fixed heat example and added authors

docs/build/html/_autosummary/dynadojo.baselines.dmd.DMD.html

@@ -420,6 +420,14 @@ <h1>dynadojo.baselines.dmd.DMD<a class="headerlink" href="#dynadojo-baselines-dm
 <dt class="sig sig-object py" id="dynadojo.baselines.dmd.DMD">
 <em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">dynadojo.baselines.dmd.</span></span><span class="sig-name descname"><span class="pre">DMD</span></span><a class="headerlink" href="#dynadojo.baselines.dmd.DMD" title="Link to this definition">#</a></dt>
 <dd><p>Bases: <a class="reference internal" href="dynadojo.abstractions.AbstractAlgorithm.html#dynadojo.abstractions.AbstractAlgorithm" title="dynadojo.abstractions.AbstractAlgorithm"><code class="xref py py-class docutils literal notranslate"><span class="pre">AbstractAlgorithm</span></code></a></p>
+<p>Dynamic mode decomposition. Implementation uses the <code class="docutils literal notranslate"><span class="pre">pydmd</span></code> library <a class="footnote-reference brackets" href="#id2" id="id1" role="doc-noteref"><span class="fn-bracket">[</span>1<span class="fn-bracket">]</span></a>.</p>
+<p class="rubric">References</p>
+<aside class="footnote-list brackets">
+<aside class="footnote brackets" id="id2" role="note">
+<span class="label"><span class="fn-bracket">[</span><a role="doc-backlink" href="#id1">1</a><span class="fn-bracket">]</span></span>
+<p><a class="reference external" href="https://pydmd.github.io/PyDMD/">https://pydmd.github.io/PyDMD/</a></p>
+</aside>
+</aside>
 <p class="rubric">Methods</p>
 <div class="table-wrapper autosummary longtable docutils container">
 <table class="autosummary longtable docutils align-default">

docs/build/html/_autosummary/dynadojo.baselines.dmd.html

@@ -141,7 +141,7 @@
           <svg class="theme-icon-when-light"><use href="#svg-sun"></use></svg>
         </button>
       </div>
-      <label class="toc-overlay-icon toc-header-icon no-toc" for="__toc">
+      <label class="toc-overlay-icon toc-header-icon" for="__toc">
         <div class="visually-hidden">Toggle table of contents sidebar</div>
         <i class="icon"><svg><use href="#svg-toc"></use></svg></i>
       </label>
@@ -408,20 +408,23 @@
               <svg class="theme-icon-when-light"><use href="#svg-sun"></use></svg>
             </button>
           </div>
-          <label class="toc-overlay-icon toc-content-icon no-toc" for="__toc">
+          <label class="toc-overlay-icon toc-content-icon" for="__toc">
             <div class="visually-hidden">Toggle table of contents sidebar</div>
             <i class="icon"><svg><use href="#svg-toc"></use></svg></i>
           </label>
         </div>
         <article role="main">
           <section id="module-dynadojo.baselines.dmd">
 <span id="dynadojo-baselines-dmd"></span><h1>dynadojo.baselines.dmd<a class="headerlink" href="#module-dynadojo.baselines.dmd" title="Link to this heading">#</a></h1>
+<section id="dynamic-mode-decomposition">
+<h2>Dynamic Mode Decomposition<a class="headerlink" href="#dynamic-mode-decomposition" title="Link to this heading">#</a></h2>
+</section>
 <p class="rubric">Classes</p>
 <div class="table-wrapper autosummary longtable docutils container">
 <table class="autosummary longtable docutils align-default">
 <tbody>
 <tr class="row-odd"><td><p><a class="reference internal" href="dynadojo.baselines.dmd.DMD.html#dynadojo.baselines.dmd.DMD" title="dynadojo.baselines.dmd.DMD"><code class="xref py py-obj docutils literal notranslate"><span class="pre">DMD</span></code></a></p></td>
-<td><p></p></td>
+<td><p>Dynamic mode decomposition.</p></td>
 </tr>
 </tbody>
 </table>
@@ -471,8 +474,27 @@
 
       </footer>
     </div>
-    <aside class="toc-drawer no-toc">
+    <aside class="toc-drawer">
+
 
+      <div class="toc-sticky toc-scroll">
+        <div class="toc-title-container">
+          <span class="toc-title">
+            On this page
+          </span>
+        </div>
+        <div class="toc-tree-container">
+          <div class="toc-tree">
+            <ul>
+<li><a class="reference internal" href="#">dynadojo.baselines.dmd</a><ul>
+<li><a class="reference internal" href="#dynamic-mode-decomposition">Dynamic Mode Decomposition</a></li>
+</ul>
+</li>
+</ul>
+
+          </div>
+        </div>
+      </div>
 
 
     </aside>

docs/build/html/_autosummary/dynadojo.systems.heat.HeatEquation.html

@@ -430,6 +430,27 @@ <h1>dynadojo.systems.heat.HeatEquation<a class="headerlink" href="#dynadojo-syst
 </aside>
 <p class="rubric">Example</p>
 <p>You can download the source image <a class="reference external" href="https://github.com/FlyingWorkshop/dynadojo/blob/main/graphics/dino.png">here</a>.</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
+<span class="kn">from</span> <span class="nn">PIL</span> <span class="kn">import</span> <span class="n">Image</span>
+<span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
+
+<span class="k">def</span> <span class="nf">grayscale</span><span class="p">(</span><span class="n">png_path</span><span class="p">,</span> <span class="n">basewidth</span><span class="o">=</span><span class="mi">30</span><span class="p">):</span>
+    <span class="n">image</span> <span class="o">=</span> <span class="n">Image</span><span class="o">.</span><span class="n">open</span><span class="p">(</span><span class="n">png_path</span><span class="p">)</span>
+    <span class="n">wpercent</span> <span class="o">=</span> <span class="p">(</span><span class="n">basewidth</span> <span class="o">/</span> <span class="nb">float</span><span class="p">(</span><span class="n">image</span><span class="o">.</span><span class="n">size</span><span class="p">[</span><span class="mi">0</span><span class="p">]))</span>
+    <span class="n">hsize</span> <span class="o">=</span> <span class="nb">int</span><span class="p">((</span><span class="nb">float</span><span class="p">(</span><span class="n">image</span><span class="o">.</span><span class="n">size</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span> <span class="o">*</span> <span class="nb">float</span><span class="p">(</span><span class="n">wpercent</span><span class="p">)))</span>
+    <span class="n">image</span> <span class="o">=</span> <span class="n">image</span><span class="o">.</span><span class="n">resize</span><span class="p">((</span><span class="n">basewidth</span><span class="p">,</span><span class="n">hsize</span><span class="p">),</span> <span class="n">Image</span><span class="o">.</span><span class="n">Resampling</span><span class="o">.</span><span class="n">LANCZOS</span><span class="p">)</span>
+    <span class="n">grayscale_image</span> <span class="o">=</span> <span class="n">image</span><span class="o">.</span><span class="n">convert</span><span class="p">(</span><span class="s2">&quot;L&quot;</span><span class="p">)</span>
+    <span class="n">grey</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">grayscale_image</span><span class="p">)</span>
+    <span class="k">return</span> <span class="n">grey</span>
+
+<span class="n">dino</span> <span class="o">=</span> <span class="n">grayscale</span><span class="p">(</span><span class="s2">&quot;../graphics/dino.png&quot;</span><span class="p">)</span>
+<span class="nb">print</span><span class="p">(</span><span class="n">dino</span><span class="o">.</span><span class="n">shape</span><span class="p">)</span>
+<span class="n">latent_dim</span> <span class="o">=</span> <span class="n">dino</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">**</span> <span class="mi">2</span>
+<span class="n">plt</span><span class="o">.</span><span class="n">imshow</span><span class="p">(</span><span class="n">dino</span><span class="p">,</span> <span class="n">cmap</span><span class="o">=</span><span class="s1">&#39;gray&#39;</span><span class="p">)</span>
+<span class="n">plt</span><span class="o">.</span><span class="n">axis</span><span class="p">(</span><span class="s1">&#39;off&#39;</span><span class="p">)</span>  <span class="c1"># Turn off axis labels and ticks</span>
+<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
+</pre></div>
+</div>
 <img alt="../_images/bw_dino.png" src="../_images/bw_dino.png" />
 <div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">dynadojo.systems.heat</span> <span class="kn">import</span> <span class="n">HeatEquation</span>
 <span class="kn">from</span> <span class="nn">dynadojo.wrappers</span> <span class="kn">import</span> <span class="n">SystemChecker</span>

docs/build/html/_autosummary/dynadojo.systems.lds.LDSystem.html

@@ -427,12 +427,7 @@ <h1>dynadojo.systems.lds.LDSystem<a class="headerlink" href="#dynadojo-systems-l
 <table class="autosummary longtable docutils align-default">
 <tbody>
 <tr class="row-odd"><td><p><a class="reference internal" href="#dynadojo.systems.lds.LDSystem.__init__" title="dynadojo.systems.lds.LDSystem.__init__"><code class="xref py py-obj docutils literal notranslate"><span class="pre">__init__</span></code></a>([latent_dim, embed_dim, ...])</p></td>
-<td><p><dl class="field-list simple">
-<dt class="field-odd">param latent_dim<span class="colon">:</span></dt>
-<dd class="field-odd"><p>Dimension of the latent space. Defaults to 2. Can set to large values.</p>
-</dd>
-</dl>
-</p></td>
+<td><p>Initialize the class.</p></td>
 </tr>
 <tr class="row-even"><td><p><a class="reference internal" href="#dynadojo.systems.lds.LDSystem.calc_control_cost" title="dynadojo.systems.lds.LDSystem.calc_control_cost"><code class="xref py py-obj docutils literal notranslate"><span class="pre">calc_control_cost</span></code></a>(control)</p></td>
 <td><p>Calculates the L2 norm / dimension of every vector in the control</p></td>
@@ -477,7 +472,25 @@ <h1>dynadojo.systems.lds.LDSystem<a class="headerlink" href="#dynadojo-systems-l
 <dl class="py method">
 <dt class="sig sig-object py" id="dynadojo.systems.lds.LDSystem.__init__">
 <span class="sig-name descname"><span class="pre">__init__</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">latent_dim</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">embed_dim</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">A_eigval_range</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(-1,</span> <span class="pre">1)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">A_eigvec_range</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(-1,</span> <span class="pre">1)</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#dynadojo.systems.lds.LDSystem.__init__" title="Link to this definition">#</a></dt>
-<dd><dl class="field-list simple">
+<dd><p>Initialize the class.</p>
+<p class="rubric">Example</p>
+<div class="doctest highlight-default notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">dynadojo.systems.lds</span> <span class="kn">import</span> <span class="n">LDSystem</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">dynadojo.wrappers</span> <span class="kn">import</span> <span class="n">SystemChecker</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">dynadojo.utils.lds</span> <span class="kn">import</span> <span class="n">plot</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">latent_dim</span> <span class="o">=</span> <span class="mi">9</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">embed_dim</span> <span class="o">=</span> <span class="mi">14</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">n</span> <span class="o">=</span> <span class="mi">500</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">timesteps</span> <span class="o">=</span> <span class="mi">50</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">system</span> <span class="o">=</span> <span class="n">SystemChecker</span><span class="p">(</span><span class="n">LDSystem</span><span class="p">(</span><span class="n">latent_dim</span><span class="p">,</span> <span class="n">embed_dim</span><span class="p">,</span> <span class="n">noise_scale</span><span class="o">=</span><span class="mi">0</span><span class="p">,</span> <span class="n">seed</span><span class="o">=</span><span class="mi">0</span><span class="p">))</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x0</span> <span class="o">=</span> <span class="n">system</span><span class="o">.</span><span class="n">make_init_conds</span><span class="p">(</span><span class="n">n</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">y0</span> <span class="o">=</span> <span class="n">system</span><span class="o">.</span><span class="n">make_init_conds</span><span class="p">(</span><span class="mi">30</span><span class="p">,</span> <span class="n">in_dist</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">x</span> <span class="o">=</span> <span class="n">system</span><span class="o">.</span><span class="n">make_data</span><span class="p">(</span><span class="n">x0</span><span class="p">,</span> <span class="n">timesteps</span><span class="o">=</span><span class="n">timesteps</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">y</span> <span class="o">=</span> <span class="n">system</span><span class="o">.</span><span class="n">make_data</span><span class="p">(</span><span class="n">y0</span><span class="p">,</span> <span class="n">timesteps</span><span class="o">=</span><span class="n">timesteps</span><span class="p">,</span> <span class="n">noisy</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">plot</span><span class="p">([</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">],</span> <span class="n">target_dim</span><span class="o">=</span><span class="nb">min</span><span class="p">(</span><span class="n">latent_dim</span><span class="p">,</span> <span class="mi">3</span><span class="p">),</span> <span class="n">labels</span><span class="o">=</span><span class="p">[</span><span class="s2">&quot;in&quot;</span><span class="p">,</span> <span class="s2">&quot;out&quot;</span><span class="p">],</span> <span class="n">max_lines</span><span class="o">=</span><span class="mi">15</span><span class="p">)</span>
+</pre></div>
+</div>
+<img alt="../_images/lds.png" src="../_images/lds.png" />
+<dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>latent_dim</strong> (<em>int</em><em>, </em><em>optional</em>) – Dimension of the latent space. Defaults to 2. Can set to large values.</p></li>

docs/build/html/_autosummary/dynadojo.systems.santi.html

@@ -417,7 +417,7 @@
           <section id="module-dynadojo.systems.santi">
 <span id="dynadojo-systems-santi"></span><h1>dynadojo.systems.santi<a class="headerlink" href="#module-dynadojo.systems.santi" title="Link to this heading">#</a></h1>
 <section id="n-body-system">
-<h2>N-Body System<a class="headerlink" href="#n-body-system" title="Link to this heading">#</a></h2>
+<h2>N-Body System.<a class="headerlink" href="#n-body-system" title="Link to this heading">#</a></h2>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
 <p>The name <cite>santi</cite> is a reference to the Chinese name for the 3-body problem and the famous eponymous novel from Cixin Liu.</p>
@@ -491,7 +491,7 @@ <h2>N-Body System<a class="headerlink" href="#n-body-system" title="Link to this
           <div class="toc-tree">
             <ul>
 <li><a class="reference internal" href="#">dynadojo.systems.santi</a><ul>
-<li><a class="reference internal" href="#n-body-system">N-Body System</a></li>
+<li><a class="reference internal" href="#n-body-system">N-Body System.</a></li>
 </ul>
 </li>
 </ul>