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Documenter.jl committed Apr 2, 2024
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2 changes: 1 addition & 1 deletion dev/.documenter-siteinfo.json
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{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-03-27T08:59:14","documenter_version":"1.3.0"}}
{"documenter":{"julia_version":"1.10.2","generation_timestamp":"2024-04-02T16:57:32","documenter_version":"1.3.0"}}
2 changes: 1 addition & 1 deletion dev/conversion.html
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<!DOCTYPE html>
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Conversion · MPI Files</title><meta name="title" content="Conversion · MPI Files"/><meta property="og:title" content="Conversion · MPI Files"/><meta property="twitter:title" content="Conversion · MPI Files"/><meta name="description" content="Documentation for MPI Files."/><meta property="og:description" content="Documentation for MPI Files."/><meta property="twitter:description" content="Documentation for MPI Files."/><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="search_index.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="index.html"><img src="assets/logo.png" alt="MPI Files logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="index.html">MPI Files</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li><a class="tocitem" href="index.html">Home</a></li><li><a class="tocitem" href="gettingStarted.html">Getting Started</a></li><li><a class="tocitem" href="lowlevel.html">Low Level Interface</a></li><li class="is-active"><a class="tocitem" href="conversion.html">Conversion</a></li><li><a class="tocitem" href="measurements.html">Measurements</a></li><li><a class="tocitem" href="systemmatrix.html">System Matrices</a></li><li><a class="tocitem" href="frequencyFilter.html">Frequency Filter</a></li><li><a class="tocitem" href="reconstruction.html">Reconstruction Results</a></li><li><a class="tocitem" href="transferfunction.html">Transfer Functions</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href="conversion.html">Conversion</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="conversion.html">Conversion</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/MagneticParticleImaging/MPIFiles.jl" title="View the repository on GitHub"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">GitHub</span></a><a class="docs-navbar-link" href="https://github.com/MagneticParticleImaging/MPIFiles.jl/blob/master/docs/src/conversion.md" title="Edit source on GitHub"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="Conversion"><a class="docs-heading-anchor" href="#Conversion">Conversion</a><a id="Conversion-1"></a><a class="docs-heading-anchor-permalink" href="#Conversion" title="Permalink"></a></h1><p>With the support for reading different file formats and the ability to store data in the MDF, it is also possible to convert files into MDF. This can be done by calling</p><pre><code class="language-julia hljs">saveasMDF(filenameOut, filenameIn)</code></pre><p>The second argument can alternatively also be an <code>MPIFile</code> handle.</p><p>Alternatively, there is also a more low level interface which gives the user the control to change parameters before storing. This look like this</p><pre><code class="language-julia hljs">params = loadDataset(f)
# do something with params
saveasMDF(filenameOut, params)</code></pre><p>Here, <code>f</code> is an <code>MPIFile</code> handle and the command <code>loadDataset</code> loads the entire dataset including all parameters into a Julia <code>Dict</code>, which can be modified by the user. After modification one can store the data by passing the <code>Dict</code> as the second argument to the <code>saveasMDF</code> function.</p><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>The parameters in the <code>Dict</code> returned by <code>loadDataset</code> have the same keys as the corresponding accessor functions listed in the <a href="lowlevel.html#Low-Level-Interface">Low Level Interface</a>.</p></div></div></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="lowlevel.html">« Low Level Interface</a><a class="docs-footer-nextpage" href="measurements.html">Measurements »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.3.0 on <span class="colophon-date" title="Wednesday 27 March 2024 08:59">Wednesday 27 March 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
saveasMDF(filenameOut, params)</code></pre><p>Here, <code>f</code> is an <code>MPIFile</code> handle and the command <code>loadDataset</code> loads the entire dataset including all parameters into a Julia <code>Dict</code>, which can be modified by the user. After modification one can store the data by passing the <code>Dict</code> as the second argument to the <code>saveasMDF</code> function.</p><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>The parameters in the <code>Dict</code> returned by <code>loadDataset</code> have the same keys as the corresponding accessor functions listed in the <a href="lowlevel.html#Low-Level-Interface">Low Level Interface</a>.</p></div></div></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="lowlevel.html">« Low Level Interface</a><a class="docs-footer-nextpage" href="measurements.html">Measurements »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.3.0 on <span class="colophon-date" title="Tuesday 2 April 2024 16:57">Tuesday 2 April 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
2 changes: 1 addition & 1 deletion dev/frequencyFilter.html
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numUsedFreqs=-1,
stepsize=1,
maxMixingOrder=-1,
sortByMixFactors=false)</code></pre><p>Usually one will apply an SNR threshold <code>SNRThresh &gt; 1.5</code> and a <code>minFreq</code> that is larger than the excitation frequencies. The frequencies are specified in Hz. Also useful is the opportunity to select specific receive channels by specifying <code>recChannels</code>.</p><p>The return value of <code>filterFrequencies</code> is of type <code>Vector{Int64}</code> and can be directly passed to <code>getMeasurements</code>, <code>getMeasurementsFD</code>, and <code>getSystemMatrix</code>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="systemmatrix.html">« System Matrices</a><a class="docs-footer-nextpage" href="reconstruction.html">Reconstruction Results »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.3.0 on <span class="colophon-date" title="Wednesday 27 March 2024 08:59">Wednesday 27 March 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
sortByMixFactors=false)</code></pre><p>Usually one will apply an SNR threshold <code>SNRThresh &gt; 1.5</code> and a <code>minFreq</code> that is larger than the excitation frequencies. The frequencies are specified in Hz. Also useful is the opportunity to select specific receive channels by specifying <code>recChannels</code>.</p><p>The return value of <code>filterFrequencies</code> is of type <code>Vector{Int64}</code> and can be directly passed to <code>getMeasurements</code>, <code>getMeasurementsFD</code>, and <code>getSystemMatrix</code>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="systemmatrix.html">« System Matrices</a><a class="docs-footer-nextpage" href="reconstruction.html">Reconstruction Results »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.3.0 on <span class="colophon-date" title="Tuesday 2 April 2024 16:57">Tuesday 2 April 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
2 changes: 1 addition & 1 deletion dev/gettingStarted.html
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[:, :, 1] =
0.014 0.014 0.0</code></pre><p>Now let us load some measurement data. This can be done by calling</p><pre><code class="language-julia hljs">u = getMeasurementsFD(f, frames=1:100, numAverages=100)</code></pre><p>Then we can display the data using the PyPlot package</p><pre><code class="language-julia hljs">using PyPlot
figure(6, figsize=(6,4))
semilogy(abs.(u[1:400,1,1,1]))</code></pre><p><img src="assets/spectrum1.png" alt="Spectrum"/></p><p>This shows a typical spectrum for a 2D Lissajous sampling pattern. The <code>getMeasurementsFD</code> is a high level interface for loading MPI data, which has several parameters that allow to customize the loading process. Details on loading measurement data are outlined in <a href="measurements.html#Measurements">Measurements</a>.</p><p>In the following we will first discuss the low level interface.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="index.html">« Home</a><a class="docs-footer-nextpage" href="lowlevel.html">Low Level Interface »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.3.0 on <span class="colophon-date" title="Wednesday 27 March 2024 08:59">Wednesday 27 March 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
semilogy(abs.(u[1:400,1,1,1]))</code></pre><p><img src="assets/spectrum1.png" alt="Spectrum"/></p><p>This shows a typical spectrum for a 2D Lissajous sampling pattern. The <code>getMeasurementsFD</code> is a high level interface for loading MPI data, which has several parameters that allow to customize the loading process. Details on loading measurement data are outlined in <a href="measurements.html#Measurements">Measurements</a>.</p><p>In the following we will first discuss the low level interface.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="index.html">« Home</a><a class="docs-footer-nextpage" href="lowlevel.html">Low Level Interface »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.3.0 on <span class="colophon-date" title="Tuesday 2 April 2024 16:57">Tuesday 2 April 2024</span>. Using Julia version 1.10.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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