build based on 8a60db9

dev/SENSE/index.html

@@ -31,4 +31,4 @@
 
 # do reconstruction
 Ireco = reconstruction(acqData, params)
-</code></pre><p>Below one can see the orignal phantom on the left and the reconstruction on the right:</p><p><img src="../assets/phantom.png" alt="Phantom"/> <img src="../assets/senseReco.png" alt="Reconstruction"/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../offresonance/">« Offresonance</a><a class="docs-footer-nextpage" href="../compressedSensing/">Compressed Sensing »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Wednesday 12 July 2023 07:29">Wednesday 12 July 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+</code></pre><p>Below one can see the orignal phantom on the left and the reconstruction on the right:</p><p><img src="../assets/phantom.png" alt="Phantom"/> <img src="../assets/senseReco.png" alt="Reconstruction"/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../offresonance/">« Offresonance</a><a class="docs-footer-nextpage" href="../compressedSensing/">Compressed Sensing »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Wednesday 12 July 2023 07:30">Wednesday 12 July 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/acquisitionData/index.html

@@ -13,4 +13,4 @@
  subsampleIndices::Vector{Array{Int64}}
  encodingSize::Vector{Int64}
  fov::Vector{Float64}
-end</code></pre><p>It consists of the sequence informations stored in a dictionary, the k-space trajectory, the k-space data, and several parameters describing the dimension of the data and some additional index vectors.</p><p>The k-space data <code>kdata</code> has three dimensions encoding</p><ol><li>dim : contrasts/echoes</li><li>dim : slices</li><li>dim : repetitions</li></ol><p>Each element is a matrix encoding</p><ol><li>dim : k-space nodes</li><li>dim : channels/coils</li></ol><p>In case of undersampled data, the subsampling indices are stored in <code>subsampleIndices</code>. One check if the data is undersampled by checking if <code>isempty(subsampleIndices)</code>.</p><p>The encoded space is stored in the field <code>encodingSize</code>. It is especially relevant for non-Cartesian trajectories where it is not clear upfront, how large the grid size for reconstruction should be chosen. Finally <code>fov</code> describes the physical lengths of the encoding grid.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../overview/">« Overview</a><a class="docs-footer-nextpage" href="../filehandling/">File Handling »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Wednesday 12 July 2023 07:29">Wednesday 12 July 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+end</code></pre><p>It consists of the sequence informations stored in a dictionary, the k-space trajectory, the k-space data, and several parameters describing the dimension of the data and some additional index vectors.</p><p>The k-space data <code>kdata</code> has three dimensions encoding</p><ol><li>dim : contrasts/echoes</li><li>dim : slices</li><li>dim : repetitions</li></ol><p>Each element is a matrix encoding</p><ol><li>dim : k-space nodes</li><li>dim : channels/coils</li></ol><p>In case of undersampled data, the subsampling indices are stored in <code>subsampleIndices</code>. One check if the data is undersampled by checking if <code>isempty(subsampleIndices)</code>.</p><p>The encoded space is stored in the field <code>encodingSize</code>. It is especially relevant for non-Cartesian trajectories where it is not clear upfront, how large the grid size for reconstruction should be chosen. Finally <code>fov</code> describes the physical lengths of the encoding grid.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../overview/">« Overview</a><a class="docs-footer-nextpage" href="../filehandling/">File Handling »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Wednesday 12 July 2023 07:30">Wednesday 12 July 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/compressedSensing/index.html

@@ -36,4 +36,4 @@
 params[:tolInner] = 1.e-2
 params[:normalizeReg] = true
 
-img_tv = reconstruction(acqDataSub, params)</code></pre><p>Lets compare the results, left the regular SENSE reconstruction and right the TV reglarized solution:</p><p><img src="../assets/kneeCG.png" alt="SENSE"/> <img src="../assets/kneeTV.png" alt="TV"/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../SENSE/">« Parallel Imaging</a><a class="docs-footer-nextpage" href="../custom/">Customize »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Wednesday 12 July 2023 07:29">Wednesday 12 July 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+img_tv = reconstruction(acqDataSub, params)</code></pre><p>Lets compare the results, left the regular SENSE reconstruction and right the TV reglarized solution:</p><p><img src="../assets/kneeCG.png" alt="SENSE"/> <img src="../assets/kneeTV.png" alt="TV"/></p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../SENSE/">« Parallel Imaging</a><a class="docs-footer-nextpage" href="../custom/">Customize »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Wednesday 12 July 2023 07:30">Wednesday 12 July 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/custom/index.html

@@ -64,4 +64,4 @@
 img_d = reconstruction(acqData,params)</code></pre><p>For comparison, let us perform the same reconstruction as above but with a Wavelet transform</p><pre><code class="language-julia">delete!(params, :sparseTrafo)
 params[:sparseTrafoName] = &quot;Wavelet&quot;
 
-img_w = reconstruction(acqData,params)</code></pre><p>The following pictures shows the wavelet based CS reconstruction on the left and the dictionary based CS reconstruction on the right:</p><p><img src="../assets/brainWavelet.png" alt="BrainWavelet"/> <img src="../assets/brainDict.png" alt="BrainDict"/></p><p>For reference, the original data is shown here:</p><p><img src="../assets/brainOrig.png" alt="BrainOrig"/></p><p>One can clearly see that the dictionary approach performs better than a simple Wavelet L1 prior.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../compressedSensing/">« Compressed Sensing</a><a class="docs-footer-nextpage" href="../generated/examples/01-binning/">Binning »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Wednesday 12 July 2023 07:29">Wednesday 12 July 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+img_w = reconstruction(acqData,params)</code></pre><p>The following pictures shows the wavelet based CS reconstruction on the left and the dictionary based CS reconstruction on the right:</p><p><img src="../assets/brainWavelet.png" alt="BrainWavelet"/> <img src="../assets/brainDict.png" alt="BrainDict"/></p><p>For reference, the original data is shown here:</p><p><img src="../assets/brainOrig.png" alt="BrainOrig"/></p><p>One can clearly see that the dictionary approach performs better than a simple Wavelet L1 prior.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../compressedSensing/">« Compressed Sensing</a><a class="docs-footer-nextpage" href="../generated/examples/01-binning/">Binning »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Wednesday 12 July 2023 07:30">Wednesday 12 July 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/filehandling/index.html

@@ -9,4 +9,4 @@
 save(fout, raw)</code></pre><p>which will generate an ISMRMRD file containing the data.</p><h2 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></h2><p>It should now be no surprise that MRIReco.jl does also allow for file conversion:</p><pre><code class="language-julia">f = BrukerFile(&quot;brukerfileCart&quot;)
 raw = RawAcquisitionData(f)
 fout = ISMRMRDFile(&quot;outputfile.h5&quot;)
-save(fout, raw)</code></pre><p>Currently, this is only limited to converting Bruker files into ISMRMRD files but the infrastructure is not limited to that.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../acquisitionData/">« Acquisition Data</a><a class="docs-footer-nextpage" href="../image/">Images »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Wednesday 12 July 2023 07:29">Wednesday 12 July 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+save(fout, raw)</code></pre><p>Currently, this is only limited to converting Bruker files into ISMRMRD files but the infrastructure is not limited to that.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../acquisitionData/">« Acquisition Data</a><a class="docs-footer-nextpage" href="../image/">Images »</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></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> on <span class="colophon-date" title="Wednesday 12 July 2023 07:30">Wednesday 12 July 2023</span>. Using Julia version 1.9.2.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>