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Update docs now that cdtools is public
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‎_sources/intro.rst.txt‎

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Introduction to CDTools
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-----------------------
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CDTools is a python library for ptychography and CDI reconstructions, using an automatic differentiation based approach.
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`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.
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.. _`CDTools`: https://github.com/cdtools-developers/cdtools
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.. code-block:: python
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‎_static/searchtools.js‎

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htmlToText: (htmlString, anchor) => {
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const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
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for (const removalQuery of [".headerlinks", "script", "style"]) {
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for (const removalQuery of [".headerlink", "script", "style"]) {
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htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() });
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}
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if (anchor) {
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for (const [title, foundTitles] of Object.entries(allTitles)) {
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if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) {
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for (const [file, id] of foundTitles) {
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let score = Math.round(100 * queryLower.length / title.length)
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const score = Math.round(Scorer.title * queryLower.length / title.length);
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const boost = titles[file] === title ? 1 : 0; // add a boost for document titles
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normalResults.push([
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docNames[file],
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titles[file] !== title ? `${titles[file]} > ${title}` : title,
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id !== null ? "#" + id : "",
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null,
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score,
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score + boost,
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filenames[file],
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]);
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}

‎datasets.html‎

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<!DOCTYPE html>
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<html class="writer-html5" lang="en" data-content_root="./">
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<head>
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<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
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<meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>Datasets &mdash; CDTools 0.2.0 documentation</title>
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<li class="toctree-l3"><a class="reference internal" href="#cdtools.datasets.Ptycho2DDataset.from_cxi"><code class="docutils literal notranslate"><span class="pre">Ptycho2DDataset.from_cxi()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="#cdtools.datasets.Ptycho2DDataset.to_cxi"><code class="docutils literal notranslate"><span class="pre">Ptycho2DDataset.to_cxi()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="#cdtools.datasets.Ptycho2DDataset.inspect"><code class="docutils literal notranslate"><span class="pre">Ptycho2DDataset.inspect()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="#cdtools.datasets.Ptycho2DDataset.plot_mean_pattern"><code class="docutils literal notranslate"><span class="pre">Ptycho2DDataset.plot_mean_pattern()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="#cdtools.datasets.Ptycho2DDataset.split"><code class="docutils literal notranslate"><span class="pre">Ptycho2DDataset.split()</span></code></a></li>
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<li class="toctree-l3"><a class="reference internal" href="#cdtools.datasets.Ptycho2DDataset.pad"><code class="docutils literal notranslate"><span class="pre">Ptycho2DDataset.pad()</span></code></a></li>
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</ul>
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<dl class="py method">
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<dt class="sig sig-object py" id="cdtools.datasets.Ptycho2DDataset.inspect">
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<span class="sig-name descname"><span class="pre">inspect</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">logarithmic</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">units</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'um'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log_offset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cdtools.datasets.Ptycho2DDataset.inspect" title="Link to this definition"></a></dt>
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<span class="sig-name descname"><span class="pre">inspect</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">logarithmic</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">units</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'um'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log_offset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plot_mean_pattern</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cdtools.datasets.Ptycho2DDataset.inspect" title="Link to this definition"></a></dt>
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<dd><p>Launches an interactive plot for perusing the data</p>
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<p>This launches an interactive plotting tool in matplotlib that
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shows the spatial map constructed from the integrated intensity
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position.</p>
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</dd></dl>
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<dl class="py method">
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<dt class="sig sig-object py" id="cdtools.datasets.Ptycho2DDataset.plot_mean_pattern">
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<span class="sig-name descname"><span class="pre">plot_mean_pattern</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">log_offset</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">1</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#cdtools.datasets.Ptycho2DDataset.plot_mean_pattern" title="Link to this definition"></a></dt>
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<dd><p>Plots the mean diffraction pattern across the dataset</p>
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<p>The output is normalized so that the summed intensity on the
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detector is equal to the total intensity of light that passed
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through the sample within each detector conjugate field of view.</p>
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<p>The plot is plotted as log base 10 of the output plus log_offset.
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By default, log_offset is set equal to 1, which is a good level for
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shot-noise limited data captured in units of photons. More
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generally, log_offset should be set roughly at the background noise
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level.</p>
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</dd></dl>
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<dl class="py method">
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<dt class="sig sig-object py" id="cdtools.datasets.Ptycho2DDataset.split">
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<span class="sig-name descname"><span class="pre">split</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#cdtools.datasets.Ptycho2DDataset.split" title="Link to this definition"></a></dt>

‎examples.html‎

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<!DOCTYPE html>
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<html class="writer-html5" lang="en" data-content_root="./">
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<meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
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<title>Examples &mdash; CDTools 0.2.0 documentation</title>

‎general.html‎

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<title>General Reference &mdash; CDTools 0.2.0 documentation</title>

‎genindex.html‎

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<li><a href="tools/initializers.html#cdtools.tools.initializers.calc_object_setup">calc_object_setup() (in module cdtools.tools.initializers)</a>
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</li>
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<li><a href="tools/analysis.html#cdtools.tools.analysis.calc_rms_error">calc_rms_error() (in module cdtools.tools.analysis)</a>
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</li>
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<li><a href="tools/analysis.html#cdtools.tools.analysis.calc_spectral_info">calc_spectral_info() (in module cdtools.tools.analysis)</a>
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</li>
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<li><a href="tools/plotting.html#cdtools.tools.plotting.plot_colorized">plot_colorized() (in module cdtools.tools.plotting)</a>
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</li>
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<li><a href="tools/plotting.html#cdtools.tools.plotting.plot_imag">plot_imag() (in module cdtools.tools.plotting)</a>
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</li>
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<li><a href="datasets.html#cdtools.datasets.Ptycho2DDataset.plot_mean_pattern">plot_mean_pattern() (cdtools.datasets.Ptycho2DDataset method)</a>
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</li>
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<li><a href="tools/plotting.html#cdtools.tools.plotting.plot_nanomap">plot_nanomap() (in module cdtools.tools.plotting)</a>
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‎index.html‎

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<title>Introduction to CDTools &mdash; CDTools 0.2.0 documentation</title>
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</div>
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<section id="introduction-to-cdtools">
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<h1>Introduction to CDTools<a class="headerlink" href="#introduction-to-cdtools" title="Link to this heading"></a></h1>
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<p>CDTools is a python library for ptychography and CDI reconstructions, using an automatic differentiation based approach.</p>
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<p><a class="reference external" href="https://github.com/cdtools-developers/cdtools">CDTools</a> 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>
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<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>
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<span class="kn">from</span> <span class="nn">cdtools.datasets</span> <span class="kn">import</span> <span class="n">Ptycho2DDataset</span>
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<span class="kn">from</span> <span class="nn">cdtools.models</span> <span class="kn">import</span> <span class="n">FancyPtycho</span>

‎indices_tables.html‎

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<title>Indices and tables &mdash; CDTools 0.2.0 documentation</title>

‎installation.html‎

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<title>Installation &mdash; CDTools 0.2.0 documentation</title>

‎intro.html‎

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<title>Introduction to CDTools &mdash; CDTools 0.2.0 documentation</title>
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<section id="introduction-to-cdtools">
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<h1>Introduction to CDTools<a class="headerlink" href="#introduction-to-cdtools" title="Link to this heading"></a></h1>
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<p>CDTools is a python library for ptychography and CDI reconstructions, using an automatic differentiation based approach.</p>
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<p><a class="reference external" href="https://github.com/cdtools-developers/cdtools">CDTools</a> 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>
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<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>
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<span class="kn">from</span> <span class="nn">cdtools.datasets</span> <span class="kn">import</span> <span class="n">Ptycho2DDataset</span>
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<span class="kn">from</span> <span class="nn">cdtools.models</span> <span class="kn">import</span> <span class="n">FancyPtycho</span>

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