Merge pull request #653 from AndreasBugten/kikuchidev

Add description of how to navigate RGBA images to the kikuchipy documentation
pyxem · Aug 29, 2023 · b7d626c · b7d626c
2 parents 3e0c8c0 + b240346
commit b7d626c
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diff --git a/.all-contributorsrc b/.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"
+      ]
     }
   ]
 }
diff --git a/.zenodo.json b/.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",

diff --git a/README.md b/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>

diff --git a/doc/tutorials/visualizing_patterns.ipynb b/doc/tutorials/visualizing_patterns.ipynb
@@ -116,8 +116,8 @@
    "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"
    ]
   },
   {
@@ -126,7 +126,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "s.plot(navigator=vbse_rgb, cmap=\"viridis\")"
+    "s.plot(navigator=maps_vbse_rgb, cmap=\"viridis\")"
    ]
   },
   {
@@ -135,7 +135,8 @@
    "source": [
     "## Any image\n",
     "\n",
-    "Images made into a [Signal2D](http://hyperspy.org/hyperspy-doc/current/api/hyperspy._signals.signal2d.html#hyperspy._signals.signal2d.Signal2D) can be used as navigators, like a quality metric map like the [image quality map](feature_maps.ipynb#Image-quality) calculated using [get_image_quality()](../reference/generated/kikuchipy.signals.EBSD.get_image_quality.rst)"
+    "Images made into a [Signal2D](http://hyperspy.org/hyperspy-doc/current/api/hyperspy._signals.signal2d.html#hyperspy._signals.signal2d.Signal2D) can be used as navigators.\n",
+    "For example a quality metric map such as the [image quality map](feature_maps.ipynb#Image-quality) calculated using [get_image_quality()](../reference/generated/kikuchipy.signals.EBSD.get_image_quality.rst)"
    ]
   },
   {
@@ -154,16 +155,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "iq = s.get_image_quality()\n",
-    "s_iq = hs.signals.Signal2D(iq)\n",
+    "maps_iq = s.get_image_quality()\n",
+    "s_iq = hs.signals.Signal2D(maps_iq)\n",
     "s.plot(navigator=s_iq)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We can obtain an RGB signal from an RGB image using [get_rgb_navigator()](../reference/generated/kikuchipy.draw.get_rgb_navigator.rst).\n",
+    "We obtain an RGB signal from an RGB image using [get_rgb_navigator()](../reference/generated/kikuchipy.draw.get_rgb_navigator.rst).\n",
     "Let's load an orientation map from dictionary indexing in the [pattern matching](pattern_matching.ipynb) tutorial"
    ]
   },
@@ -173,13 +174,47 @@
    "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)"
    ]
   },
   {
@@ -292,7 +327,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.9"
+   "version": "3.11.5"
   },
   "widgets": {
    "application/vnd.jupyter.widget-state+json": {

diff --git a/kikuchipy/release.py b/kikuchipy/release.py
@@ -29,6 +29,7 @@
     "Eric Prestat",
     "Erlend Mikkelsen Østvold",
     "Zhou Xu",
+    "Andreas V. Bugten",
     "Magnus Nord",
 ]
 license = "GPLv3+"