Merge pull request #306 from harripj/add_Symmetry_scatter

Add Symmetry plot method

CHANGELOG.rst

@@ -12,6 +12,9 @@ Unreleased
 
 Added
 -----
+- Point group `Symmetry` elements can now be viewed under the stereographic projection
+  using `Symmetry.plot()`. The notebook point_groups.ipynb has been added to the
+  documentation.
 - Add `reproject` argument to `Vector3d.scatter()` which reprojects vectors located on
   the hidden hemisphere to the visible hemisphere.
 - `Rotation` objects can now be checked for equality. Equality is determined by

doc/conf.py

@@ -44,11 +44,11 @@
 intersphinx_mapping = {
     "dask": ("https://docs.dask.org/en/latest", None),
     "diffpy.structure": ("https://www.diffpy.org/diffpy.structure", None),
-    "h5py": ("http://docs.h5py.org/en/stable/", None),
-    "matplotlib": ("https://matplotlib.org", None),
-    "numpy": ("https://docs.scipy.org/doc/numpy", None),
+    "h5py": ("https://docs.h5py.org/en/stable", None),
+    "matplotlib": ("https://matplotlib.org/stable", None),
+    "numpy": ("https://numpy.org/doc/stable", None),
     "python": ("https://docs.python.org/3", None),
-    "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
+    "scipy": ("https://docs.scipy.org/doc/scipy", None),
 }
 
 # Add any paths that contain templates here, relative to this directory.

doc/index.rst

@@ -23,6 +23,7 @@ Work using orix
     clustering_across_fundamental_region_boundaries.ipynb
     clustering_orientations.ipynb
     uniform_sampling_of_orientation_space.ipynb
+    point_groups.ipynb
 
 .. toctree::
     :hidden:

doc/point_groups.ipynb

@@ -0,0 +1,127 @@
+{
+    "cells": [
+        {
+            "cell_type": "markdown",
+            "metadata": {
+                "nbsphinx": "hidden"
+            },
+            "source": [
+                "This notebook is part of the orix documentation https://orix.rtfd.io. Links to the documentation won’t work from the notebook."
+            ]
+        },
+        {
+            "cell_type": "markdown",
+            "metadata": {},
+            "source": [
+                "## Visualizing point groups\n",
+                "\n",
+                "Point group symmetry operations are shown here under the stereographic projection.\n",
+                "\n",
+                "Vectors located on the upper (`z >= 0`) hemisphere are displayed as points (`o`), whereas vectors on the lower hemisphere are reprojected onto the upper hemisphere and shown as crosses (`+`) by default. For more information about plot formatting and visualization, see [Vector3d.scatter()](reference.rst#orix.vector.Vector3d.scatter).\n",
+                "\n",
+                "More explanation of these figures is provided at http://xrayweb.chem.ou.edu/notes/symmetry.html#point."
+            ]
+        },
+        {
+            "cell_type": "markdown",
+            "metadata": {},
+            "source": [
+                "For example, the `O (432)` point group:"
+            ]
+        },
+        {
+            "cell_type": "code",
+            "execution_count": null,
+            "metadata": {
+                "tags": [
+                    "nbsphinx-thumbnail"
+                ]
+            },
+            "outputs": [],
+            "source": [
+                "%matplotlib inline\n",
+                "\n",
+                "from orix.quaternion import symmetry\n",
+                "\n",
+                "symmetry.O.plot()"
+            ]
+        },
+        {
+            "cell_type": "markdown",
+            "metadata": {},
+            "source": [
+                "The stereographic projection of all point groups is shown below:"
+            ]
+        },
+        {
+            "cell_type": "code",
+            "execution_count": null,
+            "metadata": {},
+            "outputs": [],
+            "source": [
+                "from matplotlib import pyplot as plt\n",
+                "import numpy as np\n",
+                "\n",
+                "from orix import plot\n",
+                "from orix.quaternion import Rotation\n",
+                "from orix.vector import Vector3d\n",
+                "\n",
+                "schoenflies = ['C1', 'Ci', 'C2x', 'C2y', 'C2z', 'Csx', 'Csy', 'Csz', 'C2h', 'D2', 'C2v', 'D2h', 'C4', 'S4', 'C4h', 'D4', 'C4v', 'D2d', 'D4h', 'C3', 'S6', 'D3x', 'D3y', 'D3', 'C3v', 'D3d', 'C6', 'C3h', 'C6h', 'D6', 'C6v', 'D3h', 'D6h', 'T', 'Th', 'O', 'Td', 'Oh']\n",
+                "\n",
+                "assert len(symmetry._groups) == len(schoenflies)\n",
+                "\n",
+                "schoenflies = [s for s in schoenflies if not (s.endswith('x') or s.endswith('y'))]\n",
+                "\n",
+                "assert len(schoenflies) == 32\n",
+                "\n",
+                "orientation = Rotation.from_axes_angles((-1, 8, 1), np.deg2rad(65))\n",
+                "\n",
+                "fig, ax = plt.subplots(nrows=8, ncols=4, figsize=(10, 20), subplot_kw=dict(projection='stereographic'))\n",
+                "ax = ax.ravel()\n",
+                "\n",
+                "for i, s in enumerate(schoenflies):\n",
+                "    sym = getattr(symmetry, s)\n",
+                "\n",
+                "    ori_sym = sym.outer(orientation)\n",
+                "    v = (ori_sym * Vector3d.zvector())\n",
+                "    \n",
+                "    # reflection in the projection plane (x-y) is performed internally in\n",
+                "    # Symmetry.plot() or when using the `reproject=True` argument for\n",
+                "    # Vector3d.scatter()\n",
+                "    v_reproject = Vector3d(v.data.copy())\n",
+                "    v_reproject.z *= -1\n",
+                "    \n",
+                "    # the Symmetry marker formatting for vectors on the upper and lower hemisphere\n",
+                "    # can be set using `kwargs` and `reproject_scatter_kwargs`, respectively, for\n",
+                "    # 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",
+                "    # vectors on the lower hemisphere are reprojected onto the upper hemisphere and\n",
+                "    # shown as crosses\n",
+                "    ax[i].scatter(v_reproject, marker='+', ec='C0', s=150)\n",
+                "\n",
+                "    ax[i].set_title(f'${s}$ $({sym.name})$')\n",
+                "    ax[i].set_labels('a', 'b', None)\n",
+                "\n",
+                "fig.tight_layout()"
+            ]
+        }
+    ],
+    "metadata": {
+        "language_info": {
+            "codemirror_mode": {
+                "name": "ipython",
+                "version": 3
+            },
+            "file_extension": ".py",
+            "mimetype": "text/x-python",
+            "name": "python",
+            "nbconvert_exporter": "python",
+            "pygments_lexer": "ipython3",
+            "version": "3.9.7"
+        }
+    },
+    "nbformat": 4,
+    "nbformat_minor": 4
+}

doc/reference.rst

@@ -417,6 +417,7 @@ Symmetry
 .. currentmodule:: orix.quaternion.Symmetry
 .. autosummary::
     from_generators
+    plot
 .. autoclass:: orix.quaternion.Symmetry
     :show-inheritance:
     :members:

orix/quaternion/symmetry.py

@@ -451,6 +451,75 @@ def fundamental_zone(self):
         sr = SphericalRegion(n.unique())
         return sr
 
+    def plot(
+        self,
+        orientation=None,
+        reproject_scatter_kwargs=None,
+        **kwargs,
+    ):
+        """Stereographic projection of symmetry operations.
+
+        The upper hemisphere of the stereographic projection is shown.
+        Vectors on the lower hemisphere are shown after reprojection
+        onto the upper hemisphere.
+
+        Parameters
+        ----------
+        orientation : Orientation, optional
+            The symmetry operations are applied to this orientation
+            before plotting. The default value uses an orientation
+            optimized to show symmetry elements.
+        reproject_scatter_kwargs: dict, optional
+            Dictionary of keyword arguments for the reprojected scatter
+            points which is passed to
+            :meth:`~orix.plot.StereographicPlot.scatter`, which passes
+            these on to :meth:`matplotlib.axes.Axes.scatter`. The
+            default marker style for reprojected vectors is "+". Values
+            used for vector(s) on the visible hemisphere are used unless
+            another value is passed here.
+        kwargs : dict, optional
+            Keyword arguments passed to
+            :meth:`~orix.plot.StereographicPlot.scatter`, which passes
+            these on to :meth:`matplotlib.axes.Axes.scatter`.
+
+        Returns
+        -------
+        fig : matplotlib.figure.Figure
+            The created figure, returned if `return_figure` is supplied
+            as a keyword argument and is True.
+        """
+        if orientation is None:
+            # orientation chosen to mimic stereographic projections as
+            # shown: http://xrayweb.chem.ou.edu/notes/symmetry.html
+            orientation = Rotation.from_axes_angles((-1, 8, 1), np.deg2rad(65))
+        if not isinstance(orientation, Rotation):
+            raise TypeError("Orientation must be a Rotation instance.")
+        orientation = self.outer(orientation)
+
+        kwargs.setdefault("return_figure", False)
+        return_figure = kwargs.pop("return_figure")
+
+        if reproject_scatter_kwargs is None:
+            reproject_scatter_kwargs = {}
+        reproject_scatter_kwargs.setdefault("marker", "+")
+        reproject_scatter_kwargs.setdefault("label", "lower")
+
+        v = orientation * Vector3d.zvector()
+
+        figure = v.scatter(
+            return_figure=True,
+            axes_labels=("a", "b", None),
+            label="upper",
+            reproject=True,
+            reproject_scatter_kwargs=reproject_scatter_kwargs,
+            **kwargs,
+        )
+        # add symmetry name to figure title
+        figure.suptitle(f"${self.name}$")
+
+        if return_figure:
+            return figure
+
 
 # Triclinic
 C1 = Symmetry((1, 0, 0, 0))

orix/tests/quaternion/test_symmetry.py

@@ -19,6 +19,7 @@
 from copy import deepcopy
 
 from diffpy.structure.spacegroups import GetSpaceGroup
+from matplotlib import pyplot as plt
 import numpy as np
 import pytest
 
@@ -406,6 +407,33 @@ def test_hash_persistence():
     assert all(h1a == h2a for h1a, h2a in zip(h1, h2))
 
 
+@pytest.mark.parametrize("symmetry", [C1, C4, Oh])
+def test_symmetry_plot(symmetry):
+    figure = symmetry.plot(return_figure=True)
+    assert isinstance(figure, plt.Figure)
+    assert len(figure.axes) == 1
+    ax = figure.axes[0]
+    num = 1 if symmetry.is_proper else 2
+    assert len(ax.collections) == num
+    c0 = ax.collections[0]
+    assert len(c0.get_offsets()) == np.count_nonzero(~symmetry.improper)
+    assert c0.get_label().lower() == "upper"
+    if num > 1:
+        c1 = ax.collections[1]
+        assert len(c1.get_offsets()) == np.count_nonzero(symmetry.improper)
+        assert c1.get_label().lower() == "lower"
+    assert len(ax.texts) == 2
+    assert ax.texts[0].get_text() == "a"
+    assert ax.texts[1].get_text() == "b"
+    plt.close("all")
+
+
+@pytest.mark.parametrize("symmetry", [C1, C4, Oh])
+def test_symmetry_plot_raises(symmetry):
+    with pytest.raises(TypeError, match="Orientation must be a Rotation instance"):
+        _ = symmetry.plot(return_figure=True, orientation="test")
+
+
 class TestFundamentalSectorFromSymmetry:
     """Test the normals, vertices and centers of the fundamental sector
     for all 32 crystallographic point groups.