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mjo22 committed Apr 11, 2024
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6 changes: 3 additions & 3 deletions 404.html
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<link rel="icon" href="/cryojax/assets/images/favicon.png">
<meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.15">
<meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.17">



<title>cryoJAX</title>



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<link rel="stylesheet" href="/cryojax/assets/stylesheets/main.bcfcd587.min.css">



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<script id="__config" type="application/json">{"base": "/cryojax/", "features": ["navigation.sections", "toc.integrate"], "search": "/cryojax/assets/javascripts/workers/search.b8dbb3d2.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}}</script>


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code.doc-symbol-module::after {
content: "mod";
}
}

.doc-signature .autorefs {
color: inherit;
border-bottom: 1px dotted currentcolor;
}
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<link rel="icon" href="../../assets/images/favicon.png">
<meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.15">
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<title>Read a particle stack - cryoJAX</title>



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<script id="__config" type="application/json">{"base": "../..", "features": ["navigation.sections", "toc.integrate"], "search": "../../assets/javascripts/workers/search.b8dbb3d2.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}}</script>


<script src="../../assets/javascripts/bundle.bd41221c.min.js"></script>
<script src="../../assets/javascripts/bundle.1e8ae164.min.js"></script>

<script src="../../javascripts/mathjax.js"></script>

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6 changes: 3 additions & 3 deletions examples/simulate-helix/index.html
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<title>Simulate helix - cryoJAX</title>



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<script id="__config" type="application/json">{"base": "../..", "features": ["navigation.sections", "toc.integrate"], "search": "../../assets/javascripts/workers/search.b8dbb3d2.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}}</script>


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<title>Test multiatom - cryoJAX</title>



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<script id="__config" type="application/json">{"base": "../..", "features": ["navigation.sections", "toc.integrate"], "search": "../../assets/javascripts/workers/search.b8dbb3d2.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}}</script>


<script src="../../assets/javascripts/bundle.bd41221c.min.js"></script>
<script src="../../assets/javascripts/bundle.1e8ae164.min.js"></script>

<script src="../../javascripts/mathjax.js"></script>

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<link rel="icon" href="assets/images/favicon.png">
<meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.15">
<meta name="generator" content="mkdocs-1.5.3, mkdocs-material-9.5.17">



<title>cryoJAX</title>



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Expand Down Expand Up @@ -626,11 +626,11 @@ <h2 id="quick-example">Quick example<a class="headerlink" href="#quick-example"
<span class="n">defocus_u_in_angstroms</span><span class="o">=</span><span class="mf">10000.0</span><span class="p">,</span>
<span class="n">defocus_v_in_angstroms</span><span class="o">=</span><span class="mf">9800.0</span><span class="p">,</span>
<span class="n">astigmatism_angle</span><span class="o">=</span><span class="mf">10.0</span><span class="p">,</span>
<span class="n">voltage_in_kilovolts</span><span class="o">=</span><span class="mf">300.0</span><span class="p">,</span>
<span class="n">amplitude_contrast_ratio</span><span class="o">=</span><span class="mf">0.1</span><span class="p">)</span>
<span class="n">optics</span> <span class="o">=</span> <span class="n">cs</span><span class="o">.</span><span class="n">WeakPhaseOptics</span><span class="p">(</span><span class="n">ctf</span><span class="p">,</span> <span class="n">envelope</span><span class="o">=</span><span class="n">op</span><span class="o">.</span><span class="n">FourierGaussian</span><span class="p">(</span><span class="n">b_factor</span><span class="o">=</span><span class="mf">5.0</span><span class="p">))</span> <span class="c1"># b_factor is given in Angstroms^2</span>
<span class="c1"># ... these are stored in the Instrument</span>
<span class="n">instrument</span> <span class="o">=</span> <span class="n">cs</span><span class="o">.</span><span class="n">Instrument</span><span class="p">(</span><span class="n">optics</span><span class="p">)</span>
<span class="n">voltage_in_kilovolts</span> <span class="o">=</span> <span class="mf">300.0</span>
<span class="n">instrument</span> <span class="o">=</span> <span class="n">cs</span><span class="o">.</span><span class="n">Instrument</span><span class="p">(</span><span class="n">voltage_in_kilovolts</span><span class="p">,</span> <span class="n">optics</span><span class="p">)</span>
</code></pre></div>
<p>The <code>CTF</code> has all parameters used in CTFFIND4, which take their default values if not
explicitly configured here. Finally, we can instantiate the <code>ImagePipeline</code> and simulate an image.</p>
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<script id="__config" type="application/json">{"base": ".", "features": ["navigation.sections", "toc.integrate"], "search": "assets/javascripts/workers/search.b8dbb3d2.min.js", "translations": {"clipboard.copied": "Copied to clipboard", "clipboard.copy": "Copy to clipboard", "search.result.more.one": "1 more on this page", "search.result.more.other": "# more on this page", "search.result.none": "No matching documents", "search.result.one": "1 matching document", "search.result.other": "# matching documents", "search.result.placeholder": "Type to start searching", "search.result.term.missing": "Missing", "select.version": "Select version"}}</script>


<script src="assets/javascripts/bundle.bd41221c.min.js"></script>
<script src="assets/javascripts/bundle.1e8ae164.min.js"></script>

<script src="javascripts/mathjax.js"></script>

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