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<section id="introduction-to-cdtools">
<h1>Introduction to CDTools<a class="headerlink" href="#introduction-to-cdtools" title="Link to this heading"></a></h1>
<p>CDTools is an open source python library for ptychography and CDI reconstructions, using an automatic differentiation based approach. It is distributed under an MIT (a.k.a. Expat) license.</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">matplotlib</span> <span class="kn">import</span> <span class="n">pyplot</span> <span class="k">as</span> <span class="n">plt</span>
<span class="kn">from</span> <span class="nn">cdtools.datasets</span> <span class="kn">import</span> <span class="n">Ptycho2DDataset</span>
<span class="kn">from</span> <span class="nn">cdtools.models</span> <span class="kn">import</span> <span class="n">FancyPtycho</span>
<span class="c1"># Load a data file</span>
<span class="n">dataset</span> <span class="o">=</span> <span class="n">Ptycho2DDataset</span><span class="o">.</span><span class="n">from_cxi</span><span class="p">(</span><span class="s1">'ptycho_data.cxi'</span><span class="p">)</span>
<span class="c1"># Look at the data inside</span>
<span class="n">dataset</span><span class="o">.</span><span class="n">inspect</span><span class="p">()</span>
<span class="c1"># Initialize a model from the data</span>
<span class="n">model</span> <span class="o">=</span> <span class="n">FancyPtycho</span><span class="o">.</span><span class="n">from_dataset</span><span class="p">(</span><span class="n">dataset</span><span class="p">)</span>
<span class="c1"># Run a reconstruction</span>
<span class="k">for</span> <span class="n">loss</span> <span class="ow">in</span> <span class="n">model</span><span class="o">.</span><span class="n">Adam_optimize</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span> <span class="n">dataset</span><span class="p">):</span>
<span class="nb">print</span><span class="p">(</span><span class="n">model</span><span class="o">.</span><span class="n">report</span><span class="p">())</span>
<span class="c1"># Save the results</span>
<span class="n">model</span><span class="o">.</span><span class="n">save_to_h5</span><span class="p">(</span><span class="s1">'ptycho_results.h5'</span><span class="p">,</span> <span class="n">dataset</span><span class="p">)</span>
<span class="c1"># And look at them!</span>
<span class="n">model</span><span class="o">.</span><span class="n">inspect</span><span class="p">(</span><span class="n">dataset</span><span class="p">)</span> <span class="c1"># See the reconstructed object, probe, etc.</span>
<span class="n">model</span><span class="o">.</span><span class="n">compare</span><span class="p">(</span><span class="n">dataset</span><span class="p">)</span> <span class="c1"># See how the simulated and measured patterns compare</span>
<span class="n">plt</span><span class="o">.</span><span class="n">show</span><span class="p">()</span>
</pre></div>
</div>
<p>CDTools makes it simple to load and inspect data stored in .cxi files. Reconstruction models for common geometries are included “out of the box”. For more advanced users, it includes a collection of differentiable functions which can beused to construct new forward models.</p>
<p>The high-level interface to CDTools - datasets and models - is built on a set of lower-level tools. These lower level tools include:</p>
<ul class="simple">
<li><p>functions for accessing stored data in .cxi files</p></li>
<li><p>plotting tools to visualize data and reconstructions</p></li>
<li><p>basic operations, like light propagators, needed for coherent diffraction</p></li>
<li><p>tools that implement basic operations - such as light propagation - relevant to coherent diffraction.</p></li>
<li><p>analysis functions for assessing the quality of reconstructions</p></li>
</ul>
<p>These functions can be used alongside the high-level interface to make fun and fancy reconstruction scripts for challenging data.</p>
<p>If you’re interested, read the docs!</p>
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