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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/ismrmrd">Debian Med / ismrmrd</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ismrmrd/-/commit/cbc6808c2860f5d9913f598cdcfe8e1adba1a4be">cbc6808c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2022-04-10T08:05:16+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.8.0</pre>
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<h4>29 changed files:</h4>
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.github/workflows/ismrmrd_matlab.yml
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<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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README.md
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doc/xml.rst
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examples/matlab/test_create_dataset.m
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examples/matlab/create_dataset.m
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examples/matlab/test_create_undersampled_dataset.m
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examples/matlab/create_undersampled_dataset.m
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examples/matlab/test_recon_dataset.m
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examples/matlab/recon_dataset.m
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include/ismrmrd/meta.h
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include/ismrmrd/xml.h
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libsrc/xml.cpp
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matlab/+ismrmrd/+xml/deserialize.m
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matlab/+ismrmrd/+xml/serialize.m
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matlab/test/xml/ismrmrd_example.xml
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schema/ismrmrd.xsd
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schema/ismrmrd_example_extended.xml
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<h4>Changes:</h4>
<li id="3afbd7ab3cb23d108a1b63a98d419788eb2f2657">
<a href="https://salsa.debian.org/med-team/ismrmrd/-/commit/cbc6808c2860f5d9913f598cdcfe8e1adba1a4be#3afbd7ab3cb23d108a1b63a98d419788eb2f2657"><strong>.github/workflows/ismrmrd_matlab.yml</strong></a>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Matlab</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml"> <span class="na" style="color: #008080;">runs-on</span><span class="pi">:</span> <span class="s" style="color: #d14;">ubuntu-latest</span></span>
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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">actions/checkout@v2</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Set up MATLAB</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">matlab-actions/setup-matlab@v1</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Run tests and generate artifacts</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="na" style="color: #008080;">uses</span><span class="pi">:</span> <span class="s" style="color: #d14;">matlab-actions/run-tests@v1</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="na" style="color: #008080;">with</span><span class="pi">:</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="na" style="color: #008080;">test-results-junit</span><span class="pi">:</span> <span class="s" style="color: #d14;">test-results/results.xml</span></span>
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24
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="na" style="color: #008080;">source-folder</span><span class="pi">:</span> <span class="s" style="color: #d14;">matlab</span></span></pre></td>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/ismrmrd/-/commit/cbc6808c2860f5d9913f598cdcfe8e1adba1a4be#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -80,12 +80,12 @@ endif ()</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC80" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#in the utility libraries, that don't affect the data format itself.</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC81" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;"># For more information see http://semver.org/</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC82" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>ISMRMRD_VERSION_MAJOR 1<span class="p">)</span></span>
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83
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC83" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>ISMRMRD_VERSION_MINOR <span class="idiff left right deletion">7</span><span class="p">)</span></span>
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84
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC84" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>ISMRMRD_VERSION_PATCH <span class="idiff left right deletion">1</span><span class="p">)</span></span>
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83
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC83" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>ISMRMRD_VERSION_MINOR <span class="idiff left right addition">8</span><span class="p">)</span></span>
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84
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC84" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>ISMRMRD_VERSION_PATCH <span class="idiff left right addition">0</span><span class="p">)</span></span>
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85
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC85" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>ISMRMRD_VERSION_STRING <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">ISMRMRD_VERSION_MAJOR</span><span class="si" style="color: #d14;">}</span>.<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">ISMRMRD_VERSION_MINOR</span><span class="si" style="color: #d14;">}</span>.<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">ISMRMRD_VERSION_PATCH</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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86
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86
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC86" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>ISMRMRD_SOVERSION <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">ISMRMRD_VERSION_MAJOR</span><span class="si" style="color: #d14;">}</span>.<span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">ISMRMRD_VERSION_MINOR</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC87" class="line" lang="cmake"></span>
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<td class="new_line diff-line-num old" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC88" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>ISMRMRD_XML_SCHEMA_SHA1 <span class="s2" style="color: #d14;">"<span class="idiff left right deletion">9f159b9cc0bbca2fefbbd059701d931426ed7176</span>"</span><span class="p">)</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC88" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">set</span><span class="p">(</span>ISMRMRD_XML_SCHEMA_SHA1 <span class="s2" style="color: #d14;">"<span class="idiff left right addition">5464ea590ded027471b0740bba7472c4919b895b</span>"</span><span class="p">)</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC89" class="line" lang="cmake"></span>
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90
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC90" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#Remove line breaks and white space that does not change the meaning of the schema</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC91" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">file</span><span class="p">(</span>STRINGS <span class="si" style="color: #d14;">${</span><span class="nv" style="color: #008080;">CMAKE_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/schema/ismrmrd.xsd SCHEMA_STRINGS<span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">#Read all strings from file</span></span>
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<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/ismrmrd/-/commit/cbc6808c2860f5d9913f598cdcfe8e1adba1a4be#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,288 +8,4 @@ Inati SJ, Naegele JD, Zwart NR, Roopchansingh V, Lizak MJ, Hansen DC, Liu CY, At</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown">Please cite this paper if you use the format.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Build instructions</span></span>
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown">The ISMRM Raw Data format is described by an XML schema and some C-style structs with fixed memory layout and as such does not have dependencies. However, it uses HDF5 files for storage and a C++ library for reading and writing the ISMRMRD files is included in this distribution. Furthermore, since the XML header is defined with an XML schema, we encourage using XML data binding when writing software using the format. To compile all components of this distribution you need:</span>
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown"><span class="p">*</span> HDF5 (version 1.8 or higher) libraries. Available from http://www.hdfgroup.org/downloads/index.html.</span>
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown"><span class="p">*</span> Boost (http://www.boost.org/)</span>
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown"><span class="p">*</span> Cmake build tool (http://www.cmake.org/)</span>
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17
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC17" class="line" lang="markdown"><span class="p">*</span> Git if you would like to use the source code archive (http://git-scm.com/)</span>
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown"><span class="p">*</span> FFTW if you would like to compile some of the example applications</span>
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC19" class="line" lang="markdown"> (http://www.fftw.org)</span>
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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC20" class="line" lang="markdown"><span class="p">*</span> Doxygen if you would like to generate API documentation (http://www.doxygen.org)</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC21" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num old" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown"><span class="gt" style="color: #a00;">> It is only necessary to install the dependencies if you wish to develop compiled C/C++ software, which uses the ISMRMRD format. The format can be read in Matlab or Python without installing any additional software.</span></span>
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23
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC23" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Linux installation</span></span>
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC26" class="line" lang="markdown">The dependencies mentioned above should be included in most linux distributions. On Ubuntu you can install all required dependencies with::</span>
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC27" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num old" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC28" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<td class="old_line diff-line-num old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC29" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">sudo </span>apt-get <span class="nt" style="color: #000080;">-y</span> <span class="nb" style="color: #0086b3;">install </span>doxygen git-core graphviz libboost-all-dev libfftw3-dev libhdf5-serial-dev</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC30" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC31" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown">After installation of dependencies, the library can be installed with:</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC33" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC35" class="line" lang="markdown">git clone https://github.com/ismrmrd/ismrmrd</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC36" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd </span>ismrmrd/</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC37" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">mkdir </span>build</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC38" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd </span>build</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC39" class="line" lang="markdown">cmake ../</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC40" class="line" lang="markdown">make</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC41" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">sudo </span>make <span class="nb" style="color: #0086b3;">install</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC42" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC43" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC44" class="line" lang="markdown">This will install the library in <span class="sb" style="color: #d14;">`/usr/local/`</span> by default. To specify</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC45" class="line" lang="markdown">an alternative installation directory, pass <span class="sb" style="color: #d14;">`-D CMAKE_INSTALL_PREFIX=<install dir>`</span> to <span class="sb" style="color: #d14;">`cmake`</span>.</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC46" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC47" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Format Details</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC48" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC49" class="line" lang="markdown">The raw data format combines a mix of flexible data structures (XML header) and fixed structures (equivalent to C-structs). A raw data set consist mainly of 2 sections:</span>
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50
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC50" class="line" lang="markdown"></span>
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51
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC51" class="line" lang="markdown"><span class="p">1.</span> A flexible XML format document that can contain an arbitrary number of fields and accommodate everything from simple values (b-values, etc.) to entire vendor protocols, etc. This purpose of this XML document is to provide parameters that may be meaningful for some experiments but not for others. This XML format is defined by an XML Schema Definition file <span class="p">[</span><span class="nv" style="color: #008080;">`schema/ismrmrd.xsd`</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/ismrmrd/ismrmrd/blob/master/schema/ismrmrd.xsd</span><span class="p">)</span>.</span>
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52
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC52" class="line" lang="markdown"><span class="p">2.</span> Raw data section. This section contains all the acquired data in the experiment. Each data item is preceded by a C-struct with encoding numbers, etc. Following this data header is a channel header and data for each acquired channel. The raw data headers are defined in a C/C++ header file <span class="p">[</span><span class="nv" style="color: #008080;">`ismrmrd.h`</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/ismrmrd/ismrmrd/blob/master/include/ismrmrd/ismrmrd.h</span><span class="p">)</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC53" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC54" class="line" lang="markdown">In addition to these sections, the ISMRMRD format also specifies an image header for storing reconstructed images and the accompanying C++ library provides a convenient way of writing such images into HDF5 files along with generic arrays for storing less well defined data structures, e.g. coil sensitivity maps or other calibration data.</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC55" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC56" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Flexible Data Header</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC57" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC58" class="line" lang="markdown">The flexible data structure is defined by the xml schema definition in <span class="p">[</span><span class="nv" style="color: #008080;">`schema/ismrmrd.xsd`</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/ismrmrd/ismrmrd/blob/master/schema/ismrmrd.xsd</span><span class="p">)</span>. An example of an XML file for a Cartesian 3D acquisition can be found <span class="p">[</span><span class="nv" style="color: #008080;">`schema/ismrmrd_example.xml`</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/ismrmrd/ismrmrd/blob/master/schema/ismrmrd_example.xml</span><span class="p">)</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC60" class="line" lang="markdown">The most critical elements for image reconstruction are contained in the <span class="sb" style="color: #d14;">`<encoding>`</span> section of the document, which describes the encoded spaced and also the target reconstructed space. Along with the <span class="sb" style="color: #d14;">`<encodingLimits>`</span> this section allows the reconstruction program to determine matrix sizes, oversampling factors, partial Fourier, etc. In the example above, data is acquired with two-fold oversampling in the read-out (<span class="sb" style="color: #d14;">`x`</span>) direction, which is reflected in the larger matrix size in the encoded space compared to the reconstruction space. The field of view is also twice as large in the encoded space. For the first phase encoding dimension (<span class="sb" style="color: #d14;">`y`</span>), we have a combination of oversampling (20%), reduced phase resolution (only 83 lines of k-space acquired, and partial Fourier sampling, which is reflected in the asymmetric center of the encoding limits of the <span class="sb" style="color: #d14;">`<kspace_encoding_step_1>`</span>. Specifically, the data lines would be placed into the encoding space like this:</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC64" class="line" lang="markdown"> |-------------------------------------|-------------------------------------------|</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC65" class="line" lang="markdown"> ****************************************************</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC66" class="line" lang="markdown"> ^ ^ ^</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC70" class="line" lang="markdown">After FFT, only the central 116 lines are kept, i.e. there is a reduced field of view in the phase encoding direction. Center and encoding limits for the readout dimension is not given in the XML header. This is to accommodate sequences where the center of the readout may change from readout to readout (alternating directions of readout). There is a field on the individual data headers (see below) to indicate the center of the readout.</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC72" class="line" lang="markdown">An experiment can have multiple encoding spaces and it is possible to indicate on each acquired data readout, which encoding space the data belongs to (see below).</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC74" class="line" lang="markdown">In addition to the defined field in the xml header, it is possible to add an arbitrary number of user defined parameters to accommodate special sequence parameters. Please consult the xml schema_ to see how user parameters are defined. Briefly, the XML header can have a section at the end which looks like:</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC77" class="line" lang="markdown"><span class="nt" style="color: #000080;"><userParameters></span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC78" class="line" lang="markdown"> <span class="nt" style="color: #000080;"><userParameterLong></span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC79" class="line" lang="markdown"> <span class="nt" style="color: #000080;"><name></span>MyVar1<span class="nt" style="color: #000080;"></name><value></span>1003<span class="nt" style="color: #000080;"></value></span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC82" class="line" lang="markdown"> <span class="nt" style="color: #000080;"><name></span>MyVar2<span class="nt" style="color: #000080;"></name><value></span>1999<span class="nt" style="color: #000080;"></value></span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC88" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC90" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Fixed Data structures</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC91" class="line" lang="markdown">Each raw data acquisition is preceded by the following fixed layout structures in <span class="p">[</span><span class="nv" style="color: #008080;">`ismrmrd.h`</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/ismrmrd/ismrmrd/blob/master/include/ismrmrd/ismrmrd.h#L225</span><span class="p">)</span>.</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC93" class="line" lang="markdown">The interpretation of some of these fields may vary from sequence to sequence, i.e. for a Cartesian sequence, <span class="sb" style="color: #d14;">`kspace_encode_step_1`</span> would be the phase encoding step, for a spiral sequence where phase encoding direction does not make sense, it would be the spiral interleave number. The <span class="sb" style="color: #d14;">`encoding_space_ref`</span> enables the user to tie an acquisition to a specific encoding space (see above) in case there are multiple, e.g. in situations where a calibration scan may be integrated in the acquisition.</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC95" class="line" lang="markdown">The flags field is a bit mask, which in principle can be used freely by the user, but suggested flag values are given in <span class="sb" style="color: #d14;">`ismrmrd.h`</span>, it is recommended not to use already designated flag bits for custom purposes. There are a set of bits reserved for prototyping (bits 57-64), please see <span class="sb" style="color: #d14;">`ismrmrd.h`</span> for details.</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC97" class="line" lang="markdown">The header contains a <span class="sb" style="color: #d14;">`trajectory_dimensions`</span> field. If the value of this field is larger than 0, it means that trajectories are stored with each individual acquisition. For a 2D acquisition, the <span class="sb" style="color: #d14;">`trajectory_dimensions`</span> would typically be 2 and the convention (for memory layout) is that the header is followed immediately by the trajectory before the complex data. There is an example of how this memory layout could be implemented with a C++ class in the <span class="sb" style="color: #d14;">`ismrmrd.h`</span> file:</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC100" class="line" lang="markdown"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Acquisition</span></span>
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103
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC103" class="line" lang="markdown"><span class="c1" style="color: #998; font-style: italic;">//....</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC105" class="line" lang="markdown"><span class="n" style="color: #333;">AcquisitionHeader</span> <span class="n" style="color: #333;">head_</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//Header, see above</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC107" class="line" lang="markdown"><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">traj_</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//Trajectory, elements = head_.trajectory_dimensions*head_.number_of_samples</span></span>
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108
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC108" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">// [kx,ky,kx,ky.....] (for head_.trajectory_dimensions = 2)</span></span>
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109
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC109" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">// [kx,ky,kz,kx,ky,kz,.....] (for head_.trajectory_dimensions = 3)</span></span>
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110
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC110" class="line" lang="markdown"></span>
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111
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC111" class="line" lang="markdown"><span class="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">data_</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//Actual data, elements = head_.number_of_samples*head_.active_channels*2</span></span>
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112
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC112" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">// [re,im,re,im,.....,re,im,re,im,.....,re,im,re,im,.....]</span></span>
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113
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC113" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">// ---channel 1-------channel 2---------channel 3-----</span></span>
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114
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC114" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC115" class="line" lang="markdown"><span class="p">};</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC116" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC118" class="line" lang="markdown">This suggested memory layout is only a suggestion. The HDF5 interface (see below) can be used to read the data into many different data structures. In fact, the user can choose to read only part of the header or not read the data, etc.</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC119" class="line" lang="markdown"></span>
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120
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC120" class="line" lang="markdown">As mentioned above, the ISMRMRD format also suggests a way to store reconstructed images (or maybe image data used for calibration). An <span class="sb" style="color: #d14;">`ImageHeader`</span> structure is defined in <span class="p">[</span><span class="nv" style="color: #008080;">`ismrmrd.h`</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/ismrmrd/ismrmrd/blob/master/include/ismrmrd/ismrmrd.h#L286</span><span class="p">)</span>.</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC121" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC122" class="line" lang="markdown">In a similar fashion to the raw data acquisition data, the intention is to store a header followed by the image data. Since image data can be in several different format (e.g. float, complex, etc.), the memory layout is less well defined but can be described as:</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC124" class="line" lang="markdown"><span class="p">```</span><span class="nl">cpp</span></span>
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125
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC125" class="line" lang="markdown"><span class="k" style="font-weight: 600;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="k" style="font-weight: 600;">typename</span> <span class="nc" style="color: #458; font-weight: 600;">T</span><span class="p">></span> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Image</span> <span class="p">{</span></span>
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126
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC126" class="line" lang="markdown"></span>
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127
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC127" class="line" lang="markdown"><span class="n" style="color: #333;">ImageHeader</span> <span class="n" style="color: #333;">head_</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//ImageHeader as defined above</span></span>
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128
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC128" class="line" lang="markdown"><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">data_</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">//Data, array of size (matrix_size[0]*matrix_size[1]*matrix_size[2]*channels),</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC129" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">//first spatial dimension is fastest changing array index, channels outer most (slowest changing).</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC130" class="line" lang="markdown"><span class="p">};</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC131" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC132" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC133" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## File Storage</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC134" class="line" lang="markdown">The ISMRM Raw Data format is stored in <span class="p">[</span><span class="nv" style="color: #008080;">HDF5 format</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.hdfgroup.org/solutions/hdf5</span><span class="p">)</span>. Briefly it is a hierarchical data format (much like a file system), which can contain multiple variable organized in groups (like folders in a file system). The variables can contain arrays of data values, custom defined structs, or simple text fields. It is the convention (but not a requirement) that the ISMRMRD datasets are stored in a group called <span class="sb" style="color: #d14;">`/dataset`</span>. The XML configuration is stored in the variable <span class="sb" style="color: #d14;">`/dataset/xml`</span> and the data is stored in <span class="sb" style="color: #d14;">`/dataset/data`</span>. HDF5 files can be viewed with the HDFView application which is available on the HDF5 website for multiple platforms. Files can also be read directly in Matlab, in fact Matlab uses (since file format v7.3) HDF5 as its internal data format in the <span class="sb" style="color: #d14;">`.mat`</span> files. As an example the data from an ISMRMRD file with name <span class="sb" style="color: #d14;">`myfile.h5`</span> can be read in matlab with a command like:</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC136" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC137" class="line" lang="markdown"> >> data = h5read('simple_gre.h5', '/dataset/data');</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC138" class="line" lang="markdown"> >> data</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC139" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC140" class="line" lang="markdown"> data =</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC142" class="line" lang="markdown"> head: [1x1 struct]</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC143" class="line" lang="markdown"> traj: {1x1281 cell}</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC144" class="line" lang="markdown"> data: {1x1281 cell}</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC146" class="line" lang="markdown"> >> data.head</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC148" class="line" lang="markdown"> ans =</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC150" class="line" lang="markdown"> version: [1x1281 uint16]</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC151" class="line" lang="markdown"> flags: [1x1281 uint64]</span>
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152
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC152" class="line" lang="markdown"> measurement_uid: [1x1281 uint32]</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC153" class="line" lang="markdown"> scan_counter: [1x1281 uint32]</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC154" class="line" lang="markdown"> acquisition_time_stamp: [1x1281 uint32]</span>
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155
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC155" class="line" lang="markdown"> physiology_time_stamp: [3x1281 uint32]</span>
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156
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC156" class="line" lang="markdown"> number_of_samples: [1x1281 uint16]</span>
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157
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC157" class="line" lang="markdown"> available_channels: [1x1281 uint16]</span>
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158
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC158" class="line" lang="markdown"> active_channels: [1x1281 uint16]</span>
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159
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC159" class="line" lang="markdown"> channel_mask: [16x1281 uint64]</span>
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160
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC160" class="line" lang="markdown"> discard_pre: [1x1281 uint16]</span>
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161
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC161" class="line" lang="markdown"> discard_post: [1x1281 uint16]</span>
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162
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC162" class="line" lang="markdown"> center_sample: [1x1281 uint16]</span>
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163
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC163" class="line" lang="markdown"> encoding_space_ref: [1x1281 uint16]</span>
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164
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC164" class="line" lang="markdown"> trajectory_dimensions: [1x1281 uint16]</span>
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<td class="old_line diff-line-num old" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
165
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC165" class="line" lang="markdown"> sample_time_us: [1x1281 single]</span>
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<td class="old_line diff-line-num old" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
166
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC166" class="line" lang="markdown"> position: [3x1281 single]</span>
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<td class="old_line diff-line-num old" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
167
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC167" class="line" lang="markdown"> read_dir: [3x1281 single]</span>
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<td class="old_line diff-line-num old" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
168
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC168" class="line" lang="markdown"> phase_dir: [3x1281 single]</span>
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<td class="old_line diff-line-num old" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
169
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC169" class="line" lang="markdown"> slice_dir: [3x1281 single]</span>
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<td class="old_line diff-line-num old" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
170
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC170" class="line" lang="markdown"> patient_table_position: [3x1281 single]</span>
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<td class="old_line diff-line-num old" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
171
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC171" class="line" lang="markdown"> idx: [1x1 struct]</span>
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<td class="old_line diff-line-num old" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
172
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC172" class="line" lang="markdown"> user_int: [8x1281 int32]</span>
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<td class="old_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
173
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC173" class="line" lang="markdown"> user_float: [8x1281 single]</span>
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<td class="old_line diff-line-num old" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
174
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC174" class="line" lang="markdown"></span>
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175
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC175" class="line" lang="markdown"> >></span>
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176
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC176" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="old_line diff-line-num old" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
177
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC177" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num old" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
178
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC178" class="line" lang="markdown">The HDF5 file format can be accessed from C, C++, and java using the libraries provided on the HDF5 website. The ISMRMRD distribution also comes with some C++ wrappers that can be used for easy access (read and write) from C++ programs. See below.</span>
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<td class="old_line diff-line-num old" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
179
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC179" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num old" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
180
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC180" class="line" lang="markdown">In addition to storing acquisition data and images as defined by the headers above, the HDF5 format also enables storage of generic multi-dimensional arrays. The ISMRMRD format does not explicitly define how such data should be stored, but leaves it open for the user to add variables and data as dictated by a given application.</span>
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181
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC181" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC183" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## C++ Support Library</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC184" class="line" lang="markdown">To enable easy prototyping of C++ software using the ISMRMRD data format, a simple C++ wrapper class is provided (defined in <span class="p">[</span><span class="nv" style="color: #008080;">`dataset.h`</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/ismrmrd/ismrmrd/blob/master/include/ismrmrd/dataset.h</span><span class="p">)</span>):</span>
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185
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC185" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC186" class="line" lang="markdown">Using this wrapper, C++ applications can be programmed as:</span>
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187
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC187" class="line" lang="markdown"></span>
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188
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC188" class="line" lang="markdown"><span class="p">```</span><span class="nl">cpp</span></span>
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189
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC189" class="line" lang="markdown"><span class="c1" style="color: #998; font-style: italic;">// Open dataset</span></span>
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190
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC190" class="line" lang="markdown"><span class="n" style="color: #333;">ISMRMRD</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Dataset</span> <span class="nf" style="color: #900; font-weight: 600;">d</span><span class="p">(</span><span class="n" style="color: #333;">datafile</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="s" style="color: #d14;">"dataset"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">);</span></span>
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191
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC191" class="line" lang="markdown"></span>
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192
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC192" class="line" lang="markdown"><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">xml</span><span class="p">;</span></span>
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193
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC193" class="line" lang="markdown"><span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">readHeader</span><span class="p">(</span><span class="n" style="color: #333;">xml</span><span class="p">);</span></span>
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194
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC194" class="line" lang="markdown"><span class="n" style="color: #333;">ISMRMRD</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">IsmrmrdHeader</span> <span class="n" style="color: #333;">hdr</span><span class="p">;</span></span>
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195
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC195" class="line" lang="markdown"><span class="n" style="color: #333;">ISMRMRD</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">deserialize</span><span class="p">(</span><span class="n" style="color: #333;">xml</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span><span class="n" style="color: #333;">hdr</span><span class="p">);</span></span>
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196
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC196" class="line" lang="markdown"></span>
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197
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC197" class="line" lang="markdown"><span class="c1" style="color: #998; font-style: italic;">// Do something with the header</span></span>
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198
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC198" class="line" lang="markdown"></span>
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199
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC199" class="line" lang="markdown"><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">number_of_acquisitions</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">getNumberOfAcquisitions</span><span class="p">();</span></span>
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200
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC200" class="line" lang="markdown"><span class="n" style="color: #333;">ISMRMRD</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Acquisition</span> <span class="n" style="color: #333;">acq</span><span class="p">;</span></span>
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<td class="old_line diff-line-num old" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
201
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC201" class="line" lang="markdown"><span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">number_of_acquisitions</span><span class="p">;</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">++</span><span class="p">)</span> <span class="p">{</span></span>
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202
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC202" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">// Read one acquisition at a time</span></span>
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203
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC203" class="line" lang="markdown"> <span class="n" style="color: #333;">d</span><span class="p">.</span><span class="n" style="color: #333;">readAcquisition</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">acq</span><span class="p">);</span></span>
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204
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC204" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC205" class="line" lang="markdown"> <span class="c1" style="color: #998; font-style: italic;">// Do something with the data</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC206" class="line" lang="markdown"><span class="p">}</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC207" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC208" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC209" class="line" lang="markdown">Since the XML header is defined in the <span class="sb" style="color: #d14;">`schema/ismrmrd.xsd`</span> file, it can be</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC210" class="line" lang="markdown">parsed with numerous xml parsing libraries. The ISMRMRD library includes an API</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC211" class="line" lang="markdown">that allows for programmatically deserializing, manipulating, and serializing the</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC212" class="line" lang="markdown">XML header. See the code in the <span class="p">[</span><span class="nv" style="color: #008080;">`utilities`</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/ismrmrd/ismrmrd/blob/master/utilities/</span><span class="p">)</span> directory for examples of how to</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC213" class="line" lang="markdown">use the XML API.</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC214" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC215" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## C++ Example Applications</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC216" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC217" class="line" lang="markdown">The distribution includes two example applications, one that creates a simple 2D single-channel dataset from scratch and one that reconstructs this dataset (you need FFTW installed to compile these test applications). The data generation application can be found in <span class="p">[</span><span class="nv" style="color: #008080;">`utilities/generate_cartesian_shepp_logan.cpp`</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/ismrmrd/ismrmrd/blob/master/utilities/generate_cartesian_shepp_logan.cpp</span><span class="p">)</span>:</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC218" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC219" class="line" lang="markdown">To reconstruct this synthetic dataset, you can use the test reconstruction application <span class="p">[</span><span class="nv" style="color: #008080;">`utilities/recon_cartesian_2d.cpp`</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/ismrmrd/ismrmrd/blob/master/utilities/recon_cartesian_2d.cpp</span><span class="p">)</span>:</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC220" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC221" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC222" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## External use of ISMRMRD C++ library in other projects</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC223" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC224" class="line" lang="markdown">To use ISMRMRD for your externally developed projects, add the following to your CMakeLists.txt file:</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC225" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC226" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC227" class="line" lang="markdown">find_package( ISMRMRD REQUIRED )</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC228" class="line" lang="markdown">link_directories( ${ISMRMRD_LIBRARY_DIRS} )</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC229" class="line" lang="markdown">include_directories( ${ISMRMRD_INCLUDE_DIRS} )</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC230" class="line" lang="markdown">target_link_libraries( mytarget ${ISMRMRD_LIBRARIES} )</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC231" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC232" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC233" class="line" lang="markdown">then when configuring your package use set the following cmake variables (command line variant shown):</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC234" class="line" lang="markdown"></span>
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235
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC235" class="line" lang="markdown"><span class="p">```</span></span>
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236
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC236" class="line" lang="markdown">cmake -DISMRMRD_DIR:PATH=<path to build/install tree of ISMRMRD> <path to my source tree></span>
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237
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC237" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC238" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC239" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Matlab Example Code and Datasets</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC240" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC241" class="line" lang="markdown">The <span class="sb" style="color: #d14;">`examples`</span> folder contains some matlab code to illustrate simple interaction with the ISMRMRD data format. Go to the <span class="sb" style="color: #d14;">`examples/data`</span> folder and type the following to download the data::</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC242" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC243" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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244
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC244" class="line" lang="markdown">wget https://sourceforge.net/projects/ismrmrd/files/data/3D_partial_fourier.h5</span>
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245
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC245" class="line" lang="markdown">wget https://sourceforge.net/projects/ismrmrd/files/data/simple_gre.h5</span>
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246
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC246" class="line" lang="markdown">wget https://sourceforge.net/projects/ismrmrd/files/data/simple_spiral.h5</span>
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247
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC247" class="line" lang="markdown"><span class="p">```</span></span>
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248
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC248" class="line" lang="markdown"></span>
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249
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC249" class="line" lang="markdown">For instance, to reconstruct a 2D Cartesian acquisition (10 image repetitions), type (from the <span class="sb" style="color: #d14;">`examples/matlab`</span> folder):</span>
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250
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC250" class="line" lang="markdown"></span>
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251
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC251" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="old_line diff-line-num old" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
252
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC252" class="line" lang="markdown">>> images = simple_cartesian_recon('../data/simple_gre.h5');</span>
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253
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC253" class="line" lang="markdown">Reconstructing image 1....done</span>
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254
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC254" class="line" lang="markdown">Reconstructing image 2....done</span>
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<td class="old_line diff-line-num old" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
255
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC255" class="line" lang="markdown">Reconstructing image 3....done</span>
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<td class="old_line diff-line-num old" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
256
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC256" class="line" lang="markdown">Reconstructing image 4....done</span>
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257
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC257" class="line" lang="markdown">Reconstructing image 5....done</span>
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258
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC258" class="line" lang="markdown">Reconstructing image 6....done</span>
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259
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC259" class="line" lang="markdown">Reconstructing image 7....done</span>
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260
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC260" class="line" lang="markdown">Reconstructing image 8....done</span>
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261
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC261" class="line" lang="markdown">Reconstructing image 9....done</span>
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<td class="old_line diff-line-num old" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
262
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC262" class="line" lang="markdown">Reconstructing image 10....done</span>
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<td class="old_line diff-line-num old" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
263
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC263" class="line" lang="markdown">>></span>
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264
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC264" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="old_line diff-line-num old" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
265
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC265" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num old" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
266
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC266" class="line" lang="markdown">You should see one of the reconstructed images display. An example is also given of a 3D acquisition with partial Fourier, phase and slice oversampling, etc. Reconstruct this dataset with:</span>
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267
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC267" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num old" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
268
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC268" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="old_line diff-line-num old" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
269
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC269" class="line" lang="markdown">>> images = simple_cartesian_recon('../data/3D_partial_fourier.h5');</span>
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<td class="old_line diff-line-num old" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
270
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC270" class="line" lang="markdown">Reconstructing image 1....done</span>
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<td class="old_line diff-line-num old" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
271
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC271" class="line" lang="markdown"><span class="p">```</span></span>
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272
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC272" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num old" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
273
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC273" class="line" lang="markdown">The center slice of the volume should be displayed at the end of the reconstruction.</span>
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274
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC274" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num old" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
275
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC275" class="line" lang="markdown">Finally, there is also a spiral dataset. This dataset illustrates how the flexible section of the <span class="sb" style="color: #d14;">`<trajectoryDescription>`</span> can be used to add user defined parameters and an identifier to describe the trajectory. This dataset is also an example of storing the trajectory with the data for direct reconstruction. Reconstruct this dataset with:</span>
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276
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC276" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num old" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
277
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC277" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="old_line diff-line-num old" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
278
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC278" class="line" lang="markdown">>> images = simple_spiral_recon('../data/simple_spiral.h5');</span>
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<td class="old_line diff-line-num old" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
279
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC279" class="line" lang="markdown">Reconstructing image 1....done</span>
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<td class="old_line diff-line-num old" data-linenumber="280" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
280
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC280" class="line" lang="markdown">Reconstructing image 2....done</span>
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<td class="old_line diff-line-num old" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
281
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC281" class="line" lang="markdown">Reconstructing image 3....done</span>
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<td class="old_line diff-line-num old" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
282
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC282" class="line" lang="markdown">Reconstructing image 4....done</span>
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<td class="old_line diff-line-num old" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
283
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC283" class="line" lang="markdown">Reconstructing image 5....done</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC284" class="line" lang="markdown">Reconstructing image 6....done</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC285" class="line" lang="markdown">Reconstructing image 7....done</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC286" class="line" lang="markdown">Reconstructing image 8....done</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC287" class="line" lang="markdown">Reconstructing image 9....done</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC288" class="line" lang="markdown">Reconstructing image 10....done</span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC289" class="line" lang="markdown">>></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC290" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC291" class="line" lang="markdown"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC292" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Python implementation</span></span>
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293
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC293" class="line" lang="markdown">The Python implementation of the API is maintained in ## Other <span class="p">[</span><span class="nv" style="color: #008080;">ismrmrd-python</span><span class="p">](</span><span class="sx" style="color: #d14;">https://www.github.com/ismrmrd/ismrmrd-python</span><span class="p">)</span></span>
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294
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC294" class="line" lang="markdown"></span>
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295
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11
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown">Please the <span class="p">[</span><span class="nv" style="color: #008080;">ISMRMRD documentation</span><span class="p">](</span><span class="sx" style="color: #d14;">https://ismrmrd.readthedocs.io</span><span class="p">)</span> for details.</span></pre></td>
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<a href="https://salsa.debian.org/med-team/ismrmrd/-/commit/cbc6808c2860f5d9913f598cdcfe8e1adba1a4be#9527117c6a2a17d94b217b7122000c747b932a14"><strong>doc/.gitignore</strong></a>
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1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">_build/</span>
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2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">doxygen/</span>
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3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Doxyfile</span></pre></td>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/ismrmrd/-/commit/cbc6808c2860f5d9913f598cdcfe8e1adba1a4be#c86c7a6d9a7bc77f1c375315f47ff6952729ba5b"><strong>doc/Makefile</strong></a>
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<td class="new_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Minimal makefile for Sphinx documentation</span></span>
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<td class="new_line diff-line-num new" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="make"></span>
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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
4
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># You can set these variables from the command line, and also</span></span>
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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
5
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># from the environment for the first two.</span></span>
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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
6
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="make"><span class="nv" style="color: #008080;">SPHINXOPTS</span> <span class="o" style="font-weight: 600;">?=</span></span>
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<td class="new_line diff-line-num new" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
7
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="make"><span class="nv" style="color: #008080;">SPHINXBUILD</span> <span class="o" style="font-weight: 600;">?=</span> sphinx-build</span>
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<td class="new_line diff-line-num new" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="make"><span class="nv" style="color: #008080;">SOURCEDIR</span> <span class="o" style="font-weight: 600;">=</span> .</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="make"><span class="nv" style="color: #008080;">BUILDDIR</span> <span class="o" style="font-weight: 600;">=</span> _build</span>
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11
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Put it first so that "make" without argument is like "make help".</span></span>
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12
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="make"><span class="nl">help</span><span class="o" style="font-weight: 600;">:</span></span>
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13
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC13" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-M</span> <span class="nb" style="color: #0086b3;">help</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(SOURCEDIR)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">"</span> <span class="nv" style="color: #008080;">$(SPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(O)</span></span>
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14
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15
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC15" class="line" lang="make"><span class="nl">.PHONY</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">help Makefile</span></span>
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16
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17
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC17" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Catch-all target: route all unknown targets to Sphinx using the new</span></span>
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18
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC18" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).</span></span>
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19
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC19" class="line" lang="make"><span class="nl">%</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">Makefile</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC20" class="line" lang="make"> <span class="p">@</span><span class="nv" style="color: #008080;">$(SPHINXBUILD)</span> <span class="nt" style="color: #000080;">-M</span> <span class="nv" style="color: #008080;">$@</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(SOURCEDIR)</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(BUILDDIR)</span><span class="s2" style="color: #d14;">"</span> <span class="nv" style="color: #008080;">$(SPHINXOPTS)</span> <span class="nv" style="color: #008080;">$(O)</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/ismrmrd/-/commit/cbc6808c2860f5d9913f598cdcfe8e1adba1a4be#cb342c6815d4fbd8ef564a526e9dbd697d2bde40"><strong>doc/api.rst</strong></a>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ISMRMRD API</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">###########</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">The project includes both a C and A C++ API:</span>
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<li id="b7c00b7004069a7c3c9343b2c549d773de462f11">
<a href="https://salsa.debian.org/med-team/ismrmrd/-/commit/cbc6808c2860f5d9913f598cdcfe8e1adba1a4be#b7c00b7004069a7c3c9343b2c549d773de462f11"><strong>doc/building.md</strong></a>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Build instructions</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown">The ISMRM Raw Data format is described by an XML schema and some C-style structs with fixed memory layout and as such does not have dependencies. However, it uses HDF5 files for storage and a C++ library for reading and writing the ISMRMRD files is included in this distribution. Furthermore, since the XML header is defined with an XML schema, we encourage using XML data binding when writing software using the format. To compile all components of this distribution you need:</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">*</span> HDF5 (version 1.8 or higher) libraries. Available from http://www.hdfgroup.org/downloads/index.html.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">*</span> Boost (http://www.boost.org/)</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p">*</span> Cmake build tool (http://www.cmake.org/)</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p">*</span> Git if you would like to use the source code archive (http://git-scm.com/)</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">*</span> FFTW if you would like to compile some of the example applications</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"> (http://www.fftw.org)</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">*</span> Doxygen if you would like to generate API documentation (http://www.doxygen.org)</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="gt" style="color: #a00;">> It is only necessary to install the dependencies if you wish to develop compiled C/C++ software, which uses the ISMRMRD format. The format can be read in Matlab or Python without installing any additional software.</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Linux installation</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown">The dependencies mentioned above should be included in most linux distributions. On Ubuntu you can install all required dependencies with::</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC19" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC20" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">sudo </span>apt-get <span class="nt" style="color: #000080;">-y</span> <span class="nb" style="color: #0086b3;">install </span>doxygen git-core graphviz libboost-all-dev libfftw3-dev libhdf5-serial-dev</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"></span>
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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown">After installation of dependencies, the library can be installed with:</span>
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25
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="p">```</span><span class="nl">bash</span></span>
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26
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown">git clone https://github.com/ismrmrd/ismrmrd</span>
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27
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd </span>ismrmrd/</span>
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28
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC28" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">mkdir </span>build</span>
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29
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">cd </span>build</span>
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30
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC30" class="line" lang="markdown">cmake ../</span>
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31
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC31" class="line" lang="markdown">make</span>
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32
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"><span class="nb" style="color: #0086b3;">sudo </span>make <span class="nb" style="color: #0086b3;">install</span></span>
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33
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC33" class="line" lang="markdown"><span class="p">```</span></span>
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34
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown"></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown">This will install the library in <span class="sb" style="color: #d14;">`/usr/local/`</span> by default. To specify</span>
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36
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown">an alternative installation directory, pass <span class="sb" style="color: #d14;">`-D CMAKE_INSTALL_PREFIX=<install dir>`</span> to <span class="sb" style="color: #d14;">`cmake`</span>.</span>
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38
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39
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## External use of ISMRMRD C++ library in other projects</span></span>
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40
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"></span>
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41
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC41" class="line" lang="markdown">To use ISMRMRD for your externally developed projects, add the following to your CMakeLists.txt file:</span>
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42
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC42" class="line" lang="markdown"></span>
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43
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC43" class="line" lang="markdown"><span class="p">```</span></span>
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44
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC44" class="line" lang="markdown">find_package( ISMRMRD REQUIRED )</span>
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45
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC45" class="line" lang="markdown">link_directories( ${ISMRMRD_LIBRARY_DIRS} )</span>
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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
46
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC46" class="line" lang="markdown">include_directories( ${ISMRMRD_INCLUDE_DIRS} )</span>
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47
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC47" class="line" lang="markdown">target_link_libraries( mytarget ${ISMRMRD_LIBRARIES} )</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"><span class="p">```</span></span>
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49
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC49" class="line" lang="markdown"></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown">then when configuring your package use set the following cmake variables (command line variant shown):</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC52" class="line" lang="markdown"><span class="p">```</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC53" class="line" lang="markdown">cmake -DISMRMRD_DIR:PATH=<path to build/install tree of ISMRMRD> <path to my source tree></span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/ismrmrd/-/commit/cbc6808c2860f5d9913f598cdcfe8e1adba1a4be#d4985f7d843648ff16232f586d05914fa309a4a6"><strong>doc/c-api.rst</strong></a>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">C API</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">######</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> :project: ISMRMRD</span>
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<a href="https://salsa.debian.org/med-team/ismrmrd/-/commit/cbc6808c2860f5d9913f598cdcfe8e1adba1a4be#df0576cbb783bc50b36e1efa3cbe0564a26c8295"><strong>doc/conf.py</strong></a>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Configuration file for the Sphinx documentation builder.</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># This file only contains a selection of the most common options. For a full</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># https://www.sphinx-doc.org/en/master/usage/configuration.html</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -- Path setup --------------------------------------------------------------</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If extensions (or modules to document with autodoc) are in another directory,</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># add these directories to sys.path here. If the directory is relative to the</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># documentation root, use os.path.abspath to make it absolute, like shown here.</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># import os</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># import sys</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC15" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># sys.path.insert(0, os.path.abspath('.'))</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -- Doxygen generation</span></span>
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18
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC19" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">pathlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Path</span></span>
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20
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC20" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</span></span>
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21
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22
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="n" style="color: #333;">this_folder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">).</span><span class="n" style="color: #333;">parent</span></span>
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24
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">configureDoxyfile</span><span class="p">(</span><span class="n" style="color: #333;">input_dir</span><span class="p">,</span> <span class="n" style="color: #333;">output_dir</span><span class="p">):</span></span>
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25
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC25" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">this_folder</span><span class="o" style="font-weight: 600;">/</span><span class="s" style="color: #d14;">'Doxyfile.in'</span><span class="p">,</span> <span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="nb" style="color: #0086b3;">file</span> <span class="p">:</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC26" class="line" lang="python"> <span class="n" style="color: #333;">filedata</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>
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27
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">filedata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filedata</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'@CMAKE_SOURCE_DIR@'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">input_dir</span><span class="p">))</span></span>
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29
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">filedata</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">filedata</span><span class="p">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'@CMAKE_CURRENT_BINARY_DIR@'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">output_dir</span><span class="p">))</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="s" style="color: #d14;">'Doxyfile'</span><span class="p">,</span> <span class="s" style="color: #d14;">'w'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="nb" style="color: #0086b3;">file</span><span class="p">:</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="nb" style="color: #0086b3;">file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">filedata</span><span class="p">)</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC34" class="line" lang="python"><span class="n" style="color: #333;">doxygen_inputdir</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">this_folder</span><span class="o" style="font-weight: 600;">/</span><span class="s" style="color: #d14;">".."</span><span class="p">).</span><span class="n" style="color: #333;">resolve</span><span class="p">()</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC35" class="line" lang="python"><span class="n" style="color: #333;">doxygen_output</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">this_folder</span><span class="o" style="font-weight: 600;">/</span><span class="s" style="color: #d14;">"doxygen"</span><span class="p">).</span><span class="n" style="color: #333;">resolve</span><span class="p">()</span></span>
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36
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC36" class="line" lang="python"></span>
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37
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC37" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">Path</span><span class="p">(</span><span class="n" style="color: #333;">this_folder</span><span class="o" style="font-weight: 600;">/</span><span class="s" style="color: #d14;">"doxygen"</span><span class="p">).</span><span class="n" style="color: #333;">exists</span><span class="p">():</span></span>
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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
38
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">configureDoxyfile</span><span class="p">(</span><span class="n" style="color: #333;">doxygen_inputdir</span><span class="p">,</span> <span class="n" style="color: #333;">doxygen_output</span><span class="p">)</span></span>
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39
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_call</span><span class="p">(</span><span class="s" style="color: #d14;">'doxygen'</span><span class="p">,</span> <span class="n" style="color: #333;">cwd</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">this_folder</span><span class="p">)</span></span>
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40
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41
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC41" class="line" lang="python"><span class="n" style="color: #333;">breathe_projects</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'ISMRMRD'</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">doxygen_output</span><span class="o" style="font-weight: 600;">/</span><span class="s" style="color: #d14;">"xml"</span><span class="p">)}</span></span>
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42
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC42" class="line" lang="python"><span class="n" style="color: #333;">breathe_default_project</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'ISMRMRD'</span></span>
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43
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44
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC44" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -- Project information -----------------------------------------------------</span></span>
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45
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46
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC46" class="line" lang="python"><span class="n" style="color: #333;">project</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'ISMRMRD'</span></span>
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<td class="new_line diff-line-num new" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
47
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC47" class="line" lang="python"><span class="n" style="color: #333;">copyright</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'2022, ISMRMRD Working Group'</span></span>
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48
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC48" class="line" lang="python"><span class="n" style="color: #333;">author</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'ISMRMRD Working Group'</span></span>
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49
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50
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51
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC51" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -- General configuration ---------------------------------------------------</span></span>
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52
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53
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC53" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Add any Sphinx extension module names here, as strings. They can be</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC54" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># extensions coming with Sphinx (named 'sphinx.ext.*') or your custom</span></span>
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55
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC55" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># ones.</span></span>
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56
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC56" class="line" lang="python"><span class="n" style="color: #333;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'breathe'</span><span class="p">,</span> <span class="s" style="color: #d14;">'myst_parser'</span><span class="p">]</span></span>
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57
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58
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC58" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Add any paths that contain templates here, relative to this directory.</span></span>
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59
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC59" class="line" lang="python"><span class="n" style="color: #333;">templates_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'_templates'</span><span class="p">]</span></span>
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60
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61
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC61" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># List of patterns, relative to source directory, that match files and</span></span>
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62
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC62" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># directories to ignore when looking for source files.</span></span>
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63
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC63" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># This pattern also affects html_static_path and html_extra_path.</span></span>
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64
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC64" class="line" lang="python"><span class="n" style="color: #333;">exclude_patterns</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'_build'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Thumbs.db'</span><span class="p">,</span> <span class="s" style="color: #d14;">'.DS_Store'</span><span class="p">]</span></span>
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65
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66
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67
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC67" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -- Options for HTML output -------------------------------------------------</span></span>
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68
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69
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC69" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The theme to use for HTML and HTML Help pages. See the documentation for</span></span>
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70
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC70" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># a list of builtin themes.</span></span>
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71
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC71" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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72
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC72" class="line" lang="python"><span class="n" style="color: #333;">html_theme</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'sphinx_rtd_theme'</span></span>
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73
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74
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC74" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Add any paths that contain custom static files (such as style sheets) here,</span></span>
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75
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC75" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># relative to this directory. They are copied after the builtin static files,</span></span>
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76
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC76" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># so a file named "default.css" will overwrite the builtin "default.css".</span></span>
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77
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC77" class="line" lang="python"><span class="n" style="color: #333;">html_static_path</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">'_static'</span><span class="p">]</span></span></pre></td>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">C++ API</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> :project: ISMRMRD</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">To enable easy prototyping of C++ software using the ISMRMRD data format, a simple C++ wrapper class is provided (defined in `dataset.h <https://github.com/ismrmrd/ismrmrd/blob/master/include/ismrmrd/dataset.h>_.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Using this wrapper, C++ applications can be programmed as::</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> // Open dataset</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> ISMRMRD::Dataset d(datafile.c_str(), "dataset", false);</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> std::string xml;</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> ISMRMRD::IsmrmrdHeader hdr;</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> ISMRMRD::deserialize(xml.c_str(),hdr);</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> // Do something with the header</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> unsigned int number_of_acquisitions = d.getNumberOfAcquisitions();</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> ISMRMRD::Acquisition acq;</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> for (unsigned int i = 0; i < number_of_acquisitions; i++) {</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> // Read one acquisition at a time</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> d.readAcquisition(i, acq);</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> // Do something with the data</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> }</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">Since the XML header is defined in the `schema/ismrmrd.xsd` file, it can be</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">parsed with numerous xml parsing libraries. The ISMRMRD library includes an API</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">that allows for programmatically deserializing, manipulating, and serializing the</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">XML header. See the code in the `utilities <https://github.com/ismrmrd/ismrmrd/blob/master/utilities/>`_ directory for examples of how to use the XML API.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">************************</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">The distribution includes two example applications, one that creates a simple 2D single-channel dataset from scratch and one that reconstructs this dataset (you need FFTW installed to compile these test applications). The data generation application can be found in `utilities/generate_cartesian_shepp_logan.cpp <https://github.com/ismrmrd/ismrmrd/blob/master/utilities/generate_cartesian_shepp_logan.cpp>`_:</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">To reconstruct this synthetic dataset, you can use the test reconstruction application `utilities/recon_cartesian_2d.cpp <https://github.com/ismrmrd/ismrmrd/blob/master/utilities/recon_cartesian_2d.cpp>`_.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">External use of ISMRMRD C++ library in other projects</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">To use ISMRMRD for your externally developed projects, add the following to your CMakeLists.txt file::</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> find_package( ISMRMRD REQUIRED )</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> include_directories( ${ISMRMRD_INCLUDE_DIR} )</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> target_link_libraries( mytarget ISMRMRD::ISMRMRD )</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">then when configuring your package use set the following cmake variables (command line variant shown)::</span>
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<li id="ab7bf64f8a8059baac8aaafc4bffe49434b5dd1c">
<a href="https://salsa.debian.org/med-team/ismrmrd/-/commit/cbc6808c2860f5d9913f598cdcfe8e1adba1a4be#ab7bf64f8a8059baac8aaafc4bffe49434b5dd1c"><strong>doc/filestorage.rst</strong></a>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">HDF5 File Storage</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">The ISMRM Raw Data format can really be stored in any format that you choose, but most commonly it is stored in `HDF5 format https://www.hdfgroup.org/solutions/hdf5`_. Briefly it is a hierarchical data format (much like a file system), which can contain multiple variable organized in groups (like folders in a file system). The variables can contain arrays of data values, custom defined structs, or simple text fields. It is the convention (but not a requirement) that the ISMRMRD datasets are stored in a group called `/dataset`. The XML configuration is stored in the variable `/dataset/xml` and the data is stored in `/dataset/data`. HDF5 files can be viewed with the HDFView application which is available on the HDF5 website for multiple platforms. Many programming languages also have support for working with HDF5 files. </span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">In Python, the `h5py <https://www.h5py.org/>`_ package can be used to read the files::</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> import h5py</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> import numpy as np</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> f = h5py.File('testdata.h5')</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> acq = np.array(f['dataset']['data'][0])</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> { k: acq['head'][k] for k in acq['head'].dtype.fields.keys() }</span>
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13
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> {'version': array(1, dtype=uint16),</span>
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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> 'flags': array(64, dtype=uint64),</span>
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16
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> 'measurement_uid': array(0, dtype=uint32),</span>
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17
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> 'scan_counter': array(0, dtype=uint32),</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> 'acquisition_time_stamp': array(0, dtype=uint32),</span>
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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> 'physiology_time_stamp': array([0, 0, 0], dtype=uint32),</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> 'number_of_samples': array(512, dtype=uint16),</span>
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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> 'available_channels': array(8, dtype=uint16),</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> 'active_channels': array(8, dtype=uint16),</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> 'channel_mask': array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], dtype=uint64),</span>
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24
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> 'discard_pre': array(0, dtype=uint16),</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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25
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> 'discard_post': array(0, dtype=uint16),</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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26
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> 'center_sample': array(256, dtype=uint16),</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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27
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> 'encoding_space_ref': array(0, dtype=uint16),</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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28
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> 'trajectory_dimensions': array(0, dtype=uint16),</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> 'sample_time_us': array(5., dtype=float32),</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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30
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> 'position': array([0., 0., 0.], dtype=float32),</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
31
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> 'read_dir': array([0., 0., 0.], dtype=float32),</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
32
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> 'phase_dir': array([0., 0., 0.], dtype=float32),</span>
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33
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> 'slice_dir': array([0., 0., 0.], dtype=float32),</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
34
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> 'patient_table_position': array([0., 0., 0.], dtype=float32),</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
35
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> 'idx': array((0, 0, 0, 0, 0, 0, 0, 0, 0, [0, 0, 0, 0, 0, 0, 0, 0]),</span>
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<td class="new_line diff-line-num new" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
36
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> dtype=[('kspace_encode_step_1', '<u2'), ('kspace_encode_step_2', '<u2'), ('average', '<u2'), ('slice', '<u2'), ('contrast', '<u2'), ('phase', '<u2'), ('repetition', '<u2'), ('set', '<u2'), ('segment', '<u2'), ('user', '<u2', (8,))]),</span>
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<td class="new_line diff-line-num new" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
37
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> 'user_int': array([0, 0, 0, 0, 0, 0, 0, 0], dtype=int32),</span>
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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
38
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> 'user_float': array([0., 0., 0., 0., 0., 0., 0., 0.], dtype=float32)}</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">There is also a dedicated python libarary for working with the ISMRMRD files. The Python implementation of the API is maintained in `ismrmrd-python <https://www.github.com/ismrmrd/ismrmrd-python>_`</span>
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41
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42
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">Files can also be read directly in Matlab, in fact Matlab uses (since file format v7.3) HDF5 as its internal data format in the `.mat` files. As an example the data from an ISMRMRD file with name `myfile.h5` can be read in Matlab with a command like::</span>
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43
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44
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> >> data = h5read('simple_gre.h5', '/dataset/data');</span>
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45
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> >> data</span>
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46
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47
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> data =</span>
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48
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49
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> head: [1x1 struct]</span>
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50
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> traj: {1x1281 cell}</span>
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51
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> data: {1x1281 cell}</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> >> data.head</span>
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55
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> ans =</span>
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56
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57
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> version: [1x1281 uint16]</span>
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58
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> flags: [1x1281 uint64]</span>
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59
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> measurement_uid: [1x1281 uint32]</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> scan_counter: [1x1281 uint32]</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> acquisition_time_stamp: [1x1281 uint32]</span>
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62
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> physiology_time_stamp: [3x1281 uint32]</span>
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63
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> number_of_samples: [1x1281 uint16]</span>
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64
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> available_channels: [1x1281 uint16]</span>
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65
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> active_channels: [1x1281 uint16]</span>
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66
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> channel_mask: [16x1281 uint64]</span>
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67
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> discard_pre: [1x1281 uint16]</span>
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68
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> discard_post: [1x1281 uint16]</span>
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69
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> center_sample: [1x1281 uint16]</span>
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70
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> encoding_space_ref: [1x1281 uint16]</span>
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71
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> trajectory_dimensions: [1x1281 uint16]</span>
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72
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> sample_time_us: [1x1281 single]</span>
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73
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> position: [3x1281 single]</span>
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74
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> read_dir: [3x1281 single]</span>
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75
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> phase_dir: [3x1281 single]</span>
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76
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> slice_dir: [3x1281 single]</span>
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<td class="old_line diff-line-num new" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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77
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> patient_table_position: [3x1281 single]</span>
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78
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> idx: [1x1 struct]</span>
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79
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> user_int: [8x1281 int32]</span>
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80
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> user_float: [8x1281 single]</span>
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81
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"></span>
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82
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> >></span>
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83
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
84
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">The HDF5 file format can be accessed from C, C++, and java using the libraries provided on the HDF5 website. The ISMRMRD distribution also comes with some C++ wrappers that can be used for easy access (read and write) from C++ programs. </span>
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85
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86
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<a href="https://salsa.debian.org/med-team/ismrmrd/-/commit/cbc6808c2860f5d9913f598cdcfe8e1adba1a4be#1bbcd8980c541f52998ccf56da078edd2ca6a2d0"><strong>doc/index.rst</strong></a>
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1
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ISMRM Raw Data Format (ISMRMRD)</span>
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2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">################################</span>
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3
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">A prerequisite for sharing magnetic resonance (imaging) reconstruction algorithms and code is a common raw data format. The ISMRMRD project describes such a common raw data format, which attempts to capture the data fields that are required to describe the magnetic resonance experiment with enough detail to reconstruct images. The repository also contains a C/C++ library for working with the format. This standard was developed by a subcommittee of the ISMRM Sedona 2013 workshop and is described in detail in:</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Inati SJ, Naegele JD, Zwart NR, Roopchansingh V, Lizak MJ, Hansen DC, Liu CY, Atkinson D, Kellman P, Kozerke S, Xue H, Campbell-Washburn AE, Sørensen TS, Hansen MS. ISMRM Raw data format: A proposed standard for MRI raw datasets. `Magn Reson Med. 2017 Jan;77(1):411-421. <https://onlinelibrary.wiley.com/doi/10.1002/mrm.26089>`_</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Please cite this paper if you use the format.</span>
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16
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18
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19
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1
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2
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3
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4
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5
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6
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7
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="batchfile"><span class="k" style="font-weight: 600;">if</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">%SPHINXBUILD%</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">(</span></span>
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8
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC8" class="line" lang="batchfile"> <span class="kd" style="font-weight: 600;">set</span> <span class="kd" style="font-weight: 600;">SPHINXBUILD</span><span class="o" style="font-weight: 600;">=</span><span class="kd" style="font-weight: 600;">sphinx</span><span class="na" style="color: #008080;">-build</span></span>
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9
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10
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC10" class="line" lang="batchfile"><span class="kd" style="font-weight: 600;">set</span> <span class="kd" style="font-weight: 600;">SOURCEDIR</span><span class="o" style="font-weight: 600;">=</span>.</span>
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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="batchfile"><span class="kd" style="font-weight: 600;">set</span> <span class="kd" style="font-weight: 600;">BUILDDIR</span><span class="o" style="font-weight: 600;">=</span>_build</span>
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12
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="batchfile"></span>
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13
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC13" class="line" lang="batchfile"><span class="k" style="font-weight: 600;">if</span> <span class="s2" style="color: #d14;">"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">%</span><span class="s2" style="color: #d14;">1"</span> <span class="o" style="font-weight: 600;">==</span> <span class="s2" style="color: #d14;">""</span> <span class="k" style="font-weight: 600;">goto</span> <span class="nb" style="color: #0086b3;">help</span></span>
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14
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC14" class="line" lang="batchfile"></span>
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<td class="new_line diff-line-num new" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
15
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC15" class="line" lang="batchfile"><span class="nv" style="color: #008080;">%SPHINXBUILD%</span> <span class="o" style="font-weight: 600;">></span><span class="kd" style="font-weight: 600;">NUL</span> <span class="m" style="color: #099;">2</span><span class="o" style="font-weight: 600;">></span><span class="kd" style="font-weight: 600;">NUL</span></span>
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<td class="new_line diff-line-num new" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC16" class="line" lang="batchfile"><span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">errorlevel</span> <span class="m" style="color: #099;">9009</span> <span class="o" style="font-weight: 600;">(</span></span>
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<td class="new_line diff-line-num new" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
17
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC17" class="line" lang="batchfile"> <span class="nb" style="color: #0086b3;">echo</span>.</span>
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<td class="new_line diff-line-num new" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
18
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC18" class="line" lang="batchfile"> <span class="nb" style="color: #0086b3;">echo</span>.The <span class="s1" style="color: #d14;">'sphinx-build'</span> <span class="kd" style="font-weight: 600;">command</span> <span class="kd" style="font-weight: 600;">was</span> <span class="ow" style="font-weight: 600;">not</span> <span class="kd" style="font-weight: 600;">found</span>. <span class="kd" style="font-weight: 600;">Make</span> <span class="kd" style="font-weight: 600;">sure</span> <span class="kd" style="font-weight: 600;">you</span> <span class="kd" style="font-weight: 600;">have</span> <span class="kd" style="font-weight: 600;">Sphinx</span></span>
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<td class="new_line diff-line-num new" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
19
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC19" class="line" lang="batchfile"> <span class="nb" style="color: #0086b3;">echo</span>.installed<span class="o" style="font-weight: 600;">,</span> <span class="kd" style="font-weight: 600;">then</span> <span class="kd" style="font-weight: 600;">set</span> <span class="kd" style="font-weight: 600;">the</span> <span class="kd" style="font-weight: 600;">SPHINXBUILD</span> <span class="kd" style="font-weight: 600;">environment</span> <span class="kd" style="font-weight: 600;">variable</span> <span class="kd" style="font-weight: 600;">to</span> <span class="kd" style="font-weight: 600;">point</span></span>
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<td class="new_line diff-line-num new" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC20" class="line" lang="batchfile"> <span class="nb" style="color: #0086b3;">echo</span>.to <span class="kd" style="font-weight: 600;">the</span> <span class="kd" style="font-weight: 600;">full</span> <span class="nb" style="color: #0086b3;">path</span> <span class="kd" style="font-weight: 600;">of</span> <span class="kd" style="font-weight: 600;">the</span> <span class="s1" style="color: #d14;">'sphinx-build'</span> <span class="kd" style="font-weight: 600;">executable</span>. <span class="kd" style="font-weight: 600;">Alternatively</span> <span class="kd" style="font-weight: 600;">you</span></span>
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<td class="new_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC21" class="line" lang="batchfile"> <span class="nb" style="color: #0086b3;">echo</span>.may <span class="kd" style="font-weight: 600;">add</span> <span class="kd" style="font-weight: 600;">the</span> <span class="kd" style="font-weight: 600;">Sphinx</span> <span class="kd" style="font-weight: 600;">directory</span> <span class="kd" style="font-weight: 600;">to</span> <span class="kd" style="font-weight: 600;">PATH</span>.</span>
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22
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC22" class="line" lang="batchfile"> <span class="nb" style="color: #0086b3;">echo</span>.</span>
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<td class="new_line diff-line-num new" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC23" class="line" lang="batchfile"> <span class="nb" style="color: #0086b3;">echo</span>.If <span class="kd" style="font-weight: 600;">you</span> <span class="kd" style="font-weight: 600;">don</span><span class="s1" style="color: #d14;">'t have Sphinx installed, grab it from</span></span>
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24
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC24" class="line" lang="batchfile"><span class="s1" style="color: #d14;"> echo.https://www.sphinx-doc.org/</span></span>
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<td class="new_line diff-line-num new" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
25
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC25" class="line" lang="batchfile"><span class="s1" style="color: #d14;"> exit /b 1</span></span>
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26
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC26" class="line" lang="batchfile"><span class="s1" style="color: #d14;">)</span></span>
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27
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC27" class="line" lang="batchfile"><span class="s1" style="color: #d14;"></span></span>
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<td class="new_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
28
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC28" class="line" lang="batchfile"><span class="nv" style="color: #008080;">%SPHINXBUILD%</span><span class="s1" style="color: #d14;"> -M </span><span class="err" style="color: #a61717; background-color: #e3d2d2;">%</span><span class="s1" style="color: #d14;">1 </span><span class="nv" style="color: #008080;">%SOURCEDIR%</span><span class="s1" style="color: #d14;"> </span><span class="nv" style="color: #008080;">%BUILDDIR%</span><span class="s1" style="color: #d14;"> </span><span class="nv" style="color: #008080;">%SPHINXOPTS%</span><span class="s1" style="color: #d14;"> </span><span class="nv" style="color: #008080;">%O%</span><span class="s1" style="color: #d14;"></span></span>
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<td class="new_line diff-line-num new" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
29
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC29" class="line" lang="batchfile"><span class="s1" style="color: #d14;">goto end</span></span>
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30
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31
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC31" class="line" lang="batchfile"><span class="s1" style="color: #d14;">:help</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC32" class="line" lang="batchfile"><span class="nv" style="color: #008080;">%SPHINXBUILD%</span><span class="s1" style="color: #d14;"> -M help </span><span class="nv" style="color: #008080;">%SOURCEDIR%</span><span class="s1" style="color: #d14;"> </span><span class="nv" style="color: #008080;">%BUILDDIR%</span><span class="s1" style="color: #d14;"> </span><span class="nv" style="color: #008080;">%SPHINXOPTS%</span><span class="s1" style="color: #d14;"> </span><span class="nv" style="color: #008080;">%O%</span><span class="s1" style="color: #d14;"></span></span>
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<a href="https://salsa.debian.org/med-team/ismrmrd/-/commit/cbc6808c2860f5d9913f598cdcfe8e1adba1a4be#82401113062cb44368daabb1a60d95d081eadd17"><strong>doc/meta.rst</strong></a>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Meta API</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">#########</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">.. doxygengroup:: meta</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> :project: ISMRMRD</span>
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<a href="https://salsa.debian.org/med-team/ismrmrd/-/commit/cbc6808c2860f5d9913f598cdcfe8e1adba1a4be#b1cf159591d5cd14b430ac01f75371424a4d5637"><strong>doc/overview.rst</strong></a>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Overview</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">#########</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">The raw data format combines a mix of flexible data structures (XML header) and fixed structures (equivalent to C-structs). A raw data set consist mainly of 2 sections:</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">1. A flexible XML format document that can contain an arbitrary number of fields and accommodate everything from simple values (b-values, etc.) to entire vendor protocols, etc. This purpose of this XML document is to provide parameters that may be meaningful for some experiments but not for others. This XML format is defined by an XML Schema Definition file `schema/ismrmrd.xsd <https://github.com/ismrmrd/ismrmrd/blob/master/schema/ismrmrd.xsd>`_.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">2. Raw data section. This section contains all the acquired data in the experiment. Each data item is preceded by a C-struct with encoding numbers, etc. Following this data header is a channel header and data for each acquired channel. The raw data headers are defined in a C/C++ header file `ismrmrd.h <https://github.com/ismrmrd/ismrmrd/blob/master/include/ismrmrd/ismrmrd.h>`_</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">In addition to these sections, the ISMRMRD format also specifies an image header for storing reconstructed images and the accompanying C++ library provides a convenient way of writing such images into HDF5 files along with generic arrays for storing less well defined data structures, e.g. coil sensitivity maps or other calibration data.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Flexible Data Header</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">********************</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">The flexible data structure is defined by the xml schema definition in `schema/ismrmrd.xsd <https://github.com/ismrmrd/ismrmrd/blob/master/schema/ismrmrd.xsd>`_. An example of an XML file for a Cartesian 3D acquisition can be found `schema/ismrmrd_example.xml <https://github.com/ismrmrd/ismrmrd/blob/master/schema/ismrmrd_example.xml>_</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">The most critical elements for image reconstruction are contained in the `<encoding>` section of the document, which describes the encoded spaced and also the target reconstructed space. Along with the `<encodingLimits>` this section allows the reconstruction program to determine matrix sizes, oversampling factors, partial Fourier, etc. In the example above, data is acquired with two-fold oversampling in the read-out (`x`) direction, which is reflected in the larger matrix size in the encoded space compared to the reconstruction space. The field of view is also twice as large in the encoded space. For the first phase encoding dimension (`y`), we have a combination of oversampling (20%), reduced phase resolution (only 83 lines of k-space acquired, and partial Fourier sampling, which is reflected in the asymmetric center of the encoding limits of the `<kspace_encoding_step_1>`. Specifically, the data lines would be placed into the encoding space like this::</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> |-------------------------------------|-------------------------------------------|</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">After FFT, only the central 116 lines are kept, i.e. there is a reduced field of view in the phase encoding direction. Center and encoding limits for the readout dimension is not given in the XML header. This is to accommodate sequences where the center of the readout may change from readout to readout (alternating directions of readout). There is a field on the individual data headers (see below) to indicate the center of the readout.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">An experiment can have multiple encoding spaces and it is possible to indicate on each acquired data readout, which encoding space the data belongs to (see below).</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">In addition to the defined field in the xml header, it is possible to add an arbitrary number of user defined parameters to accommodate special sequence parameters. Please consult the xml `schema <https://github.com/ismrmrd/ismrmrd/blob/master/schema/ismrmrd.xsd>`_ to see how user parameters are defined. Briefly, the XML header can have a section at the end which looks like::</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"> <userParameters></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> <name>MyVar1</name><value>1003</value></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> <name>MyVar2</name><value>1999</value></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> <name>MyDoubleVar</name><value>87.6676</value></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">Each raw data acquisition is preceded by the following fixed layout structures in `ismrmrd.h <https://github.com/ismrmrd/ismrmrd/blob/master/include/ismrmrd/ismrmrd.h#L225>`_.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">The interpretation of some of these fields may vary from sequence to sequence, i.e. for a Cartesian sequence, `kspace_encode_step_1` would be the phase encoding step, for a spiral sequence where phase encoding direction does not make sense, it would be the spiral interleave number. The `encoding_space_ref` enables the user to tie an acquisition to a specific encoding space (see above) in case there are multiple, e.g. in situations where a calibration scan may be integrated in the acquisition.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">The flags field is a bit mask, which in principle can be used freely by the user, but suggested flag values are given in `ismrmrd.h`, it is recommended not to use already designated flag bits for custom purposes. There are a set of bits reserved for prototyping (bits 57-64), please see `ismrmrd.h` for details.</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">The header contains a `trajectory_dimensions` field. If the value of this field is larger than 0, it means that trajectories are stored with each individual acquisition. For a 2D acquisition, the `trajectory_dimensions` would typically be 2 and the convention (for memory layout) is that the header is followed immediately by the trajectory before the complex data. There is an example of how this memory layout could be implemented with a C++ class in the `ismrmrd.h` file::</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> class Acquisition</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> AcquisitionHeader head_; //Header, see above</span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> float* traj_; //Trajectory, elements = head_.trajectory_dimensions*head_.number_of_samples</span>
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61
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> // [kx,ky,kx,ky.....] (for head_.trajectory_dimensions = 2)</span>
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62
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> // [kx,ky,kz,kx,ky,kz,.....] (for head_.trajectory_dimensions = 3)</span>
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63
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"></span>
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64
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> float* data_; //Actual data, elements = head_.number_of_samples*head_.active_channels*2</span>
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65
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> // [re,im,re,im,.....,re,im,re,im,.....,re,im,re,im,.....]</span>
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66
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> // ---channel 1-------channel 2---------channel 3-----</span>
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67
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68
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> };</span>
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69
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70
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">This suggested memory layout is only a suggestion. The HDF5 interface (see below) can be used to read the data into many different data structures. In fact, the user can choose to read only part of the header or not read the data, etc.</span>
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71
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72
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">As mentioned above, the ISMRMRD format also suggests a way to store reconstructed images (or maybe image data used for calibration). An `ImageHeader` structure is defined in `ismrmrd.h <https://github.com/ismrmrd/ismrmrd/blob/master/include/ismrmrd/ismrmrd.h#L286>_.</span>
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73
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74
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">In a similar fashion to the raw data acquisition data, the intention is to store a header followed by the image data. Since image data can be in several different format (e.g. float, complex, etc.), the memory layout is less well defined but can be described as::</span>
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75
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> template <typename T> class Image {</span>
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77
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78
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> ImageHeader head_; //ImageHeader as defined above</span>
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79
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> T* data_; //Data, array of size (matrix_size[0]*matrix_size[1]*matrix_size[2]*channels),</span>
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80
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> //first spatial dimension is fastest changing array index, channels outer most (slowest changing).</span>
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81
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<a href="https://salsa.debian.org/med-team/ismrmrd/-/commit/cbc6808c2860f5d9913f598cdcfe8e1adba1a4be#73ac3f1c0f36645568b29944d795f3fa05824147"><strong>doc/requirements.txt</strong></a>
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1
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2
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">sphinx~=4.3.0</span>
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3
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -45,6 +45,7 @@ namespace ISMRMRD {</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC49" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC50" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> This class can represent a meta data value of any</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC51" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> type and it guarantees that any value will have a</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -249,6 +250,8 @@ namespace ISMRMRD {</td>
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250
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC250" class="line" lang="cpp"> <span class="n" style="color: #333;">map_t</span> <span class="n" style="color: #333;">map_</span><span class="p">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp"> <span class="p">};</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC252" class="line" lang="cpp"></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC253" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/** @} */</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC255" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//Template function instantiations</span></span>
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256
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp"> <span class="cm" style="color: #998; font-style: italic;">/*</span></span>
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257
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC257" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> template void MetaContainer::set<const char*>(const char* name, const char* value);</span></span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -260,6 +263,5 @@ namespace ISMRMRD {</td>
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260
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263
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC263" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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261
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264
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC264" class="line" lang="cpp"><span class="p">}</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC265" class="line" lang="cpp"></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC263" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** @} */</span></span>
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264
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266
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp"></span>
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265
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267
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif //ISMRMRDMETA_H</span></span></pre></td>
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<li id="ba699d29d1ce3d90b211ff331b12a06a042e5de5">
<a href="https://salsa.debian.org/med-team/ismrmrd/-/commit/cbc6808c2860f5d9913f598cdcfe8e1adba1a4be#ba699d29d1ce3d90b211ff331b12a06a042e5de5"><strong>include/ismrmrd/xml.h</strong></a>
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1
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1
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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2
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2
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @file xml.h</span></span>
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3
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3
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @defgroup xml XML API</span></span>
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4
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @{</span></span>
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5
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4
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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6
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5
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"></span>
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7
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6
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#ifndef ISMRMRDXML_H</span></span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,6 +25,10 @@</td>
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26
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"></span>
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27
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**</span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;"> * @{</span></span>
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32
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"></span>
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33
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">ISMRMRD</span></span>
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34
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC34" class="line" lang="cpp"><span class="p">{</span></span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -157,6 +160,13 @@ namespace ISMRMRD</td>
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157
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160
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp"></span>
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158
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161
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC161" class="line" lang="cpp"> <span class="p">};</span> </span>
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159
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162
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC162" class="line" lang="cpp"></span>
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163
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC163" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">threeDimensionalFloat</span></span>
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164
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC164" class="line" lang="cpp"> <span class="p">{</span> </span>
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165
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC165" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">x</span><span class="p">;</span></span>
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166
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC166" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">y</span><span class="p">;</span></span>
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167
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC167" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">z</span><span class="p">;</span></span>
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168
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC168" class="line" lang="cpp"> <span class="p">};</span></span>
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169
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160
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170
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="nc" style="color: #458; font-weight: 600;">SubjectInformation</span> </span>
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161
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171
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC171" class="line" lang="cpp"> <span class="p">{</span></span>
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162
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC172" class="line" lang="cpp"> <span class="n" style="color: #333;">Optional</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">patientName</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -194,6 +204,7 @@ namespace ISMRMRD</td>
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194
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204
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC204" class="line" lang="cpp"> <span class="n" style="color: #333;">Optional</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seriesDate</span><span class="p">;</span></span>
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195
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205
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp"> <span class="n" style="color: #333;">Optional</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seriesTime</span><span class="p">;</span></span>
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196
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206
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC206" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">patientPosition</span><span class="p">;</span></span>
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207
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC207" class="line" lang="cpp"> <span class="n" style="color: #333;">Optional</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">threeDimensionalFloat</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">relativeTablePosition</span><span class="p">;</span></span>
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197
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208
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC208" class="line" lang="cpp"> <span class="n" style="color: #333;">Optional</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">initialSeriesNumber</span><span class="p">;</span></span>
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198
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209
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"> <span class="n" style="color: #333;">Optional</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">protocolName</span><span class="p">;</span></span>
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199
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210
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC210" class="line" lang="cpp"> <span class="n" style="color: #333;">Optional</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">seriesDescription</span><span class="p">;</span></span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -420,10 +431,11 @@ namespace ISMRMRD</td>
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420
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431
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC431" class="line" lang="cpp"> <span class="p">};</span></span>
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421
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432
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC432" class="line" lang="cpp"></span>
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433
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC433" class="line" lang="cpp"></span>
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423
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC423" class="line" lang="cpp"></span>
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424
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434
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC434" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPORTISMRMRD</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">deserialize</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="n" style="color: #333;">IsmrmrdHeader</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">h</span><span class="p">);</span></span>
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425
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435
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC435" class="line" lang="cpp"> <span class="n" style="color: #333;">EXPORTISMRMRD</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">serialize</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">IsmrmrdHeader</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">h</span><span class="p">,</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">ostream</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">o</span><span class="p">);</span></span>
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC426" class="line" lang="cpp"><span class="p">}</span></span>
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436
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC436" class="line" lang="cpp"></span>
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437
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC437" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/** @} */</span></span>
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438
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC438" class="line" lang="cpp"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC441" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#endif //ISMRMRDXML_H</span></span></pre></td>
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<li id="25392c1cd8ba356261b6dab1ed022b7e4c614741">
<a href="https://salsa.debian.org/med-team/ismrmrd/-/commit/cbc6808c2860f5d9913f598cdcfe8e1adba1a4be#25392c1cd8ba356261b6dab1ed022b7e4c614741"><strong>libsrc/xml.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -118,6 +118,22 @@ namespace ISMRMRD</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC118" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"> <span class="p">}</span></span>
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120
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120
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC121" class="line" lang="cpp"> <span class="n" style="color: #333;">Optional</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">threeDimensionalFloat</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">parse_optional_threeDimensionalFloat</span><span class="p">(</span><span class="n" style="color: #333;">pugi</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">xml_node</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">child</span><span class="p">)</span> <span class="p">{</span></span>
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122
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123
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC123" class="line" lang="cpp"> <span class="n" style="color: #333;">Optional</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">threeDimensionalFloat</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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124
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125
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC125" class="line" lang="cpp"> <span class="n" style="color: #333;">pugi</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">xml_node</span> <span class="n" style="color: #333;">nc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span><span class="p">.</span><span class="n" style="color: #333;">child</span><span class="p">(</span><span class="n" style="color: #333;">child</span><span class="p">);</span></span>
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126
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC126" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">nc</span><span class="p">)</span> <span class="p">{</span></span>
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127
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC127" class="line" lang="cpp"> <span class="n" style="color: #333;">threeDimensionalFloat</span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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128
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC128" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">x</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">strtof</span><span class="p">(</span><span class="n" style="color: #333;">nc</span><span class="p">.</span><span class="n" style="color: #333;">child_value</span><span class="p">(</span><span class="s" style="color: #d14;">"x"</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">);</span></span>
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129
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC129" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">y</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">strtof</span><span class="p">(</span><span class="n" style="color: #333;">nc</span><span class="p">.</span><span class="n" style="color: #333;">child_value</span><span class="p">(</span><span class="s" style="color: #d14;">"y"</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">);</span></span>
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130
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC130" class="line" lang="cpp"> <span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">z</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">strtof</span><span class="p">(</span><span class="n" style="color: #333;">nc</span><span class="p">.</span><span class="n" style="color: #333;">child_value</span><span class="p">(</span><span class="s" style="color: #d14;">"z"</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">);</span></span>
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131
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC131" class="line" lang="cpp"> <span class="n" style="color: #333;">r</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s</span><span class="p">;</span></span>
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132
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133
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134
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC134" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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135
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136
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137
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">UserParameterLong</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">parse_user_parameter_long</span><span class="p">(</span><span class="n" style="color: #333;">pugi</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">xml_node</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">child</span><span class="p">)</span> </span>
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138
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"> <span class="p">{</span></span>
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139
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">UserParameterLong</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">r</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -373,6 +389,7 @@ namespace ISMRMRD</td>
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373
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389
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC389" class="line" lang="cpp"> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">seriesDate</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_optional_string</span><span class="p">(</span><span class="n" style="color: #333;">measurementInformation</span><span class="p">,</span> <span class="s" style="color: #d14;">"seriesDate"</span><span class="p">);</span></span>
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374
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<td class="new_line diff-line-num" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
390
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC390" class="line" lang="cpp"> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">seriesTime</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_optional_string</span><span class="p">(</span><span class="n" style="color: #333;">measurementInformation</span><span class="p">,</span> <span class="s" style="color: #d14;">"seriesTime"</span><span class="p">);</span></span>
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375
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391
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC391" class="line" lang="cpp"> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">patientPosition</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_string</span><span class="p">(</span><span class="n" style="color: #333;">measurementInformation</span><span class="p">,</span> <span class="s" style="color: #d14;">"patientPosition"</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
392
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC392" class="line" lang="cpp"> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">relativeTablePosition</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_optional_threeDimensionalFloat</span><span class="p">(</span><span class="n" style="color: #333;">measurementInformation</span><span class="p">,</span> <span class="s" style="color: #d14;">"relativeTablePosition"</span><span class="p">);</span></span>
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376
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<td class="new_line diff-line-num" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
393
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC393" class="line" lang="cpp"> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">initialSeriesNumber</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_optional_long</span><span class="p">(</span><span class="n" style="color: #333;">measurementInformation</span><span class="p">,</span> <span class="s" style="color: #d14;">"initialSeriesNumber"</span><span class="p">);</span></span>
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377
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394
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC394" class="line" lang="cpp"> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">protocolName</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_optional_string</span><span class="p">(</span><span class="n" style="color: #333;">measurementInformation</span><span class="p">,</span> <span class="s" style="color: #d14;">"protocolName"</span><span class="p">);</span></span>
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378
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395
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC395" class="line" lang="cpp"> <span class="n" style="color: #333;">info</span><span class="p">.</span><span class="n" style="color: #333;">seriesDescription</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_optional_string</span><span class="p">(</span><span class="n" style="color: #333;">measurementInformation</span><span class="p">,</span> <span class="s" style="color: #d14;">"seriesDescription"</span><span class="p">);</span></span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -601,6 +618,15 @@ namespace ISMRMRD</td>
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601
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618
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC618" class="line" lang="cpp"> <span class="n" style="color: #333;">append_node</span><span class="p">(</span><span class="n" style="color: #333;">n3</span><span class="p">,</span><span class="s" style="color: #d14;">"z"</span><span class="p">,</span><span class="n" style="color: #333;">s</span><span class="p">.</span><span class="n" style="color: #333;">fieldOfView_mm</span><span class="p">.</span><span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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602
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619
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC619" class="line" lang="cpp"> <span class="p">}</span></span>
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603
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620
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC620" class="line" lang="cpp"></span>
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<td class="new_line diff-line-num new" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
621
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC621" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">append_optional_three_dimensional_float</span><span class="p">(</span><span class="n" style="color: #333;">pugi</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">xml_node</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">child</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Optional</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">threeDimensionalFloat</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">s</span><span class="p">)</span> </span>
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622
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC622" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="new_line diff-line-num new" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
623
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC623" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">){</span></span>
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624
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC624" class="line" lang="cpp"> <span class="n" style="color: #333;">pugi</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">xml_node</span> <span class="n" style="color: #333;">n2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n</span><span class="p">.</span><span class="n" style="color: #333;">append_child</span><span class="p">(</span><span class="n" style="color: #333;">child</span><span class="p">);</span> </span>
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625
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC625" class="line" lang="cpp"> <span class="n" style="color: #333;">append_node</span><span class="p">(</span><span class="n" style="color: #333;">n2</span><span class="p">,</span><span class="s" style="color: #d14;">"x"</span><span class="p">,</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">x</span><span class="p">);</span></span>
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626
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC626" class="line" lang="cpp"> <span class="n" style="color: #333;">append_node</span><span class="p">(</span><span class="n" style="color: #333;">n2</span><span class="p">,</span><span class="s" style="color: #d14;">"y"</span><span class="p">,</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">y</span><span class="p">);</span></span>
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627
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC627" class="line" lang="cpp"> <span class="n" style="color: #333;">append_node</span><span class="p">(</span><span class="n" style="color: #333;">n2</span><span class="p">,</span><span class="s" style="color: #d14;">"z"</span><span class="p">,</span><span class="n" style="color: #333;">s</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">z</span><span class="p">);</span></span>
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628
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC628" class="line" lang="cpp"> <span class="p">}</span></span>
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629
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC629" class="line" lang="cpp"> <span class="p">}</span></span>
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604
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630
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC630" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">append_encoding_limit</span><span class="p">(</span><span class="n" style="color: #333;">pugi</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">xml_node</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">n</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">child</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Optional</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Limit</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">l</span><span class="p">)</span> </span>
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605
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631
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC631" class="line" lang="cpp"> <span class="p">{</span></span>
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632
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC632" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">l</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -695,6 +721,7 @@ namespace ISMRMRD</td>
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695
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721
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC721" class="line" lang="cpp"> <span class="n" style="color: #333;">append_optional_node</span><span class="p">(</span><span class="n" style="color: #333;">n1</span><span class="p">,</span><span class="s" style="color: #d14;">"seriesDate"</span><span class="p">,</span><span class="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">measurementInformation</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seriesDate</span><span class="p">);</span></span>
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696
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722
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC722" class="line" lang="cpp"> <span class="n" style="color: #333;">append_optional_node</span><span class="p">(</span><span class="n" style="color: #333;">n1</span><span class="p">,</span><span class="s" style="color: #d14;">"seriesTime"</span><span class="p">,</span><span class="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">measurementInformation</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seriesTime</span><span class="p">);</span></span>
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697
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<td class="new_line diff-line-num" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
723
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC723" class="line" lang="cpp"> <span class="n" style="color: #333;">append_node</span><span class="p">(</span><span class="n" style="color: #333;">n1</span><span class="p">,</span><span class="s" style="color: #d14;">"patientPosition"</span><span class="p">,</span><span class="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">measurementInformation</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">patientPosition</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
724
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC724" class="line" lang="cpp"> <span class="n" style="color: #333;">append_optional_three_dimensional_float</span><span class="p">(</span><span class="n" style="color: #333;">n1</span><span class="p">,</span><span class="s" style="color: #d14;">"relativeTablePosition"</span><span class="p">,</span><span class="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">measurementInformation</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">relativeTablePosition</span><span class="p">);</span></span>
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698
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725
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC725" class="line" lang="cpp"> <span class="n" style="color: #333;">append_optional_node</span><span class="p">(</span><span class="n" style="color: #333;">n1</span><span class="p">,</span><span class="s" style="color: #d14;">"initialSeriesNumber"</span><span class="p">,</span><span class="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">measurementInformation</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">initialSeriesNumber</span><span class="p">);</span></span>
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699
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<td class="new_line diff-line-num" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
726
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC726" class="line" lang="cpp"> <span class="n" style="color: #333;">append_optional_node</span><span class="p">(</span><span class="n" style="color: #333;">n1</span><span class="p">,</span><span class="s" style="color: #d14;">"protocolName"</span><span class="p">,</span><span class="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">measurementInformation</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">protocolName</span><span class="p">);</span></span>
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700
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727
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC727" class="line" lang="cpp"> <span class="n" style="color: #333;">append_optional_node</span><span class="p">(</span><span class="n" style="color: #333;">n1</span><span class="p">,</span><span class="s" style="color: #d14;">"seriesDescription"</span><span class="p">,</span><span class="n" style="color: #333;">h</span><span class="p">.</span><span class="n" style="color: #333;">measurementInformation</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">seriesDescription</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/ismrmrd/-/commit/cbc6808c2860f5d9913f598cdcfe8e1adba1a4be#30b182cc5bcd1cb23f8e7cf67e7ad8dca6d69921"><strong>matlab/+ismrmrd/+xml/deserialize.m</strong></a>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,6 +35,11 @@ for n = 1:numChildNodes</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC35" class="line" lang="matlab"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC36" class="line" lang="matlab"> <span class="c1" style="color: #998; font-style: italic;">%Some elements occur more than once</span></span>
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37
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC37" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isfield</span><span class="p">(</span><span class="nb" style="color: #0086b3;">info</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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38
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC38" class="line" lang="matlab"> <span class="c1" style="color: #998; font-style: italic;">% Use cell arrays for multiple valued strings and dates</span></span>
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<td class="new_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
39
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC39" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isStringType</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">isDateType</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">))</span> <span class="o" style="font-weight: 600;">&&</span> <span class="o" style="font-weight: 600;">~</span><span class="nb" style="color: #0086b3;">iscell</span><span class="p">(</span><span class="nb" style="color: #0086b3;">info</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">))</span></span>
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<td class="new_line diff-line-num new" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC40" class="line" lang="matlab"> <span class="nb" style="color: #0086b3;">info</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="nb" style="color: #0086b3;">info</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)};</span></span>
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41
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC41" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">end</span></span>
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42
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC42" class="line" lang="matlab"></span>
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38
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC43" class="line" lang="matlab"> <span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nb" style="color: #0086b3;">info</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">))</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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39
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC44" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">else</span></span>
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45
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC45" class="line" lang="matlab"> <span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -88,7 +93,7 @@ for n = 1:numChildNodes</td>
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88
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93
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC93" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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89
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94
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC94" class="line" lang="matlab"> <span class="nb" style="color: #0086b3;">info</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">char</span><span class="p">(</span><span class="n" style="color: #333;">getTextContent</span><span class="p">(</span><span class="n" style="color: #333;">theChild</span><span class="p">));</span></span>
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90
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95
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC95" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">else</span></span>
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91
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<td class="new_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC91" class="line" lang="matlab"> <span class="nb" style="color: #0086b3;">info</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)<span class="idiff left deletion">(</span></span><span class="n" style="color: #333;">num</span><span class="p"><span class="idiff right deletion">)</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">char</span><span class="p">(</span><span class="n" style="color: #333;">getTextContent</span><span class="p">(</span><span class="n" style="color: #333;">theChild</span><span class="p">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC96" class="line" lang="matlab"> <span class="nb" style="color: #0086b3;">info</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)<span class="idiff left addition">{</span></span><span class="n" style="color: #333;">num</span><span class="p"><span class="idiff right addition">}</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">char</span><span class="p">(</span><span class="n" style="color: #333;">getTextContent</span><span class="p">(</span><span class="n" style="color: #333;">theChild</span><span class="p">));</span></span>
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92
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97
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC97" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">end</span></span>
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93
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98
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC98" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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94
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99
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC99" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">end</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -106,7 +111,7 @@ for n = 1:numChildNodes</td>
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106
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111
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC111" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">num</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span></span>
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107
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112
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC112" class="line" lang="matlab"> <span class="nb" style="color: #0086b3;">info</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">char</span><span class="p">(</span><span class="n" style="color: #333;">getTextContent</span><span class="p">(</span><span class="n" style="color: #333;">theChild</span><span class="p">));</span></span>
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108
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113
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC113" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">else</span></span>
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109
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<td class="new_line diff-line-num old" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC109" class="line" lang="matlab"> <span class="nb" style="color: #0086b3;">info</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)<span class="idiff left deletion">(</span></span><span class="n" style="color: #333;">num</span><span class="p"><span class="idiff right deletion">)</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">char</span><span class="p">(</span><span class="n" style="color: #333;">getTextContent</span><span class="p">(</span><span class="n" style="color: #333;">theChild</span><span class="p">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
114
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC114" class="line" lang="matlab"> <span class="nb" style="color: #0086b3;">info</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)<span class="idiff left addition">{</span></span><span class="n" style="color: #333;">num</span><span class="p"><span class="idiff right addition">}</span></span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">char</span><span class="p">(</span><span class="n" style="color: #333;">getTextContent</span><span class="p">(</span><span class="n" style="color: #333;">theChild</span><span class="p">));</span></span>
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110
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115
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC115" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">end</span></span>
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111
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116
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC116" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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112
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117
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC117" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">end</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -166,6 +171,7 @@ function status = isCompoundType(name)</td>
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166
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171
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC171" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'accelerationFactor'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">...</span></span>
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167
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172
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC172" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'matrixSize'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">...</span></span>
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168
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173
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC173" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'fieldOfView_mm'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">...</span></span>
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174
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC174" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'relativeTablePosition'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">...</span></span>
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169
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175
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC175" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'kspace_encoding_step_0'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">...</span></span>
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170
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176
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC176" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'kspace_encoding_step_1'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">...</span></span>
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171
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177
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC177" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'kspace_encoding_step_2'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">...</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -185,7 +191,7 @@ end</td>
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185
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191
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC191" class="line" lang="matlab"><span class="k" style="font-weight: 600;">function</span> <span class="n" style="color: #333;">status</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">isNumericalType</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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186
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<td class="new_line diff-line-num" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
192
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC192" class="line" lang="matlab"> <span class="n" style="color: #333;">headerNumericalTypes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">...</span></span>
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187
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193
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC193" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'version'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">...</span></span>
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188
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<td class="new_line diff-line-num old" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC188" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'patientWeight'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">...</span></span>
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<td class="new_line diff-line-num new" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
194
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC194" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'patientWeight<span class="idiff left right addition">_kg</span>'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">...</span></span>
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189
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<td class="new_line diff-line-num" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
195
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC195" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'accessionNumber'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">...</span></span>
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190
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<td class="new_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
196
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC196" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'initialSeriesNumber'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">...</span></span>
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191
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197
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC197" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'systemFieldStrength_T'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">...</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -227,8 +233,10 @@ function status = isStringType(name)</td>
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227
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233
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC233" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'systemModel'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">...</span></span>
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228
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<td class="new_line diff-line-num" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
234
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC234" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'institutionName'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">...</span></span>
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229
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<td class="new_line diff-line-num" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
235
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC235" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'stationName'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">...</span></span>
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<td class="new_line diff-line-num new" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
236
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC236" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'deviceID'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">...</span></span>
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230
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<td class="new_line diff-line-num" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
237
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC237" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'trajectory'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">...</span></span>
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231
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<td class="new_line diff-line-num" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
238
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC238" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'identifier'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">...</span></span>
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<td class="new_line diff-line-num new" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
239
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC239" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'comment'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">...</span></span>
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232
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<td class="new_line diff-line-num" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
240
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC240" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'coilName'</span><span class="p">,</span> <span class="k" style="font-weight: 600;">...</span></span>
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233
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<td class="new_line diff-line-num" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
241
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC241" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'calibrationMode'</span><span class="p">,</span><span class="k" style="font-weight: 600;">...</span></span>
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234
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242
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC242" class="line" lang="matlab"> <span class="s1" style="color: #d14;">'interleavingDimension'</span><span class="p">,</span><span class="k" style="font-weight: 600;">...</span></span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -43,6 +43,7 @@ if isfield(header,'measurementInformation')</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC43" class="line" lang="matlab"> <span class="n" style="color: #333;">append_optional</span><span class="p">(</span><span class="n" style="color: #333;">docNode</span><span class="p">,</span><span class="n" style="color: #333;">measurementInformationNode</span><span class="p">,</span><span class="n" style="color: #333;">measurementInformation</span><span class="p">,</span><span class="s1" style="color: #d14;">'seriesTime'</span><span class="p">);</span></span>
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44
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC44" class="line" lang="matlab"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC45" class="line" lang="matlab"> <span class="n" style="color: #333;">append_node</span><span class="p">(</span><span class="n" style="color: #333;">docNode</span><span class="p">,</span><span class="n" style="color: #333;">measurementInformationNode</span><span class="p">,</span><span class="n" style="color: #333;">measurementInformation</span><span class="p">,</span><span class="s1" style="color: #d14;">'patientPosition'</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC46" class="line" lang="matlab"> <span class="n" style="color: #333;">append_optional_three_dimensional_float</span><span class="p">(</span><span class="n" style="color: #333;">docNode</span><span class="p">,</span><span class="n" style="color: #333;">measurementInformationNode</span><span class="p">,</span><span class="n" style="color: #333;">measurementInformation</span><span class="p">,</span><span class="s1" style="color: #d14;">'relativeTablePosition'</span><span class="p">);</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC47" class="line" lang="matlab"></span>
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<td class="new_line diff-line-num" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC48" class="line" lang="matlab"> <span class="n" style="color: #333;">append_optional</span><span class="p">(</span><span class="n" style="color: #333;">docNode</span><span class="p">,</span><span class="n" style="color: #333;">measurementInformationNode</span><span class="p">,</span><span class="n" style="color: #333;">measurementInformation</span><span class="p">,</span><span class="s1" style="color: #d14;">'initialSeriesNumber'</span><span class="p">,</span><span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">int2str</span><span class="p">);</span></span>
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48
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<td class="new_line diff-line-num" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC49" class="line" lang="matlab"> <span class="n" style="color: #333;">append_optional</span><span class="p">(</span><span class="n" style="color: #333;">docNode</span><span class="p">,</span><span class="n" style="color: #333;">measurementInformationNode</span><span class="p">,</span><span class="n" style="color: #333;">measurementInformation</span><span class="p">,</span><span class="s1" style="color: #d14;">'protocolName'</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -67,6 +68,7 @@ if isfield(header,'measurementInformation')</td>
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<td class="old_line diff-line-num" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
67
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC68" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">referencedImageSequence</span><span class="p">(:)</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC69" class="line" lang="matlab"> <span class="n" style="color: #333;">append_node</span><span class="p">(</span><span class="n" style="color: #333;">docNode</span><span class="p">,</span><span class="n" style="color: #333;">referencedImageSequenceNode</span><span class="p">,</span><span class="n" style="color: #333;">ref</span><span class="p">,</span><span class="s1" style="color: #d14;">'referencedSOPInstanceUID'</span><span class="p">);</span></span>
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69
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC70" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">end</span></span>
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<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC71" class="line" lang="matlab"> <span class="n" style="color: #333;">measurementInformationNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">appendChild</span><span class="p">(</span><span class="n" style="color: #333;">referencedImageSequenceNode</span><span class="p">)</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC72" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">end</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC73" class="line" lang="matlab"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC74" class="line" lang="matlab"> <span class="n" style="color: #333;">docRootNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">appendChild</span><span class="p">(</span><span class="n" style="color: #333;">measurementInformationNode</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -93,6 +95,7 @@ if isfield(header,'acquisitionSystemInformation')</td>
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<td class="old_line diff-line-num" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC95" class="line" lang="matlab"></span>
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<td class="new_line diff-line-num" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC96" class="line" lang="matlab"> <span class="n" style="color: #333;">append_optional</span><span class="p">(</span><span class="n" style="color: #333;">docNode</span><span class="p">,</span><span class="n" style="color: #333;">acquisitionSystemInformationNode</span><span class="p">,</span><span class="n" style="color: #333;">acquisitionSystemInformation</span><span class="p">,</span><span class="s1" style="color: #d14;">'institutionName'</span><span class="p">);</span></span>
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<td class="old_line diff-line-num" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
95
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<td class="new_line diff-line-num" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC97" class="line" lang="matlab"> <span class="n" style="color: #333;">append_optional</span><span class="p">(</span><span class="n" style="color: #333;">docNode</span><span class="p">,</span><span class="n" style="color: #333;">acquisitionSystemInformationNode</span><span class="p">,</span><span class="n" style="color: #333;">acquisitionSystemInformation</span><span class="p">,</span><span class="s1" style="color: #d14;">'stationName'</span><span class="p">,</span><span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">num2str</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC98" class="line" lang="matlab"> <span class="n" style="color: #333;">append_optional</span><span class="p">(</span><span class="n" style="color: #333;">docNode</span><span class="p">,</span><span class="n" style="color: #333;">acquisitionSystemInformationNode</span><span class="p">,</span><span class="n" style="color: #333;">acquisitionSystemInformation</span><span class="p">,</span><span class="s1" style="color: #d14;">'deviceID'</span><span class="p">,</span><span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">num2str</span><span class="p">);</span></span>
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96
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99
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC99" class="line" lang="matlab"> <span class="n" style="color: #333;">docRootNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">appendChild</span><span class="p">(</span><span class="n" style="color: #333;">acquisitionSystemInformationNode</span><span class="p">);</span></span>
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97
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100
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC100" class="line" lang="matlab"><span class="k" style="font-weight: 600;">end</span></span>
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98
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101
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC101" class="line" lang="matlab"></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -105,7 +108,7 @@ if ~isfield(header,'encoding')</td>
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105
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<td class="new_line diff-line-num" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
108
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC108" class="line" lang="matlab"> <span class="nb" style="color: #0086b3;">error</span><span class="p">(</span><span class="s1" style="color: #d14;">'Illegal header: missing encoding section'</span><span class="p">);</span></span>
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106
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109
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC109" class="line" lang="matlab"><span class="k" style="font-weight: 600;">end</span></span>
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107
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110
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC110" class="line" lang="matlab"></span>
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108
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<td class="new_line diff-line-num old" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC108" class="line" lang="matlab"><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">enc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encoding</span><span class="p">(:)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
111
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC111" class="line" lang="matlab"><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">enc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encoding</span><span class="p">(:)</span><span class="o" style="font-weight: 600;"><span class="idiff left right addition">'</span></span></span>
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109
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112
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC112" class="line" lang="matlab"> <span class="n" style="color: #333;">node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">docNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">createElement</span><span class="p">(</span><span class="s1" style="color: #d14;">'encoding'</span><span class="p">);</span></span>
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110
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113
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC113" class="line" lang="matlab"></span>
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111
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114
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC114" class="line" lang="matlab"> <span class="n" style="color: #333;">append_encoding_space</span><span class="p">(</span><span class="n" style="color: #333;">docNode</span><span class="p">,</span><span class="n" style="color: #333;">node</span><span class="p">,</span><span class="s1" style="color: #d14;">'encodedSpace'</span><span class="p">,</span><span class="n" style="color: #333;">enc</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">encodedSpace</span><span class="p">);</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="129" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -126,7 +129,6 @@ for enc = header.encoding(:)</td>
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126
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129
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC129" class="line" lang="matlab"> <span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">appendChild</span><span class="p">(</span><span class="n" style="color: #333;">n2</span><span class="p">);</span></span>
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127
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130
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC130" class="line" lang="matlab"></span>
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128
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131
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC131" class="line" lang="matlab"> <span class="n" style="color: #333;">append_node</span><span class="p">(</span><span class="n" style="color: #333;">docNode</span><span class="p">,</span><span class="n" style="color: #333;">node</span><span class="p">,</span><span class="n" style="color: #333;">enc</span><span class="p">,</span><span class="s1" style="color: #d14;">'trajectory'</span><span class="p">);</span></span>
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129
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC129" class="line" lang="matlab"> <span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">appendChild</span><span class="p">(</span><span class="n" style="color: #333;">n2</span><span class="p">);</span></span>
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130
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132
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC132" class="line" lang="matlab"></span>
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131
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133
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC133" class="line" lang="matlab"> <span class="c1" style="color: #998; font-style: italic;">% sometimes the encoding has the fields, but they are empty</span></span>
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132
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134
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC134" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isfield</span><span class="p">(</span><span class="n" style="color: #333;">enc</span><span class="p">,</span><span class="s1" style="color: #d14;">'trajectoryDescription'</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -279,6 +281,16 @@ function append_encoding_space(docNode,subnode,name,encodedSpace)</td>
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279
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281
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC281" class="line" lang="matlab"> <span class="n" style="color: #333;">subnode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">appendChild</span><span class="p">(</span><span class="n" style="color: #333;">n2</span><span class="p">);</span></span>
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280
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282
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC282" class="line" lang="matlab"><span class="k" style="font-weight: 600;">end</span></span>
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283
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC283" class="line" lang="matlab"></span>
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284
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC284" class="line" lang="matlab"><span class="k" style="font-weight: 600;">function</span> <span class="n" style="color: #333;">append_optional_three_dimensional_float</span><span class="p">(</span><span class="n" style="color: #333;">docNode</span><span class="p">,</span> <span class="n" style="color: #333;">subnode</span><span class="p">,</span> <span class="n" style="color: #333;">subheader</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
285
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC285" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isfield</span><span class="p">(</span><span class="n" style="color: #333;">subheader</span><span class="p">,</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
286
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC286" class="line" lang="matlab"> <span class="n" style="color: #333;">n2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">docNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">createElement</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
287
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC287" class="line" lang="matlab"> <span class="n" style="color: #333;">threeDimensionalFloat</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subheader</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="nb" style="color: #0086b3;">matlab</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lang</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">makeValidName</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
288
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC288" class="line" lang="matlab"> <span class="n" style="color: #333;">append_optional</span><span class="p">(</span><span class="n" style="color: #333;">docNode</span><span class="p">,</span><span class="n" style="color: #333;">n2</span><span class="p">,</span><span class="n" style="color: #333;">threeDimensionalFloat</span><span class="p">,</span><span class="s1" style="color: #d14;">'x'</span><span class="p">,</span><span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">num2str</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
289
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC289" class="line" lang="matlab"> <span class="n" style="color: #333;">append_optional</span><span class="p">(</span><span class="n" style="color: #333;">docNode</span><span class="p">,</span><span class="n" style="color: #333;">n2</span><span class="p">,</span><span class="n" style="color: #333;">threeDimensionalFloat</span><span class="p">,</span><span class="s1" style="color: #d14;">'y'</span><span class="p">,</span><span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">num2str</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
290
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC290" class="line" lang="matlab"> <span class="n" style="color: #333;">append_optional</span><span class="p">(</span><span class="n" style="color: #333;">docNode</span><span class="p">,</span><span class="n" style="color: #333;">n2</span><span class="p">,</span><span class="n" style="color: #333;">threeDimensionalFloat</span><span class="p">,</span><span class="s1" style="color: #d14;">'z'</span><span class="p">,</span><span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">num2str</span><span class="p">);</span></span>
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<td class="new_line diff-line-num new" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
291
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC291" class="line" lang="matlab"> <span class="n" style="color: #333;">subnode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">appendChild</span><span class="p">(</span><span class="n" style="color: #333;">n2</span><span class="p">);</span></span>
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292
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC292" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">end</span></span>
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293
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC293" class="line" lang="matlab"><span class="k" style="font-weight: 600;">end</span></span>
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282
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294
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC294" class="line" lang="matlab"></span>
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283
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295
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC295" class="line" lang="matlab"><span class="k" style="font-weight: 600;">function</span> <span class="n" style="color: #333;">append_optional</span><span class="p">(</span><span class="n" style="color: #333;">docNode</span><span class="p">,</span><span class="n" style="color: #333;">subnode</span><span class="p">,</span><span class="n" style="color: #333;">subheader</span><span class="p">,</span><span class="n" style="color: #333;">name</span><span class="p">,</span><span class="n" style="color: #333;">tostr</span><span class="p">)</span></span>
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284
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296
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC296" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isfield</span><span class="p">(</span><span class="n" style="color: #333;">subheader</span><span class="p">,</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="303" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -291,6 +303,9 @@ function append_optional(docNode,subnode,subheader,name,tostr)</td>
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291
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303
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC303" class="line" lang="matlab"><span class="k" style="font-weight: 600;">end</span></span>
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292
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304
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC304" class="line" lang="matlab"></span>
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293
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305
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC305" class="line" lang="matlab"><span class="k" style="font-weight: 600;">function</span> <span class="n" style="color: #333;">append_node</span><span class="p">(</span><span class="n" style="color: #333;">docNode</span><span class="p">,</span><span class="n" style="color: #333;">subnode</span><span class="p">,</span><span class="n" style="color: #333;">subheader</span><span class="p">,</span><span class="n" style="color: #333;">name</span><span class="p">,</span><span class="n" style="color: #333;">tostr</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
306
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC306" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">~</span><span class="nb" style="color: #0086b3;">exist</span><span class="p">(</span><span class="s1" style="color: #d14;">'tostr'</span><span class="p">,</span> <span class="s1" style="color: #d14;">'var'</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
307
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC307" class="line" lang="matlab"> <span class="n" style="color: #333;">tostr</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">char</span><span class="p">;</span></span>
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<td class="new_line diff-line-num new" data-linenumber="308" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
308
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC308" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">end</span></span>
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294
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309
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC309" class="line" lang="matlab"></span>
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295
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310
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC310" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">ischar</span><span class="p">(</span><span class="n" style="color: #333;">subheader</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">))</span></span>
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296
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311
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC311" class="line" lang="matlab"> <span class="n" style="color: #333;">n1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">docNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">createElement</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -302,8 +317,11 @@ function append_node(docNode,subnode,subheader,name,tostr)</td>
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302
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317
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC317" class="line" lang="matlab"> <span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subheader</span><span class="o" style="font-weight: 600;">.</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)(:);</span></span>
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303
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318
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC318" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">thisval</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">)</span></span>
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304
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319
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC319" class="line" lang="matlab"> <span class="n" style="color: #333;">n1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">docNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">createElement</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">);</span></span>
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305
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC305" class="line" lang="matlab"> <span class="n" style="color: #333;">n1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">appendChild</span><span class="k" style="font-weight: 600;">...</span></span>
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306
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<td class="new_line diff-line-num old" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC306" class="line" lang="matlab"> <span class="p">(</span><span class="n" style="color: #333;">docNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">createTextNode</span><span class="p">(</span><span class="n" style="color: #333;">tostr</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">(</span><span class="n" style="color: #333;">thisval</span><span class="p">))));</span></span>
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320
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC320" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">iscell</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">)</span></span>
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<td class="new_line diff-line-num new" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
321
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC321" class="line" lang="matlab"> <span class="n" style="color: #333;">n1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">appendChild</span><span class="p">(</span><span class="n" style="color: #333;">docNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">createTextNode</span><span class="p">(</span><span class="n" style="color: #333;">tostr</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">{</span><span class="n" style="color: #333;">thisval</span><span class="p">})));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
322
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC322" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">else</span></span>
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<td class="new_line diff-line-num new" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
323
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC323" class="line" lang="matlab"> <span class="n" style="color: #333;">n1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">appendChild</span><span class="p">(</span><span class="n" style="color: #333;">docNode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">createTextNode</span><span class="p">(</span><span class="n" style="color: #333;">tostr</span><span class="p">(</span><span class="n" style="color: #333;">val</span><span class="p">(</span><span class="n" style="color: #333;">thisval</span><span class="p">))));</span></span>
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<td class="new_line diff-line-num new" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
324
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC324" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">end</span></span>
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307
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325
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC325" class="line" lang="matlab"> <span class="n" style="color: #333;">subnode</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">appendChild</span><span class="p">(</span><span class="n" style="color: #333;">n1</span><span class="p">);</span></span>
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308
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326
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC326" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">end</span></span>
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309
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327
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC327" class="line" lang="matlab"> <span class="k" style="font-weight: 600;">end</span></span>
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<a href="https://salsa.debian.org/med-team/ismrmrd/-/commit/cbc6808c2860f5d9913f598cdcfe8e1adba1a4be#12358198cb5bfc8757e826c6b1f39316abd7a4ca"><strong>matlab/test/xml/ismrmrd_example.xml</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,14 +8,13 @@</td>
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8
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8
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC8" class="line" lang="xml"> <span class="nt" style="color: #000080;"><systemVendor></span>SIEMENS<span class="nt" style="color: #000080;"></systemVendor></span></span>
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9
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9
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC9" class="line" lang="xml"> <span class="nt" style="color: #000080;"><systemModel></span>Avanto<span class="nt" style="color: #000080;"></systemModel></span></span>
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10
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10
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC10" class="line" lang="xml"> <span class="nt" style="color: #000080;"><systemFieldStrength_T></span>1.494<span class="nt" style="color: #000080;"></systemFieldStrength_T></span></span>
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11
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<td class="new_line diff-line-num old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb"><pre style="margin: 0;">-<span id="LC11" class="line" lang="xml"> <span class="nt" style="color: #000080;"><receiverChannels></span>32<span class="nt" style="color: #000080;"></receiverChannels></span></span>
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12
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11
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC11" class="line" lang="xml"> <span class="nt" style="color: #000080;"><relativeReceiverNoiseBandwidth></span>0.79<span class="nt" style="color: #000080;"></relativeReceiverNoiseBandwidth></span></span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -62,6 +61,7 @@</td>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC64" class="line" lang="xml"> <span class="nt" style="color: #000080;"><trajectory></span>cartesian<span class="nt" style="color: #000080;"></trajectory></span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC67" class="line" lang="xml"> <span class="nt" style="color: #000080;"><kspace_encoding_step_1></span>1<span class="nt" style="color: #000080;"></kspace_encoding_step_1></span></span>
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<a href="https://salsa.debian.org/med-team/ismrmrd/-/commit/cbc6808c2860f5d9913f598cdcfe8e1adba1a4be#f822e7a2589360e91d393fdedfbaa7c8086400e5"><strong>schema/ismrmrd.xsd</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC65" class="line" lang="xml"> <span class="nt" style="color: #000080;"><xs:element</span> <span class="na" style="color: #008080;">minOccurs=</span><span class="s" style="color: #d14;">"0"</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"seriesDate"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"xs:date"</span> <span class="nt" style="color: #000080;">/></span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC66" class="line" lang="xml"> <span class="nt" style="color: #000080;"><xs:element</span> <span class="na" style="color: #008080;">minOccurs=</span><span class="s" style="color: #d14;">"0"</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"seriesTime"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"xs:time"</span> <span class="nt" style="color: #000080;">/></span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC67" class="line" lang="xml"> <span class="nt" style="color: #000080;"><xs:element</span> <span class="na" style="color: #008080;">minOccurs=</span><span class="s" style="color: #d14;">"1"</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"patientPosition"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"patientPositionType"</span> <span class="nt" style="color: #000080;">/></span></span>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC68" class="line" lang="xml"> <span class="nt" style="color: #000080;"><xs:element</span> <span class="na" style="color: #008080;">minOccurs=</span><span class="s" style="color: #d14;">"0"</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"relativeTablePosition"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"threeDimensionalFloat"</span> <span class="nt" style="color: #000080;">/></span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC69" class="line" lang="xml"> <span class="nt" style="color: #000080;"><xs:element</span> <span class="na" style="color: #008080;">minOccurs=</span><span class="s" style="color: #d14;">"0"</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"initialSeriesNumber"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"xs:long"</span> <span class="nt" style="color: #000080;">/></span></span>
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70
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC70" class="line" lang="xml"> <span class="nt" style="color: #000080;"><xs:element</span> <span class="na" style="color: #008080;">minOccurs=</span><span class="s" style="color: #d14;">"0"</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"protocolName"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"xs:string"</span> <span class="nt" style="color: #000080;">/></span></span>
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71
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC71" class="line" lang="xml"> <span class="nt" style="color: #000080;"><xs:element</span> <span class="na" style="color: #008080;">minOccurs=</span><span class="s" style="color: #d14;">"0"</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"seriesDescription"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"xs:string"</span> <span class="nt" style="color: #000080;">/></span></span>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -144,6 +145,15 @@</td>
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145
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC145" class="line" lang="xml"> <span class="nt" style="color: #000080;"></xs:sequence></span></span>
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146
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC146" class="line" lang="xml"> <span class="nt" style="color: #000080;"></xs:complexType></span></span>
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147
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC147" class="line" lang="xml"></span>
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148
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC148" class="line" lang="xml"> <span class="nt" style="color: #000080;"><xs:complexType</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"threeDimensionalFloat"</span><span class="nt" style="color: #000080;">></span></span>
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149
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC149" class="line" lang="xml"> <span class="nt" style="color: #000080;"><xs:sequence></span></span>
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150
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC150" class="line" lang="xml"> <span class="nt" style="color: #000080;"><xs:element</span> <span class="na" style="color: #008080;">maxOccurs=</span><span class="s" style="color: #d14;">"1"</span> <span class="na" style="color: #008080;">minOccurs=</span><span class="s" style="color: #d14;">"1"</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"x"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"xs:float"</span> <span class="nt" style="color: #000080;">/></span></span>
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151
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC151" class="line" lang="xml"> <span class="nt" style="color: #000080;"><xs:element</span> <span class="na" style="color: #008080;">maxOccurs=</span><span class="s" style="color: #d14;">"1"</span> <span class="na" style="color: #008080;">minOccurs=</span><span class="s" style="color: #d14;">"1"</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"y"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"xs:float"</span> <span class="nt" style="color: #000080;">/></span></span>
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152
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC152" class="line" lang="xml"> <span class="nt" style="color: #000080;"><xs:element</span> <span class="na" style="color: #008080;">maxOccurs=</span><span class="s" style="color: #d14;">"1"</span> <span class="na" style="color: #008080;">minOccurs=</span><span class="s" style="color: #d14;">"1"</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"z"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"xs:float"</span> <span class="nt" style="color: #000080;">/></span></span>
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153
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC153" class="line" lang="xml"> <span class="nt" style="color: #000080;"></xs:sequence></span></span>
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154
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157
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC157" class="line" lang="xml"> <span class="nt" style="color: #000080;"><xs:complexType</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"limitType"</span><span class="nt" style="color: #000080;">></span></span>
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148
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158
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC158" class="line" lang="xml"> <span class="nt" style="color: #000080;"><xs:all></span></span>
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159
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC159" class="line" lang="xml"> <span class="nt" style="color: #000080;"><xs:element</span> <span class="na" style="color: #008080;">default=</span><span class="s" style="color: #d14;">"0"</span> <span class="na" style="color: #008080;">name=</span><span class="s" style="color: #d14;">"minimum"</span> <span class="na" style="color: #008080;">type=</span><span class="s" style="color: #d14;">"xs:unsignedShort"</span> <span class="nt" style="color: #000080;">/></span></span>
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<a href="https://salsa.debian.org/med-team/ismrmrd/-/commit/cbc6808c2860f5d9913f598cdcfe8e1adba1a4be#95e2e78ef653f99f17157507df48e1b04629b439"><strong>schema/ismrmrd_example_extended.xml</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC21" class="line" lang="xml"> <span class="nt" style="color: #000080;"><seriesDate></span>2012-08-13<span class="nt" style="color: #000080;"></seriesDate></span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC22" class="line" lang="xml"> <span class="nt" style="color: #000080;"><seriesTime></span>09:10:12<span class="nt" style="color: #000080;"></seriesTime></span></span>
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23
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC23" class="line" lang="xml"> <span class="nt" style="color: #000080;"><patientPosition></span>HFS<span class="nt" style="color: #000080;"></patientPosition></span></span>
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24
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC24" class="line" lang="xml"> <span class="nt" style="color: #000080;"><relativeTablePosition></span></span>
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25
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC25" class="line" lang="xml"> <span class="nt" style="color: #000080;"><x></span>0<span class="nt" style="color: #000080;"></x></span></span>
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26
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC26" class="line" lang="xml"> <span class="nt" style="color: #000080;"><y></span>0<span class="nt" style="color: #000080;"></y></span></span>
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27
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC27" class="line" lang="xml"> <span class="nt" style="color: #000080;"><z></span>10<span class="nt" style="color: #000080;"></z></span></span>
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28
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC28" class="line" lang="xml"> <span class="nt" style="color: #000080;"></relativeTablePosition></span></span>
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24
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29
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC29" class="line" lang="xml"> <span class="nt" style="color: #000080;"><initialSeriesNumber></span>1<span class="nt" style="color: #000080;"></initialSeriesNumber></span></span>
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25
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30
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC30" class="line" lang="xml"> <span class="nt" style="color: #000080;"><protocolName></span>ExampleProt<span class="nt" style="color: #000080;"></protocolName></span></span>
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26
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31
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC31" class="line" lang="xml"> <span class="nt" style="color: #000080;"><seriesDescription></span>MRIStudy1<span class="nt" style="color: #000080;"></seriesDescription></span></span>
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