version 0.1.2 removed pycifrw, added news to doc website

doc/_build/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 703cc04edf6344aa1e792f9484f86ba0
+config: 56975c2304b95edec8a1347d7679ca8a
 tags: 645f666f9bcd5a90fca523b33c5a78b7

doc/_build/html/PTO_supercrystal_hadjimichael.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Calculation of Atom Plane Curvature &mdash; TEMUL Toolkit v0.1-alpha documentation</title>
+  <title>Calculation of Atom Plane Curvature &mdash; TEMUL Toolkit v0.1.2 documentation</title>
 
 
 
@@ -28,7 +28,7 @@
       <script type="text/javascript">
           var DOCUMENTATION_OPTIONS = {
               URL_ROOT:'./',
-              VERSION:'v0.1-alpha',
+              VERSION:'v0.1.2',
               LANGUAGE:'None',
               COLLAPSE_INDEX:false,
               FILE_SUFFIX:'.html',
@@ -68,7 +68,7 @@
 
 
               <div class="version">
-                Version 0.1-alpha
+                Version 0.1.2
               </div>
 
 
@@ -192,8 +192,8 @@
 <div class="section" id="import-the-modules-and-load-the-data">
 <h2>Import the Modules and Load the Data<a class="headerlink" href="#import-the-modules-and-load-the-data" title="Permalink to this headline">¶</a></h2>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">temul.lattice_structure_tools</span> <span class="kn">import</span> <span class="n">calculate_atom_plane_curvature</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">atomap.api</span> <span class="kn">as</span> <span class="nn">am</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">hyperspy.api</span> <span class="kn">as</span> <span class="nn">hs</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">atomap.api</span> <span class="k">as</span> <span class="nn">am</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">hyperspy.api</span> <span class="k">as</span> <span class="nn">hs</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">os</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">path_to_data</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">abspath</span><span class="p">(</span><span class="s1">&#39;&#39;</span><span class="p">),</span>
 <span class="gp">... </span>            <span class="s2">&quot;publication_examples/PTO_supercrystal_hadjimichael/data&quot;</span><span class="p">)</span>
@@ -230,7 +230,7 @@ <h2>Set up the Parameters<a class="headerlink" href="#set-up-the-parameters" tit
 <span class="gp">&gt;&gt;&gt; </span><span class="n">vmin</span><span class="p">,</span> <span class="n">vmax</span> <span class="o">=</span> <span class="mi">1</span><span class="p">,</span> <span class="mi">2</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">cmap</span> <span class="o">=</span> <span class="s1">&#39;bwr&#39;</span> <span class="c1">#  see matplotlib and colorcet for more colormaps</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">title</span> <span class="o">=</span> <span class="s1">&#39;Curvature Map&#39;</span>
-<span class="gp">&gt;&gt;&gt; </span><span class="n">filename</span> <span class="o">=</span> <span class="bp">None</span> <span class="c1">#  Set to a string if you want to save the map</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">filename</span> <span class="o">=</span> <span class="kc">None</span> <span class="c1">#  Set to a string if you want to save the map</span>
 </pre></div>
 </div>
 <p>Set the extra initial fitting parameters</p>
@@ -248,12 +248,12 @@ <h2>Calculate the Curvature of Atom Planes<a class="headerlink" href="#calculate
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="_images/Curvature_Map_Example.png"><img alt="_images/Curvature_Map_Example.png" src="_images/Curvature_Map_Example.png" style="width: 619.2px; height: 153.0px;" /></a>
-<p>When using <code class="code python docutils literal notranslate"><span class="name"><span class="pre">plot_and_return_fits</span></span><span class="operator"><span class="pre">=</span></span><span class="name builtin pseudo"><span class="pre">True</span></span></code>, the function will return the curve
+<p>When using <code class="code python docutils literal notranslate"><span class="name"><span class="pre">plot_and_return_fits</span></span><span class="operator"><span class="pre">=</span></span><span class="keyword constant"><span class="pre">True</span></span></code>, the function will return the curve
 fittings, and plot each plane (plots not displayed).</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">curvature_map</span><span class="p">,</span> <span class="n">fittings</span> <span class="o">=</span> <span class="n">calculate_atom_plane_curvature</span><span class="p">(</span><span class="n">sublattice2</span><span class="p">,</span>
 <span class="gp">... </span>                    <span class="n">zone_vector_index</span><span class="p">,</span> <span class="n">sampling</span><span class="o">=</span><span class="n">sampling</span><span class="p">,</span> <span class="n">units</span><span class="o">=</span><span class="n">units</span><span class="p">,</span>
 <span class="gp">... </span>                    <span class="n">cmap</span><span class="o">=</span><span class="n">cmap</span><span class="p">,</span> <span class="n">title</span><span class="o">=</span><span class="n">title</span><span class="p">,</span> <span class="n">atom_planes</span><span class="o">=</span><span class="n">atom_planes</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">,</span>
-<span class="gp">... </span>                    <span class="n">plot_and_return_fits</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+<span class="gp">... </span>                    <span class="n">plot_and_return_fits</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
 </pre></div>
 </div>
 </div>

doc/_build/html/_sources/index.rst.txt

@@ -21,6 +21,8 @@ atomic resolution images. It is mostly built upon the data structure of
    Just navigate to the "publication_examples" folder and click on the ".ipynb" files.
 
 
+.. include:: news.rst
+
 
 .. toctree::
    :maxdepth: 2

doc/_build/html/_sources/install.rst.txt

@@ -6,7 +6,7 @@
 Installation
 ------------
 
-The TEMUL Toolkit can be installed easily with PIP.
+The TEMUL Toolkit can be installed easily with PIP (see exceptions below if you're having issues!).
 
 :bash:`$ pip install temul-toolkit`
 
@@ -15,10 +15,15 @@ Then, it can be imported with the name "temul". For example, to import the
 
 :python:`import temul.polarisation as tmlpol`
 
-Note 1: If you wish to use the :python:`simulations.py` or :python:`model_refiner.py` 
-modules, you will need to install PyPrismatic. 
 
-Note 2: If you're using any of the functions or classes that require element quantification:
+Note 1: If you want to use the :python:`io.write_cif_from_dataframe` function, you
+will need to install pyCifRW version 4.3. This requires Visual Studio.
+
+Note 2: If you wish to use the :python:`simulations.py` or :python:`model_refiner.py` 
+modules, you will need to install PyPrismatic. This requires Visual Studio and other
+dependencies.
+
+Note 3: If you're using any of the functions or classes that require element quantification:
 
    * navigate to the "temul/external" directory, copy the "atomap_devel_012" folder and paste that in your "site-packages" directory. 
    * Then, when using atomap to create sublattices and quantify elements call atomap like this: :python:`import atomap_devel_012.api as am`.

doc/_build/html/_sources/news.rst.txt

@@ -0,0 +1,24 @@
+.. _install:
+
+.. include:: define_roles.rst
+
+
+News
+----
+
+**03/11/2020: Version 0.1.2 released**
+
+This version contains minor changes from the 0.1.1 release. It removes pyCifRW
+as a dependency, due to PyCifRW requiring Microsoft Visual Studio.
+
+
+**02/11/2020: Version 0.1.1 released**
+
+This version contains many changes to the TEMUL Toolkit.
+
+    * More parameters have been added to the polarisation module's :python:`plot_polarisation_vectors` function. Check out the walkthrough :ref:`here <polarisation_vectors_tutorial>` for more info!
+    * :ref:`Interactive double Gaussian filtering <dg_visualiser_tutorial>` with the :python:`visualise_dg_filter` function in the signal_processing module. Thanks to `Michael Hennessy <https://github.com/michaelhennessyjr>`_ for the help!
+    * The :python:`calculate_atom_plane_curvature` function has been added, creating the lattice_structure_tools module.
+    * Strain, rotation, and c/a mapping can now be done :ref:`here <structure_map_tutorial>`.
+    * Masked FFT filtering to obtain iFFTs. See :ref:`this guide <masked_fft_tutorial>` to see some code!
+    * Example walk-throughs for many features of the TEMUL Toolkit are now on this website! Check out the menu on the left to get started!

doc/_build/html/_static/documentation_options.js

@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: 'v0.1-alpha',
+    VERSION: 'v0.1.2',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

doc/_build/html/api_doc.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>API documentation &mdash; TEMUL Toolkit v0.1-alpha documentation</title>
+  <title>API documentation &mdash; TEMUL Toolkit v0.1.2 documentation</title>
 
 
 
@@ -28,7 +28,7 @@
       <script type="text/javascript">
           var DOCUMENTATION_OPTIONS = {
               URL_ROOT:'./',
-              VERSION:'v0.1-alpha',
+              VERSION:'v0.1.2',
               LANGUAGE:'None',
               COLLAPSE_INDEX:false,
               FILE_SUFFIX:'.html',
@@ -69,7 +69,7 @@
 
 
               <div class="version">
-                Version 0.1-alpha
+                Version 0.1.2
               </div>
 
 

doc/_build/html/define_roles.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>&lt;no title&gt; &mdash; TEMUL Toolkit v0.1-alpha documentation</title>
+  <title>&lt;no title&gt; &mdash; TEMUL Toolkit v0.1.2 documentation</title>
 
 
 
@@ -28,7 +28,7 @@
       <script type="text/javascript">
           var DOCUMENTATION_OPTIONS = {
               URL_ROOT:'./',
-              VERSION:'v0.1-alpha',
+              VERSION:'v0.1.2',
               LANGUAGE:'None',
               COLLAPSE_INDEX:false,
               FILE_SUFFIX:'.html',
@@ -68,7 +68,7 @@
 
 
               <div class="version">
-                Version 0.1-alpha
+                Version 0.1.2
               </div>
 
 

doc/_build/html/dg_visualiser_tutorial.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Interactive Image Filtering &mdash; TEMUL Toolkit v0.1-alpha documentation</title>
+  <title>Interactive Image Filtering &mdash; TEMUL Toolkit v0.1.2 documentation</title>
 
 
 
@@ -28,7 +28,7 @@
       <script type="text/javascript">
           var DOCUMENTATION_OPTIONS = {
               URL_ROOT:'./',
-              VERSION:'v0.1-alpha',
+              VERSION:'v0.1.2',
               LANGUAGE:'None',
               COLLAPSE_INDEX:false,
               FILE_SUFFIX:'.html',
@@ -70,7 +70,7 @@
 
 
               <div class="version">
-                Version 0.1-alpha
+                Version 0.1.2
               </div>
 
 

doc/_build/html/genindex.html

@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Index &mdash; TEMUL Toolkit v0.1-alpha documentation</title>
+  <title>Index &mdash; TEMUL Toolkit v0.1.2 documentation</title>
 
 
 
@@ -29,7 +29,7 @@
       <script type="text/javascript">
           var DOCUMENTATION_OPTIONS = {
               URL_ROOT:'./',
-              VERSION:'v0.1-alpha',
+              VERSION:'v0.1.2',
               LANGUAGE:'None',
               COLLAPSE_INDEX:false,
               FILE_SUFFIX:'.html',
@@ -69,7 +69,7 @@
 
 
               <div class="version">
-                Version 0.1-alpha
+                Version 0.1.2
               </div>
 
 

doc/_build/html/index.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Welcome to TEMUL Toolkit’s documentation! &mdash; TEMUL Toolkit v0.1-alpha documentation</title>
+  <title>Welcome to TEMUL Toolkit’s documentation! &mdash; TEMUL Toolkit v0.1.2 documentation</title>
 
 
 
@@ -28,7 +28,7 @@
       <script type="text/javascript">
           var DOCUMENTATION_OPTIONS = {
               URL_ROOT:'./',
-              VERSION:'v0.1-alpha',
+              VERSION:'v0.1.2',
               LANGUAGE:'None',
               COLLAPSE_INDEX:false,
               FILE_SUFFIX:'.html',
@@ -69,7 +69,7 @@
 
 
               <div class="version">
-                Version 0.1-alpha
+                Version 0.1.2
               </div>
 
 
@@ -174,6 +174,23 @@ <h1>Welcome to TEMUL Toolkit’s documentation!<a class="headerlink" href="#welc
 <p>The TEMUL Toolkit is a suit of functions and classes for analysis and visualisation of
 atomic resolution images. It is mostly built upon the data structure of
 <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="news">
+<span id="install"></span><h2>News<a class="headerlink" href="#news" title="Permalink to this headline">¶</a></h2>
+<p><strong>03/11/2020: Version 0.1.2 released</strong></p>
+<p>This version contains minor changes from the 0.1.1 release. It removes pyCifRW
+as a dependency, due to PyCifRW requiring Microsoft Visual Studio.</p>
+<p><strong>02/11/2020: Version 0.1.1 released</strong></p>
+<p>This version contains many changes to the TEMUL Toolkit.</p>
+<blockquote>
+<div><ul class="simple">
+<li>More parameters have been added to the polarisation module’s <code class="code python docutils literal notranslate"><span class="name"><span class="pre">plot_polarisation_vectors</span></span></code> function. Check out the walkthrough <a class="reference internal" href="polarisation_vectors_tutorial.html#polarisation-vectors-tutorial"><span class="std std-ref">here</span></a> for more info!</li>
+<li><a class="reference internal" href="dg_visualiser_tutorial.html#dg-visualiser-tutorial"><span class="std std-ref">Interactive double Gaussian filtering</span></a> with the <code class="code python docutils literal notranslate"><span class="name"><span class="pre">visualise_dg_filter</span></span></code> function in the signal_processing module. Thanks to <a class="reference external" href="https://github.com/michaelhennessyjr">Michael Hennessy</a> for the help!</li>
+<li>The <code class="code python docutils literal notranslate"><span class="name"><span class="pre">calculate_atom_plane_curvature</span></span></code> function has been added, creating the lattice_structure_tools module.</li>
+<li>Strain, rotation, and c/a mapping can now be done <a class="reference internal" href="structure_map_tutorial.html#structure-map-tutorial"><span class="std std-ref">here</span></a>.</li>
+<li>Masked FFT filtering to obtain iFFTs. See <a class="reference internal" href="masked_fft_tutorial.html#masked-fft-tutorial"><span class="std std-ref">this guide</span></a> to see some code!</li>
+<li>Example walk-throughs for many features of the TEMUL Toolkit are now on this website! Check out the menu on the left to get started!</li>
+</ul>
+</div></blockquote>
 <div class="toctree-wrapper compound">
 <p class="caption"><span class="caption-text">Contents</span></p>
 <ul>
@@ -217,16 +234,20 @@ <h1>Welcome to TEMUL Toolkit’s documentation!<a class="headerlink" href="#welc
 </li>
 </ul>
 </div>
+</div>
 <div class="section" id="installation">
-<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.</p>
+<span id="id1"></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 (see exceptions below if you’re having issues!).</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>
 <p>Then, it can be imported with the name “temul”. For example, to import the
 <code class="code python docutils literal notranslate"><span class="name"><span class="pre">polarisation</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">py</span></span></code> module, use:</p>
 <p><code class="code python docutils literal notranslate"><span class="keyword namespace"><span class="pre">import</span></span> <span class="name namespace"><span class="pre">temul.polarisation</span></span> <span class="keyword"><span class="pre">as</span></span> <span class="name namespace"><span class="pre">tmlpol</span></span></code></p>
-<p>Note 1: If you wish to use the <code class="code python docutils literal notranslate"><span class="name"><span class="pre">simulations</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">py</span></span></code> or <code class="code python docutils literal notranslate"><span class="name"><span class="pre">model_refiner</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">py</span></span></code>
-modules, you will need to install PyPrismatic.</p>
-<p>Note 2: If you’re using any of the functions or classes that require element quantification:</p>
+<p>Note 1: If you want to use the <code class="code python docutils literal notranslate"><span class="name"><span class="pre">io</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">write_cif_from_dataframe</span></span></code> function, you
+will need to install pyCifRW version 4.3. This requires Visual Studio.</p>
+<p>Note 2: If you wish to use the <code class="code python docutils literal notranslate"><span class="name"><span class="pre">simulations</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">py</span></span></code> or <code class="code python docutils literal notranslate"><span class="name"><span class="pre">model_refiner</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">py</span></span></code>
+modules, you will need to install PyPrismatic. This requires Visual Studio and other
+dependencies.</p>
+<p>Note 3: If you’re using any of the functions or classes that require element quantification:</p>
 <blockquote>
 <div><ul class="simple">
 <li>navigate to the “temul/external” directory, copy the “atomap_devel_012” folder and paste that in your “site-packages” directory.</li>