ library to reconstruct, instatiate, quantify,
+  mesh, handle and visualize multidimensional (3D), multimodal data (mainly EBSD
+  orientation data).

examples/crystal_maps/create_empty_map.py

@@ -0,0 +1,14 @@
+"""
+========================
+Create empty crystal map
+========================
+
+This example shows how to create an empty crystal map, which can be useful for testing.
+"""
+
+from orix.crystal_map import CrystalMap
+
+xmap = CrystalMap.empty((5, 10))
+xmap
+
+xmap.plot("x")

examples/misorientations/misorientation_from_aligning_directions.py

@@ -64,8 +64,8 @@
 # Plot the two directions in the (unrotated) first crystal's reference
 # frame as open circles
 fig = t_cubic.scatter(
+    c="none",
     ec=["r", "b"],
-    fc="none",
     grid=True,
     axes_labels=["e1", "e2"],
     return_figure=True,

examples/orientations/orientation_from_aligning_directions.py

@@ -1,3 +1,4 @@
+# %%
 r"""
 ====================================
 Orientation from aligning directions
@@ -39,8 +40,8 @@
 
 # Plot the reference orientation sample directions as empty circles
 fig = v.scatter(
+    c="none",
     ec=["r", "b"],
-    fc="none",
     grid=True,
     axes_labels=["X", "Y"],
     return_figure=True,

examples/rotations/rotations_mapping_fundamental_sector.py

@@ -0,0 +1,58 @@
+"""
+================================================
+Rotations mapping the fundamental sector on *S2*
+================================================
+
+This example shows how to sample rotations :math:`\mathbf{R}` that when
+rotating the vector :math:`\mathbf{v_z} = (0, 0, 1)`, the resulting
+vectors cover the fundamental sector of a given Laue class.
+
+We show this by comparing the vectors we get by: 
+
+1. sampling rotations for *4/mmm* and then rotating :math:`\mathbf{v_z}`
+2. sampling all of *S2* but only keeping those within the corresponding
+   fundamental sector.
+
+Apart from the first rotation, all rotations have a Euler angle
+:math:`\phi = 0^{\circ}`.
+These "reduced" rotations are useful in template matching of spot
+patterns from the transmission electron microscope.
+"""
+
+import matplotlib.pyplot as plt
+import numpy as np
+
+from orix import plot, sampling
+from orix.quaternion import symmetry
+from orix.vector import Vector3d
+
+
+# Sample rotations with an average misorientation
+res = 2
+pg = symmetry.D4h  # 4/mmm
+
+R = sampling.get_sample_reduced_fundamental(res, point_group=pg)
+print(np.allclose(R.to_euler()[1:, 0], 0))
+
+########################################################################
+# Get vectors within the fundamental sector following the two routes
+v1 = R * Vector3d.zvector()
+
+v2 = sampling.sample_S2(res)
+v2 = v2[v2 <= pg.fundamental_sector]
+
+# Only equivalent for the same S2 sampling method
+print(np.allclose(v1.data, v2.data))
+print(v1)
+print(v2)
+
+########################################################################
+# Plot the vectors in the fundamental sector of 4/mmm
+fig, (ax0, ax1) = plt.subplots(
+    ncols=2, subplot_kw={"projection": "ipf", "symmetry": pg}, layout="tight"
+)
+ax0.scatter(v1, s=5)
+ax1.scatter(v2, c="C1", s=5)
+ax0.set_title("Rotated Z vectors", loc="left")
+ax1.set_title("Directly sampled", loc="left")
+_ = fig.suptitle("Vectors in the fundamental sector of 4/mmm", y=0.8)

examples/stereographic_projection/zoom_inset_region.py

@@ -10,7 +10,6 @@
 """
 
 import matplotlib.pyplot as plt
-from mpl_toolkits.axes_grid1.inset_locator import InsetPosition
 
 from orix import plot, projections, sampling
 from orix.vector import Vector3d
@@ -38,22 +37,19 @@
 # The zoomed inset rectangle origin (x, y), width and height
 rect = [0.15, 0.2, 0.43, 0.43]
 
-# Add a new stereographic projection axis with a grid resolution of 2
-# degrees to the figure and plot the vectors here as well
-ax_inset = fig.add_axes(rect, projection="stereographic")
-ax_inset.stereographic_grid(True, 2, 2)
-ax_inset.scatter(v2)
-ax_inset.scatter(v_ref, c="r")
-
-# Restrict the inset region to the extent vectors
+# Add a new stereographic projection axis and zoom in
+ax_inset = ax.inset_axes(rect, projection="stereographic")
 ax_inset.set(
     xlim=(x_inset.min(), x_inset.max()),
     ylim=(y_inset.min(), y_inset.max()),
 )
 
+# Add a grid of 2 degrees resolution and re-plot the vectors
+ax_inset.stereographic_grid(True, 2, 2)
+ax_inset.scatter(v2)
+ax_inset.scatter(v_ref, c="r")
+
 # Add lines indicating the inset zoom
-ip = InsetPosition(ax, rect)
-ax_inset.set_axes_locator(ip)
 ax.indicate_inset_zoom(ax_inset, edgecolor="k")
 
 # Add border to the inset region

orix/__init__.py

@@ -13,6 +13,7 @@
     "Niels Cautaerts",
     "Austin Gerlt",
     "Anders Christian Mathisen",
+    "Carter Francis",
     "Simon Høgås",
     "Alexander Clausen",
     "Viljar Johan Femoen",

orix/crystal_map/crystal_map.py

@@ -775,17 +775,6 @@ def empty(
         -------
         xmap
             Crystal map.
-
-        Examples
-        --------
-        >>> from orix.crystal_map import CrystalMap
-        >>> xmap = CrystalMap.empty((5, 10))
-        >>> xmap
-        Phase  Orientations  Name  Space group  Point group  Proper point group     Color
-            0   50 (100.0%)  None         None         None                None  tab:blue
-        Properties:
-        Scan unit: px
-        >>> xmap.plot("x")  # Increasing towards the right
         """
         d, n = create_coordinate_arrays(shape, step_sizes)
         d["rotations"] = Rotation.identity((n,))