docs: updating links to api docs 2

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/PTO_Junction_moore.html

@@ -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>

doc/_build/html/PTO_supercrystal_hadjimichael.html

@@ -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

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/polarisation_vectors_tutorial.rst.txt

@@ -193,7 +193,7 @@ Let's look at some rotated data
 Plotting Polarisation and Movement Vectors
 ==========================================
 
-The :py:func:`temul.topotem.polarisation.temul.polarisation` module allows one to visualise the
+The :py:mod:`temul.topotem.polarisation` module allows one to visualise the
 polarisation/movement of atoms in an atomic resolution image. In this tutorial,
 we will use a dummy dataset to show the different ways the
 :py:func:`temul.topotem.polarisation.plot_polarisation_vectors`

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

@@ -7,7 +7,7 @@
 Plot Lattice Structure Maps
 ===========================
 
-The :python:`temul.polarisation` module allows one to easily visualise various
+The :py:mod:`temul.topotem.polarisation` module allows one to easily visualise various
 lattice structure characteristics, such as strain, rotation of atoms along atom
 planes, and the *c*/*a* ratio in an atomic resolution image. In this tutorial,
 we will use a dummy dataset to show the different ways each map can be created.
@@ -38,7 +38,8 @@ Plot the Lattice Strain Map
 ---------------------------
 
 By inputting the calculated or theoretical atom plane separation distance as the
-:python:`theoretical_value` parameter in :python:`tml.get_strain_map` below,
+:python:`theoretical_value` parameter in
+:py:func:`temul.topotem.polarisation.get_strain_map` below,
 we can plot a strain map. The distance *l* is calculated as the distance between
 each atom plane in the given zone axis. More details on this can be found on the
 `Atomap <https://atomap.org/analysing_atom_lattices.html#distance-between-monolayers>`_
@@ -70,7 +71,8 @@ applies to all structure maps discussed in this tutorial.
 Plot the Lattice Atom Rotation Map
 ----------------------------------
 
-The :python:`rotation_of_atom_planes` function calculates the angle between
+The :py:func:`temul.topotem.polarisation.rotation_of_atom_planes` function
+calculates the angle between
 successive atoms and the horizontal for all atoms in the given zone axis. See
 `Atomap <https://atomap.org/analysing_atom_lattices.html#angle-between-atoms>`_
 for other options.
@@ -103,7 +105,8 @@ for other options.
 Plot the *c*/*a* Ratio
 ----------------------
 
-Using the :python:`ratio_of_lattice_spacings` function, we can visualise the ratio of
+Using the :py:func:`temul.topotem.polarisation.ratio_of_lattice_spacings`
+function, we can visualise the ratio of
 two sublattice zone axes. Useful for plotting the *c*/*a* Ratio.
 
 .. code-block:: python

doc/_build/html/polarisation_vectors_tutorial.html

@@ -334,7 +334,7 @@ <h2>For single Polarised Sublattices (e.g., LNO)<a class="headerlink" href="#for
 </div>
 <div class="section" id="plotting-polarisation-and-movement-vectors">
 <h1>Plotting Polarisation and Movement Vectors<a class="headerlink" href="#plotting-polarisation-and-movement-vectors" title="Permalink to this headline">¶</a></h1>
-<p>The <code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.polarisation.temul.polarisation()</span></code> module allows one to visualise the
+<p>The <a class="reference internal" href="api_doc.html#module-temul.topotem.polarisation" title="temul.topotem.polarisation"><code class="xref py py-mod docutils literal notranslate"><span class="pre">temul.topotem.polarisation</span></code></a> module allows one to visualise the
 polarisation/movement of atoms in an atomic resolution image. In this tutorial,
 we will use a dummy dataset to show the different ways the
 <a class="reference internal" href="api_doc.html#temul.topotem.polarisation.plot_polarisation_vectors" title="temul.topotem.polarisation.plot_polarisation_vectors"><code class="xref py py-func docutils literal notranslate"><span class="pre">temul.topotem.polarisation.plot_polarisation_vectors()</span></code></a>