Merge pull request #57 from PinkShnack/sort_doc_links

Make sure the api code references are working in docs

CHANGELOG

@@ -1,4 +1,5 @@
 0.1.4
+ - ref, doc: fix api doc link references
  - add initial (useable) tests in test directory
  - add CHANGELOG
  - ref: change the directory structure to include topotem (#52)

doc/PTO_Junction_moore.rst

@@ -81,8 +81,8 @@ Load the line profile positions:
     >>> line_profile_positions = np.load('line_profile_positions.npy')
 
 Note: You can also choose your own line_profile_positions with
-:python:`am.add_atoms_with_gui(image)` and use the :python:`skimage.profile_line`
-for customisability.
+:py:func:`temul.topotem.fft_mapping.choose_points_on_image` and use the
+:python:`skimage.profile_line` for customisability.
 
 
 Create the Lattice Strain Map
@@ -104,7 +104,7 @@ Note that sometimes the 0 and 1 axes directions are constructed vice versa.
 .. image:: ../publication_examples/PTO_Junction_moore/data/strain_map.png
     :scale: 50 %
 
-Plot the line profiles with :python:`temul.signal_plotting` functions and a kwarg dictionary.
+Plot the line profiles with :py:mod:`temul.signal_plotting` functions and a kwarg dictionary.
 For more details on this function, see :ref:`this tutorial <line_profile_tutorial>`.
 
 .. code-block:: python
@@ -140,7 +140,7 @@ the turning of the lattice across the junction.
     :scale: 50 %
 
 
-Plot the line profiles with :python:`temul.signal_plotting` functions and a kwarg dictionary.
+Plot the line profiles with :py:mod:`temul.signal_plotting` functions and a kwarg dictionary.
 For more details on this function, see :ref:`this tutorial <line_profile_tutorial>`.
 
 .. code-block:: python

doc/PTO_supercrystal_hadjimichael.rst

@@ -17,14 +17,16 @@ where you will find the python scripts and interactive python notebooks:
 .. image:: https://mybinder.org/badge_logo.svg
     :target: https://mybinder.org/v2/gh/PinkShnack/TEMUL/master
 
-The :python:`calculate_atom_plane_curvature` function has been adapted from the
+The :py:func:`temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature`
+function has been adapted from the
 MATLAB script written by Dr. Marios Hadjimichael for the publication
 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.
 
-The :python:`calculate_atom_plane_curvature` function in the
-:python:`temul.lattice_structure_tools` module can be used to find the curvature of the
+The :py:func:`temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature`
+function in the
+:py:mod:`temul.topotem.lattice_structure_tools` module can be used to find the curvature of the
 displacement of atoms along an atom plane in a sublattice. Using the default
 parameter :python:`func='strain_grad'`, the function will approximate the
 curvature as the strain gradient, as in cases where the first derivative is

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: 608bac64e8b48a97b902e87aaf2e9228
+config: f50bf99a7f7005c4e9d71dc02d297799
 tags: 645f666f9bcd5a90fca523b33c5a78b7

doc/_build/html/PTO_Junction_moore.html

@@ -7,7 +7,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
 
-  <title>Analysis of PTO Domain Wall Junction &mdash; TEMUL Toolkit v0.1.2 documentation</title>
+  <title>Analysis of PTO Domain Wall Junction &mdash; TEMUL Toolkit v0.1.3 documentation</title>
 
 
 
@@ -66,7 +66,7 @@
 
 
               <div class="version">
-                Version 0.1.2
+                Version 0.1.3
               </div>
 
 
@@ -236,8 +236,8 @@ <h2>Set up the Parameters<a class="headerlink" href="#set-up-the-parameters" tit
 </pre></div>
 </div>
 <p>Note: You can also choose your own line_profile_positions with
-<code class="code python docutils literal notranslate"><span class="name"><span class="pre">am</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">add_atoms_with_gui</span></span><span class="punctuation"><span class="pre">(</span></span><span class="name"><span class="pre">image</span></span><span class="punctuation"><span class="pre">)</span></span></code> and use the <code class="code python docutils literal notranslate"><span class="name"><span class="pre">skimage</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">profile_line</span></span></code>
-for customisability.</p>
+<a class="reference internal" href="api_doc.html#temul.topotem.fft_mapping.choose_points_on_image" title="temul.topotem.fft_mapping.choose_points_on_image"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.fft_mapping.choose_points_on_image()</span></code></a> and use the
+<code class="code python docutils literal notranslate"><span class="name"><span class="pre">skimage</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">profile_line</span></span></code> for customisability.</p>
 </div>
 <div class="section" id="create-the-lattice-strain-map">
 <h2>Create the Lattice Strain Map<a class="headerlink" href="#create-the-lattice-strain-map" title="Permalink to this headline">¶</a></h2>
@@ -253,7 +253,7 @@ <h2>Create the Lattice Strain Map<a class="headerlink" href="#create-the-lattice
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="_images/strain_map.png"><img alt="_images/strain_map.png" src="_images/strain_map.png" style="width: 320.0px; height: 290.5px;" /></a>
-<p>Plot the line profiles with <code class="code python docutils literal notranslate"><span class="name"><span class="pre">temul</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">signal_plotting</span></span></code> functions and a kwarg dictionary.
+<p>Plot the line profiles with <a class="reference internal" href="api_doc.html#module-temul.signal_plotting" title="temul.signal_plotting"><code class="xref py py-mod docutils literal notranslate"><span class="pre">temul.signal_plotting</span></code></a> functions and a kwarg dictionary.
 For more details on this function, see <a class="reference internal" href="line_profile_tutorial.html#line-profile-tutorial"><span class="std std-ref">this tutorial</span></a>.</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">kwargs</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;vmin&#39;</span><span class="p">:</span> <span class="n">vmin</span><span class="p">,</span> <span class="s1">&#39;vmax&#39;</span><span class="p">:</span> <span class="n">vmax</span><span class="p">,</span> <span class="s1">&#39;cmap&#39;</span><span class="p">:</span> <span class="n">cmap</span><span class="p">}</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">tml</span><span class="o">.</span><span class="n">compare_images_line_profile_one_image</span><span class="p">(</span><span class="n">strain_map</span><span class="p">,</span> <span class="n">line_profile_positions</span><span class="p">,</span>
@@ -278,7 +278,7 @@ <h2>Create the Lattice Rotation Map<a class="headerlink" href="#create-the-latti
 </pre></div>
 </div>
 <a class="reference internal image-reference" href="_images/rotation_map.png"><img alt="_images/rotation_map.png" src="_images/rotation_map.png" style="width: 320.0px; height: 290.5px;" /></a>
-<p>Plot the line profiles with <code class="code python docutils literal notranslate"><span class="name"><span class="pre">temul</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">signal_plotting</span></span></code> functions and a kwarg dictionary.
+<p>Plot the line profiles with <a class="reference internal" href="api_doc.html#module-temul.signal_plotting" title="temul.signal_plotting"><code class="xref py py-mod docutils literal notranslate"><span class="pre">temul.signal_plotting</span></code></a> functions and a kwarg dictionary.
 For more details on this function, see <a class="reference internal" href="line_profile_tutorial.html#line-profile-tutorial"><span class="std std-ref">this tutorial</span></a>.</p>
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">kwargs</span> <span class="o">=</span> <span class="p">{</span><span class="s1">&#39;vmin&#39;</span><span class="p">:</span> <span class="n">vmin</span><span class="p">,</span> <span class="s1">&#39;vmax&#39;</span><span class="p">:</span> <span class="n">vmax</span><span class="p">,</span> <span class="s1">&#39;cmap&#39;</span><span class="p">:</span> <span class="n">cmap</span><span class="p">}</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">tml</span><span class="o">.</span><span class="n">compare_images_line_profile_one_image</span><span class="p">(</span>
@@ -360,7 +360,7 @@ <h2>Map the Polarisation<a class="headerlink" href="#map-the-polarisation" title
 
   <div role="contentinfo">
     <p>
-        &#169; Copyright 2020, Eoghan O&#39;Connell.
+        &#169; Copyright 2021, Eoghan O&#39;Connell.
 
     </p>
   </div>

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 v0.1.2 documentation</title>
+  <title>Calculation of Atom Plane Curvature &mdash; TEMUL Toolkit v0.1.3 documentation</title>
 
 
 
@@ -66,7 +66,7 @@
 
 
               <div class="version">
-                Version 0.1.2
+                Version 0.1.3
               </div>
 
 
@@ -186,13 +186,15 @@
 without needing any downloads. Just click this button and navigate to that same folder,
 where you will find the python scripts and interactive python notebooks:</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>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
+<p>The <a class="reference internal" href="api_doc.html#temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature" title="temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature()</span></code></a>
+function has been adapted from the
 MATLAB script written by Dr. Marios Hadjimichael for the publication
 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
-<code class="code python docutils literal notranslate"><span class="name"><span class="pre">temul</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">lattice_structure_tools</span></span></code> module can be used to find the curvature of the
+<p>The <a class="reference internal" href="api_doc.html#temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature" title="temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature()</span></code></a>
+function in the
+<a class="reference internal" href="api_doc.html#module-temul.topotem.lattice_structure_tools" title="temul.topotem.lattice_structure_tools"><code class="xref py py-mod docutils literal notranslate"><span class="pre">temul.topotem.lattice_structure_tools</span></code></a> module can be used to find the curvature of the
 displacement of atoms along an atom plane in a sublattice. Using the default
 parameter <code class="code python docutils literal notranslate"><span class="name"><span class="pre">func</span></span><span class="operator"><span class="pre">=</span></span><span class="literal string single"><span class="pre">’strain_grad’</span></span></code>, the function will approximate the
 curvature as the strain gradient, as in cases where the first derivative is
@@ -283,7 +285,7 @@ <h2>Calculate the Curvature of Atom Planes<a class="headerlink" href="#calculate
 
   <div role="contentinfo">
     <p>
-        &#169; Copyright 2020, Eoghan O&#39;Connell.
+        &#169; Copyright 2021, Eoghan O&#39;Connell.
 
     </p>
   </div>

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

@@ -81,8 +81,8 @@ Load the line profile positions:
     >>> line_profile_positions = np.load('line_profile_positions.npy')
 
 Note: You can also choose your own line_profile_positions with
-:python:`am.add_atoms_with_gui(image)` and use the :python:`skimage.profile_line`
-for customisability.
+:py:func:`temul.topotem.fft_mapping.choose_points_on_image` and use the
+:python:`skimage.profile_line` for customisability.
 
 
 Create the Lattice Strain Map
@@ -104,7 +104,7 @@ Note that sometimes the 0 and 1 axes directions are constructed vice versa.
 .. image:: ../publication_examples/PTO_Junction_moore/data/strain_map.png
     :scale: 50 %
 
-Plot the line profiles with :python:`temul.signal_plotting` functions and a kwarg dictionary.
+Plot the line profiles with :py:mod:`temul.signal_plotting` functions and a kwarg dictionary.
 For more details on this function, see :ref:`this tutorial <line_profile_tutorial>`.
 
 .. code-block:: python
@@ -140,7 +140,7 @@ the turning of the lattice across the junction.
     :scale: 50 %
 
 
-Plot the line profiles with :python:`temul.signal_plotting` functions and a kwarg dictionary.
+Plot the line profiles with :py:mod:`temul.signal_plotting` functions and a kwarg dictionary.
 For more details on this function, see :ref:`this tutorial <line_profile_tutorial>`.
 
 .. code-block:: python

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

@@ -17,14 +17,16 @@ where you will find the python scripts and interactive python notebooks:
 .. image:: https://mybinder.org/badge_logo.svg
     :target: https://mybinder.org/v2/gh/PinkShnack/TEMUL/master
 
-The :python:`calculate_atom_plane_curvature` function has been adapted from the
+The :py:func:`temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature`
+function has been adapted from the
 MATLAB script written by Dr. Marios Hadjimichael for the publication
 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.
 
-The :python:`calculate_atom_plane_curvature` function in the
-:python:`temul.lattice_structure_tools` module can be used to find the curvature of the
+The :py:func:`temul.topotem.lattice_structure_tools.calculate_atom_plane_curvature`
+function in the
+:py:mod:`temul.topotem.lattice_structure_tools` module can be used to find the curvature of the
 displacement of atoms along an atom plane in a sublattice. Using the default
 parameter :python:`func='strain_grad'`, the function will approximate the
 curvature as the strain gradient, as in cases where the first derivative is

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.

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

@@ -7,9 +7,10 @@
 Interactive Image Filtering
 ===========================
 
-The :python:`temul.signal_processing` module allows one to filter images with a
+The :py:mod:`temul.signal_processing` module allows one to filter images with a
 double Gaussian (band-pass) filter. Apart from the base functions, it can be
-done interactively with the :python:`visualise_dg_filter` function. In this
+done interactively with the
+:py:func:`temul.signal_processing.visualise_dg_filter` function. In this
 tutorial, we will see how to use the function on experimental data.
 
 
@@ -30,8 +31,8 @@ TEMUL package.
 Interactively Filter the Experimental Image
 -------------------------------------------
 
-Run the :python:`visualise_dg_filter` function. There are lots of other parameters
-too for customisation.
+Run the :py:func:`temul.signal_processing.visualise_dg_filter` function.
+There are lots of other parameters too for customisation.
 
 .. code-block:: python
 
@@ -40,9 +41,10 @@ too for customisation.
 .. image:: tutorial_images/dg_filter_tutorial/dg_visualiser.gif
     :scale: 50 %
 
-As we can see, an interactive window appears, showing the FFT ("FFT Widget") of the image with
-the positions of the inner and outer Gaussian full width at half maximums (FWHMs).
-The inital FWHMs can be changed with the :python:`d_inner` and :python:`d_outer`
+As we can see, an interactive window appears, showing the FFT ("FFT Widget")
+of the image with the positions of the inner and outer Gaussian full width
+at half maximums (FWHMs). The inital FWHMs can be changed with the
+:python:`d_inner` and :python:`d_outer`
 parameters (limits can also be changed).
 
 To change the two FWHMs interactively
@@ -56,7 +58,8 @@ Return the Filtered Image
 -------------------------
 
 When we have suitable FWHMs for the inner and outer Gaussians, we can use
-the :python:`double_gaussian_fft_filter` function the return a filtered image.
+the :py:func:`temul.signal_processing.double_gaussian_fft_filter` function
+the return a filtered image.
 
 .. code-block:: python
 
@@ -71,6 +74,6 @@ the :python:`double_gaussian_fft_filter` function the return a filtered image.
     :scale: 50 %
 
 
-Details on the :python:`double_gaussian_fft_filter_optimised` function can be
-found in the :ref:`api_doc`.
-We hope to added some examples of this functions to this page in future.
+Details on the
+:py:func:`temul.signal_processing.double_gaussian_fft_filter_optimised`
+function can be found in the :ref:`api_doc`.