build based on 80bfc86

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2023-12-11T13:46:57","documenter_version":"1.2.1"}}
+{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2023-12-11T15:31:00","documenter_version":"1.2.1"}}

dev/basicReconstruction.html

@@ -16,4 +16,4 @@
   spectralCleaning=true, fgFrames=1:10, bgCorrectionInternal=false,
   noiseFreqThresh=0.0, kargs...)</code></pre><p>This function is responsible for loading the measurement data and potential background data that is subtracted from the measurements. For any frame to be reconstructed, the low level reconstruction routine is called.</p><h2 id="Low-Level-Reconstruction"><a class="docs-heading-anchor" href="#Low-Level-Reconstruction">Low Level Reconstruction</a><a id="Low-Level-Reconstruction-1"></a><a class="docs-heading-anchor-permalink" href="#Low-Level-Reconstruction" title="Permalink"></a></h2><p>Finally, we have arrived at the low level reconstruction routine that has the signature</p><pre><code class="language-julia hljs">function reconstruction(S, u::Array; sparseTrafo = nothing,
                         lambd=0, progress=nothing, solver = &quot;Kaczmarz&quot;,
-                        weights=nothing, kargs...)</code></pre><p>One can see that it requires the system matrix <code>S</code> and the measurements <code>u</code> to be already loaded.</p><p>We note that <code>S</code> is typeless for a reason here. For a regular reconstruction one will basically feed in an <code>Array{ComplexF32,2}</code> in here, although more precisely it will be a <code>Transposed</code> version of that type if the <code>Kaczmarz</code> algorithm is being used for efficiency reasons.</p><p>However, in case that matrix compression is applied <code>S</code> will be of type <code>SparseMatrixCSC</code>. And for <a href="multiPatch.html#Multi-Patch-Reconstruction">Multi-Patch Reconstruction</a> <code>S</code> will be of type <code>MultiPatchOperator</code>. Hence, the solvers are implemented in a very generic way and require only certain functions to be implemented. The low level reconstruction method calls one of the solvers from <a href="https://github.com/tknopp/RegularizedLeastSquares.jl">RegularizedLeastSquares.jl</a>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="overview.html">« Getting Started</a><a class="docs-footer-nextpage" href="parameters.html">Parameters »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Monday 11 December 2023 13:46">Monday 11 December 2023</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+                        weights=nothing, kargs...)</code></pre><p>One can see that it requires the system matrix <code>S</code> and the measurements <code>u</code> to be already loaded.</p><p>We note that <code>S</code> is typeless for a reason here. For a regular reconstruction one will basically feed in an <code>Array{ComplexF32,2}</code> in here, although more precisely it will be a <code>Transposed</code> version of that type if the <code>Kaczmarz</code> algorithm is being used for efficiency reasons.</p><p>However, in case that matrix compression is applied <code>S</code> will be of type <code>SparseMatrixCSC</code>. And for <a href="multiPatch.html#Multi-Patch-Reconstruction">Multi-Patch Reconstruction</a> <code>S</code> will be of type <code>MultiPatchOperator</code>. Hence, the solvers are implemented in a very generic way and require only certain functions to be implemented. The low level reconstruction method calls one of the solvers from <a href="https://github.com/tknopp/RegularizedLeastSquares.jl">RegularizedLeastSquares.jl</a>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="overview.html">« Getting Started</a><a class="docs-footer-nextpage" href="parameters.html">Parameters »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Monday 11 December 2023 15:31">Monday 11 December 2023</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/datasetStore.html

@@ -1,2 +1,2 @@
 <!DOCTYPE html>
-<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>- · MPI Reconstruction</title><meta name="title" content="- · MPI Reconstruction"/><meta property="og:title" content="- · MPI Reconstruction"/><meta property="twitter:title" content="- · MPI Reconstruction"/><meta name="description" content="Documentation for MPI Reconstruction."/><meta property="og:description" content="Documentation for MPI Reconstruction."/><meta property="twitter:description" content="Documentation for MPI Reconstruction."/><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 Reconstruction logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="index.html">MPI Reconstruction</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="overview.html">Getting Started</a></li><li><a class="tocitem" href="basicReconstruction.html">Basic Reconstruction</a></li><li><a class="tocitem" href="parameters.html">Parameters</a></li><li><a class="tocitem" href="recoResults.html">Results</a></li><li><a class="tocitem" href="multiContrast.html">Multi-Contrast</a></li><li><a class="tocitem" href="multiPatch.html">Multi-Patch</a></li><li><a class="tocitem" href="matrixCompression.html">Compression</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="datasetStore.html">-</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="datasetStore.html">-</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/MagneticParticleImaging/MPIReco.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/MPIReco.jl/blob/master/docs/src/datasetStore.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"><h2 id="Layers"><a class="docs-heading-anchor" href="#Layers">Layers</a><a id="Layers-1"></a><a class="docs-heading-anchor-permalink" href="#Layers" title="Permalink"></a></h2><p>The <code>reconstruction</code> function has several layers starting from a high level over several middle layer to low layer functions. The most high level method has the following signature `<span>$julia reconstruction(d::MDFDatasetStore, study::Study, exp::Experiment, recoParams::Dict{String,Any})$</span></p></article><nav class="docs-footer"><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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Monday 11 December 2023 13:46">Monday 11 December 2023</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>- · MPI Reconstruction</title><meta name="title" content="- · MPI Reconstruction"/><meta property="og:title" content="- · MPI Reconstruction"/><meta property="twitter:title" content="- · MPI Reconstruction"/><meta name="description" content="Documentation for MPI Reconstruction."/><meta property="og:description" content="Documentation for MPI Reconstruction."/><meta property="twitter:description" content="Documentation for MPI Reconstruction."/><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 Reconstruction logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="index.html">MPI Reconstruction</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="overview.html">Getting Started</a></li><li><a class="tocitem" href="basicReconstruction.html">Basic Reconstruction</a></li><li><a class="tocitem" href="parameters.html">Parameters</a></li><li><a class="tocitem" href="recoResults.html">Results</a></li><li><a class="tocitem" href="multiContrast.html">Multi-Contrast</a></li><li><a class="tocitem" href="multiPatch.html">Multi-Patch</a></li><li><a class="tocitem" href="matrixCompression.html">Compression</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="datasetStore.html">-</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="datasetStore.html">-</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://github.com/MagneticParticleImaging/MPIReco.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/MPIReco.jl/blob/master/docs/src/datasetStore.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"><h2 id="Layers"><a class="docs-heading-anchor" href="#Layers">Layers</a><a id="Layers-1"></a><a class="docs-heading-anchor-permalink" href="#Layers" title="Permalink"></a></h2><p>The <code>reconstruction</code> function has several layers starting from a high level over several middle layer to low layer functions. The most high level method has the following signature `<span>$julia reconstruction(d::MDFDatasetStore, study::Study, exp::Experiment, recoParams::Dict{String,Any})$</span></p></article><nav class="docs-footer"><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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.2.1 on <span class="colophon-date" title="Monday 11 December 2023 15:30">Monday 11 December 2023</span>. Using Julia version 1.9.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>