Geometrical and kinematical Kikuchi pattern simulations for all point groups

.github/workflows/build.yml

@@ -48,7 +48,7 @@ jobs:
           - os: ubuntu-latest
             python-version: 3.7
             OLDEST_SUPPORTED_VERSION: true
-            DEPENDENCIES: dask==2021.8.1 diffsims==0.4.0 hyperspy==1.7 matplotlib==3.3 numba==0.52 numpy==1.19 orix==0.9.0 scikit-image==0.16.2
+            DEPENDENCIES: dask==2021.8.1 diffsims==0.5.0 hyperspy==1.7 matplotlib==3.3 numba==0.52 numpy==1.19 orix==0.9.0 scikit-image==0.16.2
             LABEL: -oldest
     steps:
       - uses: actions/checkout@v2

CHANGELOG.rst

@@ -24,8 +24,11 @@ Added
 - ``EBSDMasterPattern.plot_spherical()`` for plotting a master pattern in the
   stereographic projection on the 3D sphere.
   (`#536 <https://github.com/pyxem/kikuchipy/pull/536>`_)
-- A new package dependency on `pyvista` for 3D plotting and on `pythreejs` for the docs
-  are introduced. (`#536 <https://github.com/pyxem/kikuchipy/pull/536>`_)
+- Projection of master pattern in the stereographic projection to the square Lambert
+  projection via ``EBSDMasterPattern.to_lambert()``.
+  (`#536 <https://github.com/pyxem/kikuchipy/pull/536>`_)
+- New package dependencies on ``pyvista`` for 3D plotting and on ``pythreejs`` for the
+  docs are introduced. (`#536 <https://github.com/pyxem/kikuchipy/pull/536>`_)
 - Reduce time and memory use of the following ``kikuchipy.signals.EBSD`` methods by
   using ``hyperspy.signal.BaseSignal.map()``: ``remove_static_background()``,
   ``remove_dynamic_background()`` and ``get_image_quality()``.
@@ -38,21 +41,40 @@ Added
 
 Changed
 -------
+- Valid ``EBSDMasterPattern.hemisphere`` values from ``"north"`` and ``"south"`` to
+  ``"upper"`` and ``"lower"``, respectively, to be in line with `orix`.
+  (`#537 <https://github.com/pyxem/kikuchipy/pull/537>`_)
+- Increase minimal version of diffsims to 0.5.
+  (`#537 <https://github.com/pyxem/kikuchipy/pull/537>`_)
 - Chunking of EBSD signal navigation dimensions in
   ``EBSD.average_neighbour_patterns()`` to reduce memory use.
   (`#532 <https://github.com/pyxem/kikuchipy/pull/532>`_)
 - Remove requirement that the crystal map used for EBSD refinement has identical step
   size(s) to the EBSD signal's navigation axes. This raised an error previously, but now
   only emits a warning. (`#531 <https://github.com/pyxem/kikuchipy/pull/531>`_)
-- Restrict minimal version of HyperSpy to 1.7.
+- Increase minimal version of HyperSpy to 1.7.
   (`#527 <https://github.com/pyxem/kikuchipy/pull/527>`_)
-- Restrict minimal version of SciPy to 1.7.
+- Increase minimal version of SciPy to 1.7.
   (`#504 <https://github.com/pyxem/kikuchipy/pull/504>`_)
 
 Deprecated
 ----------
+- The ``kikuchipy.simulations.GeometricalEBSDSimulation`` class is deprecated and will
+  be removed in version 0.7. Obtain
+  ``kikuchipy.simulations.GeometricalKikuchiPatternSimulation``  via
+  ``kikuchipy.simulations.KikuchiPatternSimulator.on_detector()`` instead. The
+  ``kikuchipy.simulations.features`` module is also deprecated and will be removed in
+  version 0.7. Obtain Kikuchi line and zone axis detector/gnomonic coordinates of a
+  simulation via ``lines_coordinates()`` and ``zone_axes_coordinates()`` instead.
+  (`#537 <https://github.com/pyxem/kikuchipy/pull/537>`_)
+- The ``kikuchipy.generators.EBSDSimulationGenerator`` class is deprecated and will be
+  removed in version 0.7. Use the ``kikuchipy.simulations.KikuchiPatternSimulator``
+  class instead. (`#537 <https://github.com/pyxem/kikuchipy/pull/537>`_)
+- The ``kikuchipy.crystallography.matrices`` module is depreacted and will be removed in
+  version 0.7, access the matrices via :class:`diffpy.structure.Lattice` attributes
+  instead. (`#537 <https://github.com/pyxem/kikuchipy/pull/537>`_)
 - The following functions for processing of pattern chunks in the
-  ``kikuchipy.pattern.chunk`` module are deprecated in 0.6 and will be removed in 0.7:
+  ``kikuchipy.pattern.chunk`` module are deprecated and will be removed in version 0.7:
   ``get_image_quality()``, ``remove_dynamic_background()`` and
   ``remove_static_background()``. Use the ``EBSD`` class for processing of many
   patterns. (`#527 <https://github.com/pyxem/kikuchipy/pull/527>`_,
@@ -66,6 +88,8 @@ Removed
 
 Fixed
 -----
+- Plotting of geometrical simulation markers on rectangular patterns.
+  (`#537 <https://github.com/pyxem/kikuchipy/pull/537>`_)
 - Hopefully prevent EBSD refinement tests using random data to fail on Azure.
   (`#465 <https://github.com/pyxem/kikuchipy/pull/465>`_)
 

CONTRIBUTING.rst

@@ -71,7 +71,7 @@ Code style
 ==========
 
 The code making up kikuchipy is formatted closely following the `Style Guide for Python
-Code <https://www.python.org/dev/peps/pep-0008/>`_ with `The Black Code style
+Code <https://peps.python.org/pep-0008/>`_ with `The Black Code style
 <https://black.readthedocs.io/en/stable/the_black_code_style/current_style.html>`_. We
 use `pre-commit <https://pre-commit.com>`_ to run ``black`` automatically prior to each
 local commit. Please install it in your environment::
@@ -82,7 +82,7 @@ Next time you commit some code, your code will be formatted inplace according to
 ``black``.
 
 Note that ``black`` won't format `docstrings
-<https://www.python.org/dev/peps/pep-0257/>`_. We follow the `numpydoc
+<https://peps.python.org/pep-0257/>`_. We follow the `numpydoc
 <https://numpydoc.readthedocs.io/en/latest/format.html#docstring-standard>`_ standard.
 
 Comment lines should preferably be limited to 72 characters.
@@ -132,7 +132,7 @@ Add and commit your created, modified or deleted files::
 The ``-s`` makes sure that you sign your commit with your `GitHub-registered email
 <https://github.com/settings/emails>`_ as the author. You can set this up following
 `this GitHub guide
-<https://help.github.com/en/github/setting-up-and-managing-your-github-user-account/setting-your-commit-email-address>`_.
+<https://docs.github.com/en/account-and-profile/setting-up-and-managing-your-personal-account-on-github/managing-email-preferences/setting-your-commit-email-address>`_.
 
 Keeping your branch up-to-date
 ==============================
@@ -161,8 +161,9 @@ Update your remote branch::
     git push -u origin your-awesome-feature-name
 
 You can then make a `pull request
-<https://guides.github.com/activities/forking/#making-a-pull-request>`_ to kikuchipy's
-``develop`` branch for new features and ``main`` branch for bug fixes. Good job!
+<https://docs.github.com/en/get-started/quickstart/contributing-to-projects#making-a-pull-request>`_
+to kikuchipy's ``develop`` branch for new features and ``main`` branch for bug fixes.
+Good job!
 
 Building and writing documentation
 ==================================
@@ -245,7 +246,7 @@ the documentation doesn't take too long to build, either by us locally or the Re
 Docs GitHub action. To check that the notebooks with stored cell outputs are compatible
 with the current API, we run a scheduled GitHub Action every Monday morning which checks
 that the notebooks run OK and that they produce the same output now as when they were
-last executed. We use `nbval <https://nbval.readthedocs.io>`_ for this.
+last executed. We use `nbval <https://nbval.readthedocs.io/en/latest/>`_ for this.
 
 Deprecations
 ============
@@ -277,8 +278,9 @@ answers. Install necessary dependencies to run the tests::
 
     pip install --editable .[tests]
 
-Some useful `fixtures <https://docs.pytest.org/en/latest/fixture.html>`_, like a dummy
-scan and corresponding background pattern, are available in the ``conftest.py`` file.
+Some useful `fixtures <https://docs.pytest.org/en/latest/explanation/fixtures.html>`_,
+like a dummy scan and corresponding background pattern, are available in the
+``conftest.py`` file.
 
 .. note::
 
@@ -309,7 +311,7 @@ e.g. when you're creating or updating a test. But remember to run the full test
 before pushing!
 
 Docstring examples are tested `with pytest
-<https://docs.pytest.org/en/stable/doctest.html>`_ as well::
+<https://docs.pytest.org/en/stable/how-to/doctest.html>`_ as well::
 
     pytest --doctest-modules --ignore-glob=kikuchipy/*/tests
 

doc/bibliography.bib

@@ -106,6 +106,25 @@ @phdthesis{lassen1994automated
 	title = {{Automated Determanation of Crystal Orientations from Electron Backscattering Patterns}},
 	year = {1994}
 }
+@book{kirkland1998advanced,
+	author = {Kirkland, Earl J},
+	publisher = {Springer},
+	title = {{Advanced computing in electron microscopy}},
+	volume = {12},
+	year = {1998},
+	doi = {10.1007/978-1-4757-4406-4}
+}
+@article{lobato2014accurate,
+	author = {Lobato, Ivan and {Van Dyck}, Dirk},
+	journal = {Acta Crystallographica Section A: Foundations and Advances},
+	number = {6},
+	pages = {636–649},
+	publisher = {International Union of Crystallography},
+	title = {{An accurate parameterization for scattering factors, electron densities and electrostatic potentials for neutral atoms that obey all physical constraints}},
+	volume = {70},
+	year = {2014},
+	doi = {10.1107/S205327331401643X}
+}
 @article{marquardt2017quantitative,
 	author = {Marquardt, Katharina and {De Graef}, Marc and Singh, Saransh and Marquardt, Hauke and Rosenthal, Anja and Koizuimi, Sanae},
 	doi = {10.2138/am-2017-6062},

doc/index.rst

@@ -3,7 +3,7 @@ kikuchipy
 =========
 
 .. Launch binder
-.. image:: https://mybinder.org/badge_logo.svg
+.. image:: https://static.mybinder.org/badge_logo.svg
     :target: https://mybinder.org/v2/gh/pyxem/kikuchipy/HEAD
     :alt: Launch binder
 
@@ -28,11 +28,11 @@ kikuchipy
 
 .. PyPI version
 .. image:: https://img.shields.io/pypi/v/kikuchipy.svg
-    :target: https://pypi.python.org/pypi/kikuchipy
+    :target: https://pypi.org/project/kikuchipy/
     :alt: PyPI version
 
 .. Downloads per month
-.. image:: https://pepy.tech/badge/kikuchipy/month
+.. image:: https://static.pepy.tech/badge/kikuchipy/month
     :target: https://pepy.tech/project/kikuchipy
     :alt: Downloads per month
 
@@ -54,7 +54,7 @@ multi-dimensional data analysis provided by the HyperSpy library.
   Notebooks with many links to detailed explanations of the input parameters and output
   of functions and class methods (the API reference). The notebooks can be inspected
   statically on the web page or via `nbviewer
-  <https://nbviewer.jupyter.org/github/pyxem/kikuchipy/tree/develop/doc/user_guide/>`_,
+  <https://nbviewer.org/github/pyxem/kikuchipy/tree/develop/doc/user_guide/>`_,
   downloaded and run locally, or run interactively in the browser by clicking the Binder
   link above and navigating to the `doc/user_guide` directory. We hope you find them
   useful!
@@ -87,7 +87,7 @@ multi-dimensional data analysis provided by the HyperSpy library.
     user_guide/feature_maps.ipynb
     user_guide/virtual_backscatter_electron_imaging.ipynb
     user_guide/pattern_matching.ipynb
-    user_guide/geometrical_ebsd_simulations.ipynb
+    user_guide/kikuchi_pattern_simulations.ipynb
     user_guide/multivariate_analysis.ipynb
     user_guide/metadata_structure.ipynb
 

doc/reference.rst

@@ -613,8 +613,38 @@ simulations
 .. currentmodule:: kikuchipy.simulations
 
 .. autosummary::
-    GeometricalEBSDSimulation
+    KikuchiPatternSimulator
+    GeometricalKikuchiPatternSimulation
     features
+    GeometricalEBSDSimulation
+
+KikuchiPatternSimulator
+-----------------------
+
+.. currentmodule:: kikuchipy.simulations.KikuchiPatternSimulator
+
+.. autosummary::
+    calculate_master_pattern
+    on_detector
+    plot
+
+.. autoclass:: kikuchipy.simulations.KikuchiPatternSimulator
+    :members:
+
+GeometricalKikuchiPatternSimulation
+-----------------------------------
+
+.. currentmodule:: kikuchipy.simulations.GeometricalKikuchiPatternSimulation
+
+.. autosummary::
+    as_collections
+    as_markers
+    lines_coordinates
+    plot
+    zone_axes_coordinates
+
+.. autoclass:: kikuchipy.simulations.GeometricalKikuchiPatternSimulation
+    :members:
 
 GeometricalEBSDSimulation
 -------------------------