Change left/right symmetry in reduction of (mis)orientations to fundamental zone

CHANGELOG.rst

@@ -11,18 +11,30 @@ Unreleased
 
 Added
 -----
+- ``Vector3d.get_path()`` class method to get vectors between two or more vectors.
 
 Changed
 -------
+- The ``reduce()`` method (replacing ``map_into_symmetry_reduced_zone()``) for
+  the ``Misorientation`` and ``Orientation`` classes now apply symmetry operators in the
+  opposite order of what was done previously.
+- The ``convention`` parameter in ``from_euler()`` and ``to_euler()`` will be removed in
+  the next minor release, 0.13, instead of release 1.0 as previously stated.
 
 Deprecated
 ----------
+- ``map_into_symmetry_reduced_zone()`` is deprecated since 0.12 and will be removed in
+  0.13. Use ``reduce()`` instead.
 
 Removed
 -------
+- ``verbose`` parameter in ``reduce()``
+  (replacing ``map_into_symmetry_reduced_zone()``).
 
 Fixed
 -----
+- Transparency of polar stereographic grid lines can now be controlled by Matplotlib's
+  ``grid.alpha``, just like the azimuth grid lines.
 
 2023-03-14 - version 0.11.1
 ===========================

doc/conf.py

@@ -61,7 +61,6 @@
     "nbval": ("https://nbval.readthedocs.io/en/latest", None),
     "numpy": ("https://numpy.org/doc/stable", None),
     "numpydoc": ("https://numpydoc.readthedocs.io/en/latest", None),
-    "pymicro": ("https://pymicro.readthedocs.io/projects/pymicro/en/latest", None),
     "pytest": ("https://docs.pytest.org/en/stable", None),
     "python": ("https://docs.python.org/3", None),
     "pyxem": ("https://pyxem.readthedocs.io/en/latest", None),

doc/tutorials/clustering_across_fundamental_region_boundaries.ipynb

@@ -75,21 +75,21 @@
     "cluster1 = Rotation.random_vonmises(n_orientations, alpha=alpha)\n",
     "\n",
     "# Cluster 2\n",
-    "centre2 = Rotation.from_axes_angles((1, 0, 0), np.pi / 4)\n",
+    "centre2 = Rotation.from_axes_angles((1, 0, 0), -45, degrees=True)\n",
     "cluster2 = Rotation.random_vonmises(\n",
     "    n_orientations, alpha=alpha, reference=centre2\n",
     ")\n",
     "\n",
     "# Cluster 3\n",
-    "centre3 = Rotation.from_axes_angles((1, 1, 0), np.pi / 3)\n",
+    "centre3 = Rotation.from_axes_angles((1, 1, 0), -60, degrees=True)\n",
     "cluster3 = Rotation.random_vonmises(\n",
     "    n_orientations, alpha=alpha, reference=centre3\n",
     ")\n",
     "\n",
     "# Stack and map into the Oh fundamental zone\n",
     "ori = Orientation.stack([cluster1, cluster2, cluster3]).flatten()\n",
     "ori.symmetry = Oh\n",
-    "ori = ori.map_into_symmetry_reduced_zone()"
+    "ori = ori.reduce()"
    ]
   },
   {
@@ -102,7 +102,7 @@
     "\n",
     "### Perform clustering without application of crystal symmetry\n",
     "\n",
-    "Compute misorientations, i.e. distance between orientations"
+    "Compute misorientation angles, i.e. distance between orientations, without symmetry"
    ]
   },
   {
@@ -116,11 +116,8 @@
     "# Remove symmetry by setting it to point group 1 (identity operation)\n",
     "ori_without_symmetry = Orientation(ori.data, symmetry=C1)\n",
     "\n",
-    "# Misorientations\n",
-    "mori1 = (~ori_without_symmetry).outer(ori_without_symmetry)\n",
-    "\n",
     "# Misorientation angles\n",
-    "D1 = mori1.angle"
+    "D1 = ori_without_symmetry.angle_with_outer(ori_without_symmetry)"
    ]
   },
   {
@@ -136,6 +133,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "D1 = D1.astype(np.float32)\n",
     "dbscan_naive = DBSCAN(eps=0.3, min_samples=10, metric=\"precomputed\").fit(D1)\n",
     "print(\"Labels:\", np.unique(dbscan_naive.labels_))"
    ]
@@ -155,12 +153,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mori2 = (~ori).outer(ori)\n",
-    "\n",
-    "mori2.symmetry = Oh\n",
-    "mori2 = mori2.map_into_symmetry_reduced_zone()\n",
-    "\n",
-    "D2 = mori2.angle"
+    "D2 = ori.angle_with_outer(ori)"
    ]
   },
   {
@@ -176,9 +169,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "D2 = D2.astype(np.float32)\n",
     "dbscan = DBSCAN(\n",
     "    eps=np.deg2rad(17), min_samples=20, metric=\"precomputed\"\n",
-    ").fit(D2.astype(np.float32))\n",
+    ").fit(D2)\n",
     "print(\"Labels:\", np.unique(dbscan.labels_))"
    ]
   },
@@ -284,7 +278,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.8"
+   "version": "3.10.10"
   }
  },
  "nbformat": 4,

doc/tutorials/clustering_misorientations.ipynb

@@ -39,7 +39,6 @@
     "\n",
     "from orix import data, plot\n",
     "from orix.quaternion import Orientation, Misorientation, Rotation\n",
-    "from orix.quaternion.symmetry import D6\n",
     "from orix.vector import Vector3d\n",
     "\n",
     "\n",
@@ -52,7 +51,7 @@
    "source": [
     "## Import data\n",
     "\n",
-    "Load Ti orientations with the point group symmetry *D6* (*622*). We have to explicitly allow downloading from an external source."
+    "Load Ti orientations with the point group symmetry *622* (*D6*). We have to explicitly allow downloading from an external source."
    ]
   },
   {
@@ -69,7 +68,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The orientations define transformations from the sample (lab) to the crystal reference frame, i.e. the Bunge convention. The above referenced paper assumes the opposite convention, which is the one used in MTEX. So, we have to invert the orientations"
+    "Extract the symmetry"
    ]
   },
   {
@@ -78,30 +77,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ori = ~ori"
+    "sym = ori.symmetry"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Reshape the orientation mapping data to the correct spatial dimension for the scan"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "ori = ori.reshape(381, 507)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "Select a subset of the orientations with a suitable size for this demonstration"
+    "Reshape the orientation mapping data to the correct spatial dimension for the scan and select a subset of the orientations with a suitable size for this demonstration (bottom left corner)"
    ]
   },
   {
@@ -110,6 +93,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "ori = ori.reshape(381, 507)\n",
     "ori = ori[-100:, :200]"
    ]
   },
@@ -126,16 +110,15 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ckey = plot.IPFColorKeyTSL(D6)\n",
+    "ckey = plot.IPFColorKeyTSL(sym)\n",
     "\n",
-    "directions = [(1, 0, 0), (0, 1, 0)]\n",
-    "titles = [\"X\", \"Y\"]\n",
+    "directions = [(1, 0, 0), (0, 0, 1)]\n",
+    "titles = [\"X\", \"Z\"]\n",
     "\n",
     "fig, axes = plt.subplots(ncols=2, figsize=(15, 10))\n",
     "for i, ax in enumerate(axes):\n",
     "    ckey.direction = Vector3d(directions[i])\n",
-    "    # Invert because orix assumes lab2crystal when coloring orientations\n",
-    "    ax.imshow(ckey.orientation2color(~ori))\n",
+    "    ax.imshow(ckey.orientation2color(ori))\n",
     "    ax.set_title(f\"IPF-{titles[i]}\")\n",
     "    ax.axis(\"off\")\n",
     "\n",
@@ -154,7 +137,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Map the orientations into the fundamental zone (find symmetrically equivalent orientations with the smallest angle of rotation) of *D6*"
+    "Map the orientations into the Rodrigues fundamental zone (find symmetrically equivalent orientations with the smallest angle of rotation) of *622*"
    ]
   },
   {
@@ -163,14 +146,14 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ori = ori.map_into_symmetry_reduced_zone()"
+    "ori = ori.reduce()"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Compute misorientations (in the horizontal direction)"
+    "Compute misorientations $m_{AB} = g_B \\cdot g_A^{-1}$ (in the horizontal direction)"
    ]
   },
   {
@@ -179,7 +162,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mori_all = Misorientation(~ori[:, :-1] * ori[:, 1:])"
+    "mori_all = Misorientation(ori[:, :-1] * ~ori[:, 1:], symmetry=(sym, sym))"
    ]
   },
   {
@@ -203,7 +186,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Map the misorientations into the fundamental zone of (*D6*, *D6*)"
+    "Map the misorientations into the Mackenzie fundamental zone of *622-622*"
    ]
   },
   {
@@ -212,8 +195,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mori.symmetry = (D6, D6)\n",
-    "mori = mori.map_into_symmetry_reduced_zone()"
+    "mori = mori.reduce()"
    ]
   },
   {
@@ -267,6 +249,7 @@
    "outputs": [],
    "source": [
     "# Compute clusters\n",
+    "D = D.astype(np.float32)\n",
     "dbscan = DBSCAN(eps=0.05, min_samples=10, metric=\"precomputed\").fit(D)\n",
     "\n",
     "unique_labels, all_cluster_sizes = np.unique(\n",
@@ -291,9 +274,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "unique_cluster_labels = unique_labels[\n",
-    "    1:\n",
-    "]  # Without the \"no-cluster\" label -1\n",
+    "unique_cluster_labels = unique_labels[1:]  # Drop \"no-cluster\" label -1\n",
     "cluster_sizes = all_cluster_sizes[1:]\n",
     "\n",
     "rc = Rotation.from_axes_angles((0, 0, 1), 15, degrees=True)\n",
@@ -304,21 +285,21 @@
     "    mori_i = rc * mori[dbscan.labels_ == label]\n",
     "\n",
     "    # Map into the fundamental zone\n",
-    "    mori_i.symmetry = (D6, D6)\n",
-    "    mori_i = mori_i.map_into_symmetry_reduced_zone()\n",
+    "    mori_i.symmetry = (sym, sym)\n",
+    "    mori_i = mori_i.reduce()\n",
     "\n",
     "    # Get the cluster mean\n",
     "    mori_i = mori_i.mean()\n",
     "\n",
     "    # Rotate back and add to list\n",
-    "    cluster_mean_local = (~rc) * mori_i\n",
+    "    cluster_mean_local = ~rc * mori_i\n",
     "    mori_mean.append(cluster_mean_local)\n",
     "\n",
     "cluster_means = Misorientation.stack(mori_mean).flatten()\n",
     "\n",
     "# Map into the fundamental zone\n",
-    "cluster_means.symmetry = (D6, D6)\n",
-    "cluster_means = cluster_means.map_into_symmetry_reduced_zone()\n",
+    "cluster_means.symmetry = (sym, sym)\n",
+    "cluster_means = cluster_means.reduce()\n",
     "cluster_means"
    ]
   },
@@ -378,7 +359,8 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Calculate difference, defined as minimum rotation angle, between measured and theoretical values"
+    "Calculate difference, defined as minimum rotation angle, between measured and theoretical values.\n",
+    "This procedure accounts for the edges of the fundamental zone"
    ]
   },
   {
@@ -387,10 +369,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mori2 = (~twin_theory).outer(cluster_means)\n",
-    "sym_op = D6.outer(D6).unique()\n",
+    "mori2 = twin_theory.outer(cluster_means)\n",
+    "sym_ops = sym.outer(sym).unique()\n",
     "mori2_equiv = (\n",
-    "    D6.outer(~twin_theory).outer(sym_op).outer(cluster_means).outer(D6)\n",
+    "    sym.outer(twin_theory).outer(sym_ops).outer(cluster_means).outer(sym)\n",
     ")\n",
     "D2 = mori2_equiv.angle.min(axis=(0, 2, 4))"
    ]
@@ -447,7 +429,7 @@
     "cluster_sizes_scaled = 1000 * cluster_sizes / cluster_sizes.max()\n",
     "\n",
     "fig, ax = plt.subplots(\n",
-    "    figsize=(5, 5), subplot_kw=dict(projection=\"ipf\", symmetry=D6)\n",
+    "    figsize=(5, 5), subplot_kw=dict(projection=\"ipf\", symmetry=sym)\n",
     ")\n",
     "ax.scatter(\n",
     "    cluster_means.axis, c=colors, s=cluster_sizes_scaled, alpha=0.5, ec=\"k\"\n",
@@ -559,13 +541,14 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "fig3, ax3 = plt.subplots(figsize=(15, 10))\n",
     "ax3.imshow(mapping)\n",
-    "ax3.set_xticks([])\n",
-    "ax3.set_yticks([]);"
+    "ax3.set(xticks=[], yticks=[]);"
    ]
   }
  ],
@@ -585,7 +568,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.8"
+   "version": "3.10.10"
   }
  },
  "nbformat": 4,