Merge branch 'develop' into support-pyebsdindex-0-2

Signed-off-by: Håkon Wiik Ånes <hwaanes@gmail.com>

.all-contributorsrc

@@ -97,6 +97,15 @@
       "contributions": [
         "bug"
       ]
+    },
+    {
+      "login": "AndreasBugten",
+      "name": "AndreasBugten",
+      "avatar_url": "https://avatars.githubusercontent.com/u/106192446?v=4",
+      "profile": "https://github.com/AndreasBugten",
+      "contributions": [
+        "doc"
+      ]
     }
   ]
 }

.zenodo.json

@@ -27,6 +27,11 @@
       "name": "Zhou Xu",
       "affiliation": "Monash Centre for Electron Microscopy"
     },
+    {
+      "name": "Andreas V. Bugten",
+      "orcid": "0000-0003-0311-8584",
+      "affiliation": "Norwegian University of Science and Technology"
+    },
     {
       "name": "Magnus Nord",
       "orcid": "0000-0001-7981-5293",

README.md

@@ -60,15 +60,16 @@ Thanks go to these wonderful people ([emoji key](https://allcontributors.org/doc
 <table>
   <tbody>
     <tr>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/AndreasBugten"><img src="https://avatars.githubusercontent.com/u/106192446?v=4?s=100" width="100px;" alt="AndreasBugten"/><br /><sub><b>AndreasBugten</b></sub></a><br /><a href="https://github.com/pyxem/kikuchipy/commits?author=AndreasBugten" title="Documentation">📖</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/ericpre"><img src="https://avatars.githubusercontent.com/u/11851990?v=4?s=100" width="100px;" alt="Eric Prestat"/><br /><sub><b>Eric Prestat</b></sub></a><br /><a href="https://github.com/pyxem/kikuchipy/commits?author=ericpre" title="Code">💻</a> <a href="#maintenance-ericpre" title="Maintenance">🚧</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://www.ntnu.edu/employees/hakon.w.anes"><img src="https://avatars.githubusercontent.com/u/12139781?v=4?s=100" width="100px;" alt="Håkon Wiik Ånes"/><br /><sub><b>Håkon Wiik Ånes</b></sub></a><br /></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/friedkitteh"><img src="https://avatars.githubusercontent.com/u/11888052?v=4?s=100" width="100px;" alt="Lars Lervik"/><br /><sub><b>Lars Lervik</b></sub></a><br /><a href="https://github.com/pyxem/kikuchipy/issues?q=author%3Afriedkitteh" title="Bug reports">🐛</a> <a href="https://github.com/pyxem/kikuchipy/commits?author=friedkitteh" title="Code">💻</a> <a href="https://github.com/pyxem/kikuchipy/commits?author=friedkitteh" title="Documentation">📖</a> <a href="#question-friedkitteh" title="Answering Questions">💬</a> <a href="https://github.com/pyxem/kikuchipy/pulls?q=is%3Apr+reviewed-by%3Afriedkitteh" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/pyxem/kikuchipy/commits?author=friedkitteh" title="Tests">⚠️</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://www.ntnu.edu/employees/magnus.nord"><img src="https://avatars.githubusercontent.com/u/1690979?v=4?s=100" width="100px;" alt="Magnus Nord"/><br /><sub><b>Magnus Nord</b></sub></a><br /><a href="https://github.com/pyxem/kikuchipy/commits?author=magnunor" title="Documentation">📖</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/onatlandsmyr"><img src="https://avatars.githubusercontent.com/u/34620114?v=4?s=100" width="100px;" alt="Ole Natlandsmyr"/><br /><sub><b>Ole Natlandsmyr</b></sub></a><br /><a href="https://github.com/pyxem/kikuchipy/commits?author=onatlandsmyr" title="Code">💻</a> <a href="https://github.com/pyxem/kikuchipy/commits?author=onatlandsmyr" title="Documentation">📖</a> <a href="#question-onatlandsmyr" title="Answering Questions">💬</a> <a href="https://github.com/pyxem/kikuchipy/pulls?q=is%3Apr+reviewed-by%3Aonatlandsmyr" title="Reviewed Pull Requests">👀</a> <a href="https://github.com/pyxem/kikuchipy/commits?author=onatlandsmyr" title="Tests">⚠️</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/tinabe"><img src="https://avatars.githubusercontent.com/u/22915119?v=4?s=100" width="100px;" alt="Tina Bergh"/><br /><sub><b>Tina Bergh</b></sub></a><br /><a href="https://github.com/pyxem/kikuchipy/commits?author=tinabe" title="Code">💻</a> <a href="https://github.com/pyxem/kikuchipy/pulls?q=is%3Apr+reviewed-by%3Atinabe" title="Reviewed Pull Requests">👀</a></td>
-      <td align="center" valign="top" width="14.28%"><a href="https://github.com/IMBalENce"><img src="https://avatars.githubusercontent.com/u/2986794?v=4?s=100" width="100px;" alt="Zhou Xu"/><br /><sub><b>Zhou Xu</b></sub></a><br /><a href="https://github.com/pyxem/kikuchipy/issues?q=author%3AIMBalENce" title="Bug reports">🐛</a> <a href="https://github.com/pyxem/kikuchipy/commits?author=IMBalENce" title="Code">💻</a> <a href="https://github.com/pyxem/kikuchipy/commits?author=IMBalENce" title="Documentation">📖</a> <a href="https://github.com/pyxem/kikuchipy/commits?author=IMBalENce" title="Tests">⚠️</a></td>
     </tr>
     <tr>
+      <td align="center" valign="top" width="14.28%"><a href="https://github.com/IMBalENce"><img src="https://avatars.githubusercontent.com/u/2986794?v=4?s=100" width="100px;" alt="Zhou Xu"/><br /><sub><b>Zhou Xu</b></sub></a><br /><a href="https://github.com/pyxem/kikuchipy/issues?q=author%3AIMBalENce" title="Bug reports">🐛</a> <a href="https://github.com/pyxem/kikuchipy/commits?author=IMBalENce" title="Code">💻</a> <a href="https://github.com/pyxem/kikuchipy/commits?author=IMBalENce" title="Documentation">📖</a> <a href="https://github.com/pyxem/kikuchipy/commits?author=IMBalENce" title="Tests">⚠️</a></td>
       <td align="center" valign="top" width="14.28%"><a href="https://github.com/Erlendos12"><img src="https://avatars.githubusercontent.com/u/99336047?v=4?s=100" width="100px;" alt="erlenmos"/><br /><sub><b>erlenmos</b></sub></a><br /><a href="https://github.com/pyxem/kikuchipy/issues?q=author%3AErlendos12" title="Bug reports">🐛</a></td>
     </tr>
   </tbody>

doc/tutorials/visualizing_patterns.ipynb

@@ -118,8 +118,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vbse_rgb = vbse_imager.get_rgb_image(r=(3, 1), b=(3, 2), g=(3, 3))\n",
-    "vbse_rgb"
+    "maps_vbse_rgb = vbse_imager.get_rgb_image(r=(3, 1), b=(3, 2), g=(3, 3))\n",
+    "maps_vbse_rgb"
    ]
   },
   {
@@ -128,7 +128,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "s.plot(navigator=vbse_rgb, cmap=\"viridis\")"
+    "s.plot(navigator=maps_vbse_rgb, cmap=\"viridis\")"
    ]
   },
   {
@@ -176,13 +176,47 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "rgb_z = plt.imread(\n",
-    "    \"../_static/image/visualizing_patterns/ni_large_rgb_z.png\"\n",
-    ")\n",
-    "rgb_z = rgb_z[..., :3]  # Drop the alpha channel\n",
-    "s_rgb_z = kp.draw.get_rgb_navigator(rgb_z)\n",
+    "maps_ipfz = plt.imread(\"../_static/image/visualizing_patterns/ni_large_rgb_z.png\")\n",
+    "maps_ipfz = maps_ipfz[..., :3]  # Drop the alpha channel\n",
+    "s_ipfz = kp.draw.get_rgb_navigator(maps_ipfz)\n",
     "\n",
-    "s.plot(navigator=s_rgb_z, colorbar=False)"
+    "s.plot(navigator=s_ipfz, colorbar=False)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "By overlaying the image quality map on the RGB image, we can visualize crystal directions within grains and the grain morphology in the same image"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "maps_iq_1d = maps_iq.ravel()  # Flat array required by orix\n",
+    "maps_ipfz_1d = maps_ipfz.reshape(-1, 3)\n",
+    "fig = s.xmap.plot(maps_ipfz_1d, overlay=maps_iq_1d, return_figure=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "By extracting the image array, we can use this map to navigate patterns in"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "maps_ipfz_iq = fig.axes[0].images[0].get_array()\n",
+    "s_ipfz_iq = kp.draw.get_rgb_navigator(maps_ipfz_iq)\n",
+    "s.plot(s_ipfz_iq)"
    ]
   },
   {

kikuchipy/release.py

@@ -29,6 +29,7 @@
     "Eric Prestat",
     "Erlend Mikkelsen Østvold",
     "Zhou Xu",
+    "Andreas V. Bugten",
     "Magnus Nord",
 ]
 license = "GPLv3+"