Merge pull request #55 from PinkShnack/formalise_docs

Correct docs and make pass
PinkShnack · Nov 7, 2021 · c032533 · c032533
2 parents 915b55f + 71ee60c
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diff --git a/.github/workflows/CI-workflow.yml b/.github/workflows/CI-workflow.yml
@@ -26,7 +26,7 @@ jobs:
           pip install -e .
       - name: Lint with flake8
         run: |
-          flake8 temul tests --exclude temul/external,temul/example_scripts.py,code_tutorials,publication_examples
+          flake8 temul tests --exclude temul/external,temul/example_scripts.py,temul/atomap_devel_temp.py,code_tutorials,publication_examples
       - name: Test with pytest
         run: |
           pytest tests

diff --git a/README.md b/README.md
@@ -38,3 +38,13 @@ If the button does not work, try [this link instead](https://mybinder.org/v2/gh/
 | :------------------   | :-----------------------  |
 | M. Hadjimichael, Y. Li *et al*, [Metal-ferroelectric supercrystals with periodically curved metallic layers](https://www.nature.com/articles/s41563-020-00864-6), Nature Materials 2021        | publication_examples/PTO_supercrystal_hadjimichael              |
 | K. Moore *et al* [Highly charged 180 degree head-to-head domain walls in lead titanate](https://www.nature.com/articles/s42005-020-00488-x), Nature Communications Physics 2020          | publication_examples/PTO_Junction_moore                         |
+
+
+## Information for developers
+
+To build the docs, do the following::
+
+```bash
+cd doc
+make html
+```
diff --git a/doc/_build/doctrees/PTO_Junction_moore.doctree b/doc/_build/doctrees/PTO_Junction_moore.doctree
diff --git a/doc/_build/doctrees/PTO_supercrystal_hadjimichael.doctree b/doc/_build/doctrees/PTO_supercrystal_hadjimichael.doctree
diff --git a/doc/_build/doctrees/api_doc.doctree b/doc/_build/doctrees/api_doc.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/doctrees/polarisation_vectors_tutorial.doctree b/doc/_build/doctrees/polarisation_vectors_tutorial.doctree
diff --git a/doc/_build/doctrees/using_temul.doctree b/doc/_build/doctrees/using_temul.doctree
diff --git a/doc/_build/html/.buildinfo b/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: 713559574e2a71cb94ab036b601ffd09
+config: 608bac64e8b48a97b902e87aaf2e9228
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/doc/_build/html/PTO_Junction_moore.html b/doc/_build/html/PTO_Junction_moore.html
diff --git a/doc/_build/html/PTO_supercrystal_hadjimichael.html b/doc/_build/html/PTO_supercrystal_hadjimichael.html
@@ -3,33 +3,38 @@
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" >
 <head>
-  <meta charset="utf-8">
+  <meta charset="utf-8" />
 
-  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
   <title>Calculation of Atom Plane Curvature &mdash; TEMUL Toolkit v0.1.2 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" />
 
 
 
+
 
 
 
 
+
+
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
 
       <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>
         <script src="_static/jquery.js"></script>
         <script src="_static/underscore.js"></script>
         <script src="_static/doctools.js"></script>
-        <script src="_static/language_data.js"></script>
 
     <script type="text/javascript" src="_static/js/theme.js"></script>
 
@@ -51,7 +56,7 @@
 
 
 
-            <a href="index.html" class="icon icon-home" alt="Documentation Home"> TEMUL Toolkit
+            <a href="index.html" class="icon icon-home"> TEMUL Toolkit
 
 
 
@@ -104,7 +109,6 @@
 <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="PTO_Junction_moore.html">Analysis of PTO Domain Wall Junction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="api_doc.html">API documentation</a></li>
 </ul>
 
@@ -146,6 +150,8 @@
 
 
 
+
+
 <div role="navigation" aria-label="breadcrumbs navigation">
 
   <ul class="wy-breadcrumbs">
@@ -157,7 +163,7 @@
 
       <li class="wy-breadcrumbs-aside">
 
-            
+
             <a href="_sources/PTO_supercrystal_hadjimichael.rst.txt" rel="nofollow"> View page source</a>
 
 
@@ -182,7 +188,7 @@
 <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>The <code class="code python docutils literal notranslate"><span class="name"><span class="pre">calculate_atom_plane_curvature</span></span></code> function has been adapted from the
 MATLAB script written by Dr. Marios Hadjimichael for the publication
-M. Hadjimichael <em>et al</em>, <a class="reference external" href="https://www.nature.com/articles/s41563-020-00864-6">Metal-ferroelectric supercrystals with periodically
+M. Hadjimichael, Y. Li <em>et al</em>, <a class="reference external" href="https://www.nature.com/articles/s41563-020-00864-6">Metal-ferroelectric supercrystals with periodically
 curved metallic layers, Nature Materials 2020</a>.
 This MATLAB script can also be found in the same folder.</p>
 <p>The <code class="code python docutils literal notranslate"><span class="name"><span class="pre">calculate_atom_plane_curvature</span></span></code> function in the
@@ -268,37 +274,29 @@ <h2>Calculate the Curvature of Atom Planes<a class="headerlink" href="#calculate
 
           </div>
           <footer>
-
     <div class="rst-footer-buttons" role="navigation" aria-label="footer navigation">
-
-        <a href="PTO_Junction_moore.html" class="btn btn-neutral float-right" title="Analysis of PTO Domain Wall Junction" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right"></span></a>
-
-
-        <a href="structure_map_tutorial.html" class="btn btn-neutral float-left" title="Plot Lattice Structure Maps" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left"></span> Previous</a>
-
+        <a href="PTO_Junction_moore.html" class="btn btn-neutral float-right" title="Analysis of PTO Domain Wall Junction" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
+        <a href="structure_map_tutorial.html" class="btn btn-neutral float-left" title="Plot Lattice Structure Maps" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
     </div>
-
 
   <hr/>
 
   <div role="contentinfo">
     <p>
-
-        &copy; Copyright 2020, Eoghan O&#39;Connell
+        &#169; Copyright 2020, Eoghan O&#39;Connell.
 
     </p>
   </div>
 
 
 
-    Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a
+    Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
 
-    <a href="https://github.com/rtfd/sphinx_rtd_theme">theme</a>
+    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
 
     provided by <a href="https://readthedocs.org">Read the Docs</a>. 
 
 </footer>
-
         </div>
       </div>
 

diff --git a/doc/_build/html/_sources/PTO_Junction_moore.rst.txt b/doc/_build/html/_sources/PTO_Junction_moore.rst.txt
@@ -97,7 +97,7 @@ Note that sometimes the 0 and 1 axes directions are constructed vice versa.
     >>> vmax = 30
     >>> cmap = 'inferno'
     >>> theoretical_value = round(3.929/10, 3)  # units of nm
-    >>> strain_map = tmlp.get_strain_map(sublattice1, zone_vector_index_B,
+    >>> strain_map = tml.get_strain_map(sublattice1, zone_vector_index_B,
     ...                          theoretical_value, sampling=sampling,
     ...                          units=units, vmin=vmin, vmax=vmax, cmap=cmap)
 

diff --git a/doc/_build/html/_sources/PTO_supercrystal_hadjimichael.rst.txt b/doc/_build/html/_sources/PTO_supercrystal_hadjimichael.rst.txt
@@ -19,7 +19,7 @@ where you will find the python scripts and interactive python notebooks:
 
 The :python:`calculate_atom_plane_curvature` function has been adapted from the
 MATLAB script written by Dr. Marios Hadjimichael for the publication
-M. Hadjimichael *et al*, `Metal-ferroelectric supercrystals with periodically
+M. Hadjimichael, Y. Li *et al*, `Metal-ferroelectric supercrystals with periodically
 curved metallic layers, Nature Materials 2020 <https://www.nature.com/articles/s41563-020-00864-6>`_.
 This MATLAB script can also be found in the same folder.
 

diff --git a/doc/_build/html/_sources/api_doc.rst.txt b/doc/_build/html/_sources/api_doc.rst.txt
@@ -9,6 +9,9 @@ Classes
 
 Model Refiner
 =============
+.. This won't work because PyPrismatic isn't dependency
+   This of course needs to be fixed, but the fix is to
+   overhaul the Model Refiner class
 .. autoclass:: temul.model_refiner.Model_Refiner
     :members:
     :undoc-members:
@@ -17,9 +20,17 @@ Model Refiner
 Modules
 -------
 
-Polarisation
-============
-.. automodule:: temul.polarisation
+TopoTEM (Polarisation)
+======================
+.. automodule:: temul.topotem.polarisation
+    :members:
+    :undoc-members:
+
+.. automodule:: temul.topotem.fft_mapping
+    :members:
+    :undoc-members:
+
+.. automodule:: temul.topotem.lattice_structure_tools
     :members:
     :undoc-members:
 

diff --git a/doc/_build/html/_sources/news.rst.txt b/doc/_build/html/_sources/news.rst.txt
@@ -7,30 +7,52 @@ News
 ----
 
 .. new version additions:
-    Corrected atom_deviation_from_straight_line_fit function.
-    Added documentation for how to find the polarisation vectors
-    Added "code_tutorials" ipynb examples
-    Corrected plot_polarisation_vectors vector quiver key
-    Created "polar_colorwheel" `plot_style` for plot_polarisation_vectors by
-        using a HSV to RGB 2D colorwheel and mapping the angles and magnitudes to
-        these values. Used code from PixStem for colorwheel visualisation. 
-    Fixed norm and cmap scaling for the colorbar for "contour", "colorwheel" and
-        "colormap" plot_styles. Now they scale nicely and ticks can be input to all three.
-    Added invert_y_axis param for plot_polarisation_vectors function
-    plot_polarisation_vectors function now returns the Axes object
-    Added workflows webpage, .py and .ipynb files
-    Added vector correction functions
-    Added marios PTO paper links and notebook
-    Added Kalani PTO paper branch
-    
-
-**03/11/2020: Version 0.1.2 released**
+
+
+16/02/2021: Version 0.1.4 released
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+The polarisation, structure tools and fft mapping has now
+been refactored into the topotem module. The temul
+functionality remains the same i.e. ``import temul.api as tml`.
+
+
+16/02/2021: Version 0.1.3 released
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+First articles uses and citations for the TEMUL Toolkit!
+This version updated the Publication Examples folder with two newly published
+articles. The folder contains interactive and raw code on how to reproduce the
+data in the publications. Congrats to those involved!
+    * M. Hadjimichael, Y. Li *et al*, `Metal-ferroelectric supercrystals with periodically curved metallic layers, Nature Materials 2020 <https://www.nature.com/articles/s41563-020-00864-6>`_
+    * K. Moore *et al* `Highly charged 180 degree head-to-head domain walls in lead titanate, Nature Communications Physics 2020 <https://www.nature.com/articles/s42005-020-00488-x>`_
+If you have a question or issue with using the publication examples, please make
+an issue on `GitHub <https://github.com/PinkShnack/TEMUL/issues>`_.
+
+Code changes in this version:
+    * The :python:`atom_deviation_from_straight_line_fit` function has been **corrected** and expanded. For a use case, see :ref:`Finding Polarisation Vectors <polarisation_vectors_tutorial>`
+    * Corrected the :python:`plot_polarisation_vectors` function's vector quiver key.
+    * Created the "polar_colorwheel" :python:`plot_style` for :python:`plot_polarisation_vectors` by using a HSV to RGB 2D colorwheel and mapping the angles and magnitudes to these values. Used code from `PixStem <https://pixstem.org/>`_ for colorwheel visualisation. 
+    * Fixed :python:`norm` and :python:`cmap` scaling for the colorbar for the "contour", "colorwheel" and "colormap" :python:`plot_styles`. Now each of these :python:`plot_styles` scale nicely, and colorbar :python:`ticks` may be specified.
+    * Added invert_y_axis param for plot_polarisation_vectors function, useful for testing if angles are displaying correctly.
+    * :python:`plot_polarisation_vectors` function now returns a Matplotlib :python:`Axes` object, which can be used to further edit the layout/presentation of the plotted map.
+    * Added functions to correct for possible off-zone tilt in the atomic columns. Use with caution.
+
+Documentation changes in this version:
+    * Added documentation for :ref:`how to find the polarisation vectors <polarisation_vectors_tutorial>`.
+    * Added "code_tutorials" ipynb (interactive Jupyter Notebook) examples. See the `GitHub repository <https://github.com/PinkShnack/TEMUL>`_ for downloads.
+    * The :ref:`workflows <workflows>` folder in "code_tutorials/workflows" also contains starting workflows for analysis of different materials. See the `GitHub repository <https://github.com/PinkShnack/TEMUL>`_ for downloads.
+    * Added "publication_examples" tutorial ipynb (interactive Jupyter Notebook) examples. See the `GitHub repository <https://github.com/PinkShnack/TEMUL>`_ for downloads.
+
+
+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.
 
 
-**02/11/2020: Version 0.1.1 released**
+02/11/2020: Version 0.1.1 released
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 This version contains many changes to the TEMUL Toolkit.