add publised work highlghts section to the docs

PinkShnack · Nov 27, 2021 · d0e5126 · d0e5126
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diff --git a/doc/_build/doctrees/about_temul_toolkit.doctree b/doc/_build/doctrees/about_temul_toolkit.doctree
diff --git a/doc/_build/doctrees/environment.pickle b/doc/_build/doctrees/environment.pickle
diff --git a/doc/_build/doctrees/index.doctree b/doc/_build/doctrees/index.doctree
diff --git a/doc/_build/doctrees/news.doctree b/doc/_build/doctrees/news.doctree
diff --git a/doc/_build/html/_sources/about_temul_toolkit.rst.txt b/doc/_build/html/_sources/about_temul_toolkit.rst.txt
@@ -0,0 +1,9 @@
+.. _about_temul_toolkit:
+
+.. include:: define_roles.rst
+
+
+Some published results using the TEMUL Toolkit
+----------------------------------------------
+
+.. Include some images! Just copy from the papers and cite.
diff --git a/doc/_build/html/_sources/index.rst.txt b/doc/_build/html/_sources/index.rst.txt
@@ -15,6 +15,13 @@ atomic resolution images. It is mostly built upon the data structure of
 
 Interactive Examples
 --------------------
+The easiest way to try the TEMUL Toolkit is via Binder:
+`introductory Jupyter Notebook <https://hub.gke2.mybinder.org/user/pinkshnack-temul-19r27k52/lab/tree/code_tutorials/polarisation_vectors_tutorial.ipynb>`_.
+To install the TEMUL Toolkit on your own computer,
+see the :ref:`install` instructions.
+
+And there are more examples with Binder, just click the below button!
+
 .. image:: https://mybinder.org/badge_logo.svg
    :target: https://mybinder.org/v2/gh/PinkShnack/TEMUL/master
 
@@ -27,6 +34,9 @@ published scientific papers!
 Just navigate to whichever of these folders you want click on the ".ipynb" files.
 
 
+.. include:: about_temul_toolkit.rst
+
+
 .. include:: news.rst
 
 

diff --git a/doc/_build/html/_sources/news.rst.txt b/doc/_build/html/_sources/news.rst.txt
@@ -1,4 +1,4 @@
-.. _install:
+.. _news:
 
 .. include:: define_roles.rst
 

diff --git a/doc/_build/html/about_temul_toolkit.html b/doc/_build/html/about_temul_toolkit.html
@@ -0,0 +1,221 @@
+
+
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" >
+<head>
+  <meta charset="utf-8" />
+
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+
+  <title>Some published results using the TEMUL Toolkit &mdash; TEMUL Toolkit v0.1.3 documentation</title>
+
+
+
+  <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+  <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+  <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+  <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
+
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+  <!--[if lt IE 9]>
+    <script src="_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+
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+      <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
+        <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
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+        <script src="_static/doctools.js"></script>
+
+    <script type="text/javascript" src="_static/js/theme.js"></script>
+
+
+    <link rel="index" title="Index" href="genindex.html" />
+    <link rel="search" title="Search" href="search.html" /> 
+</head>
+
+<body class="wy-body-for-nav">
+
+
+  <div class="wy-grid-for-nav">
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+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+
+
+
+            <a href="index.html" class="icon icon-home"> TEMUL Toolkit
+
+
+
+          </a>
+
+
+
+
+              <div class="version">
+                Version 0.1.3
+              </div>
+
+
+
+
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+
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+        </div>
+
+
+        <div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
+
+
+
+
+
+
+              <p class="caption"><span class="caption-text">Contents</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="install.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="using_temul.html">Getting started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="workflows.html">Analysis Workflows</a></li>
+<li class="toctree-l1"><a class="reference internal" href="polarisation_vectors_tutorial.html">Finding Polarisation Vectors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="polarisation_vectors_tutorial.html#plotting-polarisation-and-movement-vectors">Plotting Polarisation and Movement Vectors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="structure_map_tutorial.html">Plot Lattice Structure Maps</a></li>
+<li class="toctree-l1"><a class="reference internal" href="PTO_supercrystal_hadjimichael.html">Calculation of Atom Plane Curvature</a></li>
+<li class="toctree-l1"><a class="reference internal" href="PTO_Junction_moore.html">Analysis of PTO Domain Wall Junction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="masked_fft_tutorial.html">Masked FFT and iFFT</a></li>
+<li class="toctree-l1"><a class="reference internal" href="line_profile_tutorial.html">Line Intensity Profile Comparisons</a></li>
+<li class="toctree-l1"><a class="reference internal" href="dg_visualiser_tutorial.html">Interactive Image Filtering</a></li>
+<li class="toctree-l1"><a class="reference internal" href="api_doc.html">API documentation</a></li>
+</ul>
+
+
+
+        </div>
+
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
+
+
+      <nav class="wy-nav-top" aria-label="top navigation">
+
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="index.html">TEMUL Toolkit</a>
+
+      </nav>
+
+
+      <div class="wy-nav-content">
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+        <div class="rst-content">
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+<div role="navigation" aria-label="breadcrumbs navigation">
+
+  <ul class="wy-breadcrumbs">
+
+      <li><a href="index.html" class="icon icon-home"></a> &raquo;</li>
+
+      <li>Some published results using the TEMUL Toolkit</li>
+
+
+      <li class="wy-breadcrumbs-aside">
+
+
+            <a href="_sources/about_temul_toolkit.rst.txt" rel="nofollow"> View page source</a>
+
+
+      </li>
+
+  </ul>
+
+
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+  <div class="section" id="some-published-results-using-the-temul-toolkit">
+<span id="about-temul-toolkit"></span><h1>Some published results using the TEMUL Toolkit<a class="headerlink" href="#some-published-results-using-the-temul-toolkit" title="Permalink to this headline">¶</a></h1>
+</div>
+
+
+           </div>
+
+          </div>
+          <footer>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>
+        &#169; Copyright 2021, Eoghan O&#39;Connell.
+
+    </p>
+  </div>
+
+
+
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+</html>
diff --git a/doc/_build/html/index.html b/doc/_build/html/index.html
@@ -178,6 +178,11 @@ <h1>Welcome to TEMUL Toolkit’s documentation!<a class="headerlink" href="#welc
 <a class="reference external" href="https://hyperspy.org/">HyperSpy</a> and <a class="reference external" href="https://atomap.org/">Atomap</a>.</p>
 <div class="section" id="interactive-examples">
 <h2>Interactive Examples<a class="headerlink" href="#interactive-examples" title="Permalink to this headline">¶</a></h2>
+<p>The easiest way to try the TEMUL Toolkit is via Binder:
+<a class="reference external" href="https://hub.gke2.mybinder.org/user/pinkshnack-temul-19r27k52/lab/tree/code_tutorials/polarisation_vectors_tutorial.ipynb">introductory Jupyter Notebook</a>.
+To install the TEMUL Toolkit on your own computer,
+see the <a class="reference internal" href="#install"><span class="std std-ref">Installation</span></a> instructions.</p>
+<p>And there are more examples with Binder, just click the below button!</p>
 <a class="reference external image-reference" href="https://mybinder.org/v2/gh/PinkShnack/TEMUL/master"><img alt="https://mybinder.org/badge_logo.svg" src="https://mybinder.org/badge_logo.svg" /></a>
 <p>Click the button above to start some data analysis
 (it may take a few minutes to load).
@@ -187,13 +192,16 @@ <h2>Interactive Examples<a class="headerlink" href="#interactive-examples" title
 published scientific papers!
 Just navigate to whichever of these folders you want click on the “.ipynb” files.</p>
 </div>
+<div class="section" id="some-published-results-using-the-temul-toolkit">
+<span id="about-temul-toolkit"></span><h2>Some published results using the TEMUL Toolkit<a class="headerlink" href="#some-published-results-using-the-temul-toolkit" title="Permalink to this headline">¶</a></h2>
+</div>
 <div class="section" id="news">
-<span id="install"></span><h2>News<a class="headerlink" href="#news" title="Permalink to this headline">¶</a></h2>
+<span id="id1"></span><h2>News<a class="headerlink" href="#news" title="Permalink to this headline">¶</a></h2>
 <div class="section" id="version-0-1-4-released">
 <h3>16/02/2021: Version 0.1.4 released<a class="headerlink" href="#version-0-1-4-released" title="Permalink to this headline">¶</a></h3>
 <p>The polarisation, structure tools and fft mapping has now
 been refactored into the topotem module. The temul
-functionality remains the same i.e. <a href="#id1"><span class="problematic" id="id2">``</span></a>import temul.api as tml`.</p>
+functionality remains the same i.e. <a href="#id2"><span class="problematic" id="id3">``</span></a>import temul.api as tml`.</p>
 </div>
 <div class="section" id="version-0-1-3-released">
 <h3>16/02/2021: Version 0.1.3 released<a class="headerlink" href="#version-0-1-3-released" title="Permalink to this headline">¶</a></h3>
@@ -324,7 +332,7 @@ <h3>02/11/2020: Version 0.1.1 released<a class="headerlink" href="#version-0-1-1
 </div>
 </div>
 <div class="section" id="installation">
-<span id="id5"></span><h2>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h2>
+<span id="install"></span><h2>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h2>
 <p>The TEMUL Toolkit can be installed easily with PIP (those using Windows may
 need to download VS C++ Build Tools, see below).</p>
 <p><code class="code bash docutils literal notranslate"><span class="pre">$</span> <span class="pre">pip</span> <span class="pre">install</span> <span class="pre">temul-toolkit</span></code></p>

diff --git a/doc/_build/html/news.html b/doc/_build/html/news.html
@@ -171,12 +171,12 @@
            <div itemprop="articleBody">
 
   <div class="section" id="news">
-<span id="install"></span><h1>News<a class="headerlink" href="#news" title="Permalink to this headline">¶</a></h1>
+<span id="id1"></span><h1>News<a class="headerlink" href="#news" title="Permalink to this headline">¶</a></h1>
 <div class="section" id="version-0-1-4-released">
 <h2>16/02/2021: Version 0.1.4 released<a class="headerlink" href="#version-0-1-4-released" title="Permalink to this headline">¶</a></h2>
 <p>The polarisation, structure tools and fft mapping has now
 been refactored into the topotem module. The temul
-functionality remains the same i.e. <a href="#id1"><span class="problematic" id="id2">``</span></a>import temul.api as tml`.</p>
+functionality remains the same i.e. <a href="#id2"><span class="problematic" id="id3">``</span></a>import temul.api as tml`.</p>
 </div>
 <div class="section" id="version-0-1-3-released">
 <h2>16/02/2021: Version 0.1.3 released<a class="headerlink" href="#version-0-1-3-released" title="Permalink to this headline">¶</a></h2>

diff --git a/doc/_build/html/objects.inv b/doc/_build/html/objects.inv
diff --git a/doc/_build/html/searchindex.js b/doc/_build/html/searchindex.js
diff --git a/doc/about_temul_toolkit.rst b/doc/about_temul_toolkit.rst
@@ -0,0 +1,9 @@
+.. _about_temul_toolkit:
+
+.. include:: define_roles.rst
+
+
+Some published results using the TEMUL Toolkit
+----------------------------------------------
+
+.. Include some images! Just copy from the papers and cite.
diff --git a/doc/index.rst b/doc/index.rst
@@ -15,6 +15,13 @@ atomic resolution images. It is mostly built upon the data structure of
 
 Interactive Examples
 --------------------
+The easiest way to try the TEMUL Toolkit is via Binder:
+`introductory Jupyter Notebook <https://hub.gke2.mybinder.org/user/pinkshnack-temul-19r27k52/lab/tree/code_tutorials/polarisation_vectors_tutorial.ipynb>`_.
+To install the TEMUL Toolkit on your own computer,
+see the :ref:`install` instructions.
+
+And there are more examples with Binder, just click the below button!
+
 .. image:: https://mybinder.org/badge_logo.svg
    :target: https://mybinder.org/v2/gh/PinkShnack/TEMUL/master
 
@@ -27,6 +34,9 @@ published scientific papers!
 Just navigate to whichever of these folders you want click on the ".ipynb" files.
 
 
+.. include:: about_temul_toolkit.rst
+
+
 .. include:: news.rst
 
 

diff --git a/doc/news.rst b/doc/news.rst
@@ -1,4 +1,4 @@
-.. _install:
+.. _news:
 
 .. include:: define_roles.rst