diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index 4aa01d7..34925a2 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2023-12-11T13:46:57","documenter_version":"1.2.1"}} \ No newline at end of file +{"documenter":{"julia_version":"1.9.4","generation_timestamp":"2023-12-11T15:31:00","documenter_version":"1.2.1"}} \ No newline at end of file diff --git a/dev/basicReconstruction.html b/dev/basicReconstruction.html index 590d946..50e50a9 100644 --- a/dev/basicReconstruction.html +++ b/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 = "Kaczmarz", - 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> diff --git a/dev/datasetStore.html b/dev/datasetStore.html index 1ebc5d4..75e1226 100644 --- a/dev/datasetStore.html +++ b/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 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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>. 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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>. 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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="MPIReco.jl"><a class="docs-heading-anchor" href="#MPIReco.jl">MPIReco.jl</a><a id="MPIReco.jl-1"></a><a class="docs-heading-anchor-permalink" href="#MPIReco.jl" title="Permalink"></a></h1><p><em>Julia package for the reconstruction of magnetic particle imaging (MPI) data</em></p><h2 id="Introduction"><a class="docs-heading-anchor" href="#Introduction">Introduction</a><a id="Introduction-1"></a><a class="docs-heading-anchor-permalink" href="#Introduction" title="Permalink"></a></h2><p>This project provides functions for the reconstruction of MPI data. The project is implemented in the programming language Julia and contains algorithms for</p><ul><li><a href="basicReconstruction.html#Basic-Reconstruction">Basic Reconstruction</a> using a system matrix based approach</li><li><a href="multiPatch.html#Multi-Patch-Reconstruction">Multi-Patch Reconstruction</a> for data that has been acquired using a focus field sequence</li><li><a href="multiContrast.html#Multi-Contrast-Reconstruction">Multi-Contrast Reconstruction</a></li><li><a href="matrixCompression.html#Matrix-Compression-Techniques">Matrix-Compression Techniques</a></li></ul><p>Key features are</p><ul><li>Frequency filtering for memory efficient reconstruction. Only frequencies used during reconstructions are loaded into memory.</li><li>Different solvers provided by the package <a href="https://github.com/tknopp/RegularizedLeastSquares.jl">RegularizedLeastSquares.jl</a></li><li>High-level until low-level reconstruction providing maximum flexibility for the user</li><li>Spectral leakage correction (implemented in <a href="https://github.com/MagneticParticleImaging/MPIFiles.jl">MPIFiles.jl</a>)</li></ul><h2 id="Installation"><a class="docs-heading-anchor" href="#Installation">Installation</a><a id="Installation-1"></a><a class="docs-heading-anchor-permalink" href="#Installation" title="Permalink"></a></h2><p>Start julia and open the package mode by entering <code>]</code>. Then enter</p><pre><code class="language-julia hljs">add MPIReco</code></pre><p>This will install the packages <code>MPIReco.jl</code> and all its dependencies. In particular this will install the core dependencies <a href="https://github.com/MagneticParticleImaging/MPIFiles.jl.git">MPIFiles</a> and <a href="https://github.com/tknopp/RegularizedLeastSquares.jl.git">RegularizedLeastSquares</a>.</p><h2 id="License-/-Terms-of-Usage"><a class="docs-heading-anchor" href="#License-/-Terms-of-Usage">License / Terms of Usage</a><a id="License-/-Terms-of-Usage-1"></a><a class="docs-heading-anchor-permalink" href="#License-/-Terms-of-Usage" title="Permalink"></a></h2><p>The source code of this project is licensed under the MIT license. This implies that you are free to use, share, and adapt it. However, please give appropriate credit by citing the project.</p><h2 id="Contact"><a class="docs-heading-anchor" href="#Contact">Contact</a><a id="Contact-1"></a><a class="docs-heading-anchor-permalink" href="#Contact" title="Permalink"></a></h2><p>If you have problems using the software, find mistakes, or have general questions please use the <a href="https://github.com/MagneticParticleImaging/MPIReco.jl/issues">issue tracker</a> to contact us.</p><h2 id="Contributors"><a class="docs-heading-anchor" href="#Contributors">Contributors</a><a id="Contributors-1"></a><a class="docs-heading-anchor-permalink" href="#Contributors" title="Permalink"></a></h2><ul><li><a href="https://www.tuhh.de/ibi/people/tobias-knopp-head-of-institute.html">Tobias Knopp</a></li><li><a href="https://www.tuhh.de/ibi/people/martin-moeddel.html">Martin Möddel</a></li><li><a href="https://www.tuhh.de/ibi/people/patryk-szwargulski.html">Patryk Szwargulski</a></li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="overview.html">Getting Started »</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>. 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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="index.html">Home</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="index.html">Home</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/index.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="MPIReco.jl"><a class="docs-heading-anchor" href="#MPIReco.jl">MPIReco.jl</a><a id="MPIReco.jl-1"></a><a class="docs-heading-anchor-permalink" href="#MPIReco.jl" title="Permalink"></a></h1><p><em>Julia package for the reconstruction of magnetic particle imaging (MPI) data</em></p><h2 id="Introduction"><a class="docs-heading-anchor" href="#Introduction">Introduction</a><a id="Introduction-1"></a><a class="docs-heading-anchor-permalink" href="#Introduction" title="Permalink"></a></h2><p>This project provides functions for the reconstruction of MPI data. The project is implemented in the programming language Julia and contains algorithms for</p><ul><li><a href="basicReconstruction.html#Basic-Reconstruction">Basic Reconstruction</a> using a system matrix based approach</li><li><a href="multiPatch.html#Multi-Patch-Reconstruction">Multi-Patch Reconstruction</a> for data that has been acquired using a focus field sequence</li><li><a href="multiContrast.html#Multi-Contrast-Reconstruction">Multi-Contrast Reconstruction</a></li><li><a href="matrixCompression.html#Matrix-Compression-Techniques">Matrix-Compression Techniques</a></li></ul><p>Key features are</p><ul><li>Frequency filtering for memory efficient reconstruction. Only frequencies used during reconstructions are loaded into memory.</li><li>Different solvers provided by the package <a href="https://github.com/tknopp/RegularizedLeastSquares.jl">RegularizedLeastSquares.jl</a></li><li>High-level until low-level reconstruction providing maximum flexibility for the user</li><li>Spectral leakage correction (implemented in <a href="https://github.com/MagneticParticleImaging/MPIFiles.jl">MPIFiles.jl</a>)</li></ul><h2 id="Installation"><a class="docs-heading-anchor" href="#Installation">Installation</a><a id="Installation-1"></a><a class="docs-heading-anchor-permalink" href="#Installation" title="Permalink"></a></h2><p>Start julia and open the package mode by entering <code>]</code>. Then enter</p><pre><code class="language-julia hljs">add MPIReco</code></pre><p>This will install the packages <code>MPIReco.jl</code> and all its dependencies. In particular this will install the core dependencies <a href="https://github.com/MagneticParticleImaging/MPIFiles.jl.git">MPIFiles</a> and <a href="https://github.com/tknopp/RegularizedLeastSquares.jl.git">RegularizedLeastSquares</a>.</p><h2 id="License-/-Terms-of-Usage"><a class="docs-heading-anchor" href="#License-/-Terms-of-Usage">License / Terms of Usage</a><a id="License-/-Terms-of-Usage-1"></a><a class="docs-heading-anchor-permalink" href="#License-/-Terms-of-Usage" title="Permalink"></a></h2><p>The source code of this project is licensed under the MIT license. This implies that you are free to use, share, and adapt it. However, please give appropriate credit by citing the project.</p><h2 id="Contact"><a class="docs-heading-anchor" href="#Contact">Contact</a><a id="Contact-1"></a><a class="docs-heading-anchor-permalink" href="#Contact" title="Permalink"></a></h2><p>If you have problems using the software, find mistakes, or have general questions please use the <a href="https://github.com/MagneticParticleImaging/MPIReco.jl/issues">issue tracker</a> to contact us.</p><h2 id="Contributors"><a class="docs-heading-anchor" href="#Contributors">Contributors</a><a id="Contributors-1"></a><a class="docs-heading-anchor-permalink" href="#Contributors" title="Permalink"></a></h2><ul><li><a href="https://www.tuhh.de/ibi/people/tobias-knopp-head-of-institute.html">Tobias Knopp</a></li><li><a href="https://www.tuhh.de/ibi/people/martin-moeddel.html">Martin Möddel</a></li><li><a href="https://www.tuhh.de/ibi/people/patryk-szwargulski.html">Patryk Szwargulski</a></li></ul></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="overview.html">Getting Started »</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>. 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href="matrixCompression.html">Compression</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="matrixCompression.html">Compression</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/matrixCompression.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="Matrix-Compression-Techniques"><a class="docs-heading-anchor" href="#Matrix-Compression-Techniques">Matrix-Compression Techniques</a><a id="Matrix-Compression-Techniques-1"></a><a class="docs-heading-anchor-permalink" href="#Matrix-Compression-Techniques" title="Permalink"></a></h1><p>The reconstruction can be accelerated by applying matrix compression. To this end, the system matrix <code>S</code> is transformed into a different domain by applying a basis transformation on the rows of the system matrix. In <code>MPIReco.jl</code>, matrix compression can be enabled by specifying <code>sparseTrafo</code> which can be <code>"DCT-IV"</code> or <code>"FFT"</code>. </p><p>The transformations can be restricted to the drive-field field-of-view by setting <code>useDFFoV = true</code>. The compression factor that controls how many coefficients are dropped after application of the transformation is controlled by the parameter <code>redFactor</code>. For instance a reduction factor of <code>redFactor = 0.01</code> will drop 99 % of the data.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="multiPatch.html">« Multi-Patch</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>. 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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/matrixCompression.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="Matrix-Compression-Techniques"><a class="docs-heading-anchor" href="#Matrix-Compression-Techniques">Matrix-Compression Techniques</a><a id="Matrix-Compression-Techniques-1"></a><a class="docs-heading-anchor-permalink" href="#Matrix-Compression-Techniques" title="Permalink"></a></h1><p>The reconstruction can be accelerated by applying matrix compression. To this end, the system matrix <code>S</code> is transformed into a different domain by applying a basis transformation on the rows of the system matrix. In <code>MPIReco.jl</code>, matrix compression can be enabled by specifying <code>sparseTrafo</code> which can be <code>"DCT-IV"</code> or <code>"FFT"</code>. </p><p>The transformations can be restricted to the drive-field field-of-view by setting <code>useDFFoV = true</code>. The compression factor that controls how many coefficients are dropped after application of the transformation is controlled by the parameter <code>redFactor</code>. For instance a reduction factor of <code>redFactor = 0.01</code> will drop 99 % of the data.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="multiPatch.html">« Multi-Patch</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>. 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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 class="is-active"><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="multiContrast.html">Multi-Contrast</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="multiContrast.html">Multi-Contrast</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/multiContrast.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="Multi-Contrast-Reconstruction"><a class="docs-heading-anchor" href="#Multi-Contrast-Reconstruction">Multi-Contrast Reconstruction</a><a id="Multi-Contrast-Reconstruction-1"></a><a class="docs-heading-anchor-permalink" href="#Multi-Contrast-Reconstruction" title="Permalink"></a></h1><p>Until now we have discussed single-contrast reconstruction in which case the reconstructed image <code>c</code> has a singleton first dimension. To perform multi-contrast reconstruction one has to specify multiple system matrices</p><pre><code class="language-julia hljs">bSFa = MPIFile(filenameA) bSFb = MPIFile(filenameB)</code></pre><p>and can then invoke</p><pre><code class="language-julia hljs">c = reconstruction([bSFa, bSFb], b; SNRThresh=5, frames=1, minFreq=80e3, - recChannels=1:2, iterations=1)</code></pre><p>Now one can access the first and second channel by <code>c[1,:,:,:]</code> and <code>c[2,:,:,:]</code>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="recoResults.html">« Results</a><a class="docs-footer-nextpage" href="multiPatch.html">Multi-Patch »</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> + recChannels=1:2, iterations=1)</code></pre><p>Now one can access the first and second channel by <code>c[1,:,:,:]</code> and <code>c[2,:,:,:]</code>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="recoResults.html">« Results</a><a class="docs-footer-nextpage" href="multiPatch.html">Multi-Patch »</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> diff --git a/dev/multiPatch.html b/dev/multiPatch.html index ff9b03f..7a50485 100644 --- a/dev/multiPatch.html +++ b/dev/multiPatch.html @@ -18,4 +18,4 @@ c4 = reconstruction(bSFs, b; SNRThresh=5, frames=1, minFreq=80e3, recChannels=1:2,iterations=1, spectralLeakageCorrection=false, mapping=mapping, systemMatrices = S, SFGridCenter=SFGridCenter, - FFPos=FFPos, FFPosSF=FFPos)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="multiContrast.html">« Multi-Contrast</a><a class="docs-footer-nextpage" href="matrixCompression.html">Compression »</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> + FFPos=FFPos, FFPosSF=FFPos)</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="multiContrast.html">« Multi-Contrast</a><a class="docs-footer-nextpage" href="matrixCompression.html">Compression »</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> diff --git a/dev/overview.html b/dev/overview.html index 484f495..c36baa2 100644 --- a/dev/overview.html +++ b/dev/overview.html @@ -12,4 +12,4 @@ recChannels=1:2, iterations=1, spectralLeakageCorrection=true) -</code></pre><p>Lets go through that script step by step. First, we create handles for the system matrix and the measurement data. Both are of the type <code>MPIFile</code> which is an abstract type that can for instance be an <code>MDFFile</code> or a <code>BrukerFile</code>.</p><p>Using the handles to the MPI datasets we can call the <code>reconstruction</code> function that has various variants depending on the types that are passed to it. Here, we exploit the multiple dispatch mechanism of julia. In addition to the file handles we also apply several reconstruction parameters using keyword arguments. In this case, we set the SNR threshold to 5 implying that only matrix rows with an SNR above 5 are used during reconstruction. The parameter <code>frame</code> decides which frame of the measured data should be reconstructed.</p><p>The object <code>c</code> is of type <code>ImageMeta</code> and contains not only the reconstructed data but also several metadata such as the reconstruction parameters being used. More details on the return type are discussed in the <a href="recoResults.html#Reconstruction-Results">Reconstruction Results</a></p><h2 id="Data-Storage"><a class="docs-heading-anchor" href="#Data-Storage">Data Storage</a><a id="Data-Storage-1"></a><a class="docs-heading-anchor-permalink" href="#Data-Storage" title="Permalink"></a></h2><p>One can store the reconstruction result into an MDF file by calling</p><pre><code class="language-julia hljs">saveRecoData("filename.mdf", c)</code></pre><p>In order to load the data one calls</p><pre><code class="language-julia hljs">c = loadRecoData("filename.mdf", c)</code></pre><p>We will next take a closer look at different forms of the <code>reconstruction</code> routine.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="index.html">« Home</a><a class="docs-footer-nextpage" href="basicReconstruction.html">Basic Reconstruction »</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> +</code></pre><p>Lets go through that script step by step. First, we create handles for the system matrix and the measurement data. Both are of the type <code>MPIFile</code> which is an abstract type that can for instance be an <code>MDFFile</code> or a <code>BrukerFile</code>.</p><p>Using the handles to the MPI datasets we can call the <code>reconstruction</code> function that has various variants depending on the types that are passed to it. Here, we exploit the multiple dispatch mechanism of julia. In addition to the file handles we also apply several reconstruction parameters using keyword arguments. In this case, we set the SNR threshold to 5 implying that only matrix rows with an SNR above 5 are used during reconstruction. The parameter <code>frame</code> decides which frame of the measured data should be reconstructed.</p><p>The object <code>c</code> is of type <code>ImageMeta</code> and contains not only the reconstructed data but also several metadata such as the reconstruction parameters being used. More details on the return type are discussed in the <a href="recoResults.html#Reconstruction-Results">Reconstruction Results</a></p><h2 id="Data-Storage"><a class="docs-heading-anchor" href="#Data-Storage">Data Storage</a><a id="Data-Storage-1"></a><a class="docs-heading-anchor-permalink" href="#Data-Storage" title="Permalink"></a></h2><p>One can store the reconstruction result into an MDF file by calling</p><pre><code class="language-julia hljs">saveRecoData("filename.mdf", c)</code></pre><p>In order to load the data one calls</p><pre><code class="language-julia hljs">c = loadRecoData("filename.mdf", c)</code></pre><p>We will next take a closer look at different forms of the <code>reconstruction</code> routine.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="index.html">« Home</a><a class="docs-footer-nextpage" href="basicReconstruction.html">Basic Reconstruction »</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>. 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href="recoResults.html">Results</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="recoResults.html">Results</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/recoResults.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="Reconstruction-Results"><a class="docs-heading-anchor" href="#Reconstruction-Results">Reconstruction Results</a><a id="Reconstruction-Results-1"></a><a class="docs-heading-anchor-permalink" href="#Reconstruction-Results" title="Permalink"></a></h1><p>The object <code>c</code> is of type <code>ImageMeta</code> and contains not only the reconstructed data but also several metadata such as the reconstruction parameters being used. c has in total 5 dimensions. The first dimension encodes multi-spectral channels. Dimensions 2-4 encode the three spatial dimensions. 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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/recoResults.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="Reconstruction-Results"><a class="docs-heading-anchor" href="#Reconstruction-Results">Reconstruction Results</a><a id="Reconstruction-Results-1"></a><a class="docs-heading-anchor-permalink" href="#Reconstruction-Results" title="Permalink"></a></h1><p>The object <code>c</code> is of type <code>ImageMeta</code> and contains not only the reconstructed data but also several metadata such as the reconstruction parameters being used. c has in total 5 dimensions. The first dimension encodes multi-spectral channels. Dimensions 2-4 encode the three spatial dimensions. 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