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<h3>
Andreas Tille pushed to branch debian/master
at <a href="https://salsa.debian.org/med-team/ciftilib">Debian Med / ciftilib</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ciftilib/commit/84a45634bfd805dfb20633034579bbe2d2110d14">84a45634</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T08:40:33Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.5.3</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ciftilib/commit/21525505fdab77d8d2a67f504a9138774f914ed0">21525505</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T08:40:38Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.5.3'
Update to upstream version '1.5.3'
with Debian dir 8f1e443bd35b8c9fdb87c072c678e8654110eb62</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ciftilib/commit/d94c49752f08c95951df745ea69ac792a3ab53c8">d94c4975</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T08:40:38Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ciftilib/commit/ffac925f7bbca782f7a28ccda96522eca8104b45">ffac925f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T08:40:38Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">debhelper 12
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ciftilib/commit/92827b3408ed7920975420b8f9dca31a35307186">92827b34</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T08:40:43Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.3.0
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ciftilib/commit/c245ed50f4bec7fe590b31b60a49967dba10dc20">c245ed50</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T08:43:57Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upstream applied patches
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ciftilib/commit/4e52611c6df94d03fa28b600a571755774e0196f">4e52611c</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T09:15:25Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not run build time tests parallel
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/ciftilib/commit/7404c968411b750315bcfa5dfc882faf771474c2">7404c968</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-01-30T09:20:23Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
</ul>
<h4>27 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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</li>
<li class="file-stats">
<a href="#9a2aa4db38d3115ed60da621e012c0efc0172aae">
CMakeLists.txt
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<li class="file-stats">
<a href="#a03b58b952b312440c771d304d42b57d0c7fb29d">
Doxyfile.in
</a>
</li>
<li class="file-stats">
<a href="#69e27356ef629022720d868ab0c0e3394775b6c1">
README
</a>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
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<li class="file-stats">
<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">
debian/compat
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<li class="file-stats">
<a href="#dc8f7a00b599b92b9f014014a779f5a4cbf5bccf">
<span class="deleted-file">
−
debian/patches/Enable-parallel-execution-of-tests.patch
</span>
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<li class="file-stats">
<a href="#75ed0086b826909d323ef1597bd300ce3f6f10af">
<span class="deleted-file">
−
debian/patches/Fix-spelling-errors-reported-by-Lintian.patch
</span>
</a>
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<span class="deleted-file">
−
debian/patches/series
</span>
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<li class="file-stats">
<a href="#1958a1278fbc887fe31daefcf65a5e57f16807b6">
example/CMakeLists.txt
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<li class="file-stats">
<a href="#4c5c68ad3b75ed24e08ddb5f2ff3720dc14fe5b7">
<span class="new-file">
+
example/datatype.cxx
</span>
</a>
</li>
<li class="file-stats">
<a href="#631c8d07f5ea23b9a9f6c57f5389dfcf94bc33b7">
src/CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#32a152aeda3110adcdbd417db5b1d26f0abecd6b">
src/Cifti/CMakeLists.txt
</a>
</li>
<li class="file-stats">
<a href="#0685fd34d9c8da41f7280e865f694d39f40305cb">
src/Cifti/CiftiBrainModelsMap.cxx
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<li class="file-stats">
<a href="#e11a4fe1e7bdb48037a91121d18a2344e323cd1f">
src/CiftiFile.cxx
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<li class="file-stats">
<a href="#1e4dfb5374146c117f65eb7fc0fe28a6f3e2de89">
src/CiftiFile.h
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<li class="file-stats">
<a href="#9eac26ae03a8483af4a93893a3a08f87f96e5219">
src/Common/AString.h
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<li class="file-stats">
<a href="#410b539d70abfc4648b1b19780a2381b1a9fcbbd">
src/Common/BinaryFile.cxx
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<li class="file-stats">
<a href="#7cdad2fbf92f42a516417164e615370fe457ac85">
src/Common/BinaryFile.h
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<li class="file-stats">
<a href="#0072de496a99688cfe175e9fb52da88c2f89573f">
src/Common/CMakeLists.txt
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<li class="file-stats">
<a href="#cef9390bac429a064229b057088c655a78a00305">
src/Nifti/CMakeLists.txt
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<li class="file-stats">
<a href="#0cd4c140b4e6b79e2c3b2cf44b91861befe56050">
src/Nifti/NiftiHeader.cxx
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<li class="file-stats">
<a href="#c8d9666779c52ffe39b1b01c4c06b8285258f0cf">
src/Nifti/NiftiHeader.h
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<a href="#7d2ec12a9cdd93000c8f8714368517127db5b64b">
src/NiftiIO.cxx
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<li class="file-stats">
<a href="#e1bc753f66e97e3c73bc3ba07e7931c56b13526c">
src/NiftiIO.h
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</ul>
<h4>Changes:</h4>
<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="19" 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">@@ -19,10 +19,11 @@ compiler:</td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">gcc</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="yaml"></span>
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<td class="diff-line-num old_line" data-linenumber="21" 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="diff-line-num new_line" data-linenumber="21" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC21" class="line" lang="yaml"><span class="na" style="color: teal;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">IGNORE_QT=false SHARED=true</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">IGNORE_QT=false SHARED=false</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">IGNORE_QT=true SHARED=true</span></span>
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<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">IGNORE_QT=true SHARED=false</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml"> <span class="na" style="color: teal;">matrix</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">IGNORE_QT=false SHARED=true</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">IGNORE_QT=false SHARED=false</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">IGNORE_QT=true SHARED=true</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">IGNORE_QT=true SHARED=false</span></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="yaml"><span class="na" style="color: teal;">before_install</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">mkdir ../build</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">@@ -30,5 +31,7 @@ before_install:</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="yaml"><span class="na" style="color: teal;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">cmake -D BUILD_SHARED_LIBS:BOOL=$SHARED -D IGNORE_QT:BOOL=$IGNORE_QT ../CiftiLib</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">export LD_LIBRARY_PATH=$(if [[ $CXX == "clang++" ]]; then echo -n '/usr/local/clang/lib'; fi)</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make -j 4</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">example/xmlinfo ../CiftiLib/example/data/ones.dscalar.nii</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ctest</span></span></pre>
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<li id="9a2aa4db38d3115ed60da621e012c0efc0172aae">
<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#9a2aa4db38d3115ed60da621e012c0efc0172aae"><strong>CMakeLists.txt</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -41,7 +41,7 @@ IF (NOT IGNORE_QT)</td>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>LIBS <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">LIBS</span><span class="si" style="color: #d14;">}</span> Qt5::Core<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;">#whatever that means</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">ADD_DEFINITIONS</span><span class="p">(</span>-DCIFTILIB_USE_QT<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CIFTILIB_PKGCONFIG_REQUIRES_LINE <span class="s2" style="color: #d14;">"Requires: Qt5Core<span class="idiff left right"> Qt5Xml</span>"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CIFTILIB_PKGCONFIG_REQUIRES_LINE <span class="s2" style="color: #d14;">"Requires: Qt5Core"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>CIFTILIB_PKGCONFIG_DEFINE <span class="s2" style="color: #d14;">"-DCIFTILIB_USE_QT"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">ENDIF</span> <span class="p">(</span>Qt5Core_FOUND<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">ENDIF</span> <span class="p">(</span>QT_FOUND<span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#a03b58b952b312440c771d304d42b57d0c7fb29d"><strong>Doxyfile.in</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">@@ -231,7 +231,7 @@ EXTENSION_MAPPING =</td>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="plaintext"># func(std::string) {}). This also make the inheritance and collaboration </span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="plaintext"># diagrams that involve STL classes more complete and accurate.</span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC234" class="line" lang="plaintext">BUILTIN_STL_SUPPORT = <span class="idiff left right">NO</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext">BUILTIN_STL_SUPPORT = <span class="idiff left right">YES</span></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="plaintext"># If you use Microsoft's C++/CLI language, you should set this option to YES to </span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="plaintext"># enable parsing support.</span>
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<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#69e27356ef629022720d868ab0c0e3394775b6c1"><strong>README</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">The CiftiLib library requires boost headers and either QT (4.8.x or 5), or libxml++ 2.17.x or newer (and its dependencies: libxml2, glib, sigc++, gtkmm and glibmm) and the boost filesystem library to compile, and optionally uses zlib if you want to use its NIfTI reading capabilities for other purposes.</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"><span class="idiff left right">It is currently set up to be compiled, along with a few simple examples, by</span> cmake:</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"><span class="idiff left right">To build it, and example executables, in the recommended "out-of-source" method using</span> cmake:</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">#start one level up from the source tree</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">#make build directory beside the source tree, enter it</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">#make <span class="idiff left right">a </span>build directory beside the source tree, enter it</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">mkdir build; cd build</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">#you may want to set the cmake variable CMAKE_BUILD_TYPE to Release or Debug before building</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">#<span class="idiff left right">NOTE: </span>you may want to set the cmake variable CMAKE_BUILD_TYPE to Release or Debug before building</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">#the default build behavior may be non-optimized and without debug symbols.</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">#run cmake to generate makefiles</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">cmake <span class="idiff left right">../CiftiLib -D CMAKE_BUILD_TYPE=Release</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">cmake <span class="idiff left right">-D CMAKE_BUILD_TYPE=Release ../CiftiLib</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">#OR</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">cmake-gui ../CiftiLib</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">#build</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">make</span>
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19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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20
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">#OPTIONAL: run tests<span class="idiff left right">, make docs</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">#OPTIONAL: run tests</span>
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">make test</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">#install library to location specified by cmake variable CMAKE_INSTALL_PREFIX</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">make install</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">#OPTIONAL: generate documentation (needs doxygen installed and on PATH)</span>
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22
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">make doc</span>
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23
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>
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24
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">The resulting library and example executables will be in subdirectories of the build directory, not in the source directory. You can install the library and headers (location controlled by cmake variable CMAKE_INSTALL_PREFIX and make variable DESTDIR) with 'make install'.</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">The build results will be in subdirectories of the build directory, not in the source directory.</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">To use the installed library, use pkg-config to get the needed directories and libraries. For instance, in cmake:</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">find_package(PkgConfig)</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">pkg_check_modules(PC_CIFTI REQUIRED CiftiLib)</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">You can then use cmake variables PC_CIFTI_LIBRARIES, PC_CIFTI_INCLUDE_DIRS, and similar, see here for descriptions:</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">https://cmake.org/cmake/help/v3.0/module/FindPkgConfig.html</span>
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25
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"></span>
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26
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext">Troubleshooting:</span>
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27
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ciftilib (1.5.3-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * debhelper 12</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> * Standards-Version: 4.3.0</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> * Do not run build time tests parallel</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 30 Jan 2019 10:15:35 +0100</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">ciftilib (1.5.1-3) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> * Team upload</span>
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<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">1</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">1<span class="idiff left right">2</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -4,13 +4,13 @@ Uploaders: Ghislain Antony Vaillant <ghisvail@gmail.com></td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Section: libs</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Priority: optional</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Build-Depends: cmake,</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> debhelper (>= 1<span class="idiff left right">1</span>~),</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> debhelper (>= 1<span class="idiff left right">2</span>~),</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> libboost-dev,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> libboost-filesystem-dev,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libxml++2.6-dev,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> zlib1g-dev</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Build-Depends-Indep: doxygen</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">1.4</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Standards-Version: 4.<span class="idiff left right">3.0</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/ciftilib</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/ciftilib.git</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Homepage: https://github.com/Washington-University/CiftiLib</span>
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<li id="dc8f7a00b599b92b9f014014a779f5a4cbf5bccf">
<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#dc8f7a00b599b92b9f014014a779f5a4cbf5bccf"><strong>debian/patches/Enable-parallel-execution-of-tests.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">From: Ghislain Antony Vaillant <ghisvail@gmail.com></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Date: Tue, 8 Nov 2016 11:28:10 +0000</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Subject: Enable parallel execution of tests.</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">---</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> example/CMakeLists.txt | 2 ++</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> 1 file changed, 2 insertions(+)</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/example/CMakeLists.txt b/example/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gh" style="color: #999;">index 71f4b0a..bc34779 100644</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/example/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/example/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -76,8 +76,10 @@ FOREACH(index RANGE ${loop_end})</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> ADD_TEST(rewrite-little-${testfile} rewrite ${CMAKE_SOURCE_DIR}/example/data/${testfile} little-${testfile} LITTLE)</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> LIST(GET cifti_le_md5s ${index} goodsum)</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> ADD_TEST(rewrite-little-md5-${testfile} ${CMAKE_COMMAND} -Dgood_sum=${goodsum} -Dcheck_file=little-${testfile} -P ${CMAKE_SOURCE_DIR}/cmake/scripts/testmd5.cmake)</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SET_TESTS_PROPERTIES(rewrite-little-md5-${testfile} PROPERTIES DEPENDS rewrite-little-${testfile})</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> ADD_TEST(rewrite-big-${testfile} rewrite ${CMAKE_SOURCE_DIR}/example/data/${testfile} big-${testfile} BIG)</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> LIST(GET cifti_be_md5s ${index} goodsum)</span>
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21
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> ADD_TEST(rewrite-big-md5-${testfile} ${CMAKE_COMMAND} -Dgood_sum=${goodsum} -Dcheck_file=big-${testfile} -P ${CMAKE_SOURCE_DIR}/cmake/scripts/testmd5.cmake)</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ SET_TESTS_PROPERTIES(rewrite-big-md5-${testfile} PROPERTIES DEPENDS rewrite-big-${testfile})</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"> ENDFOREACH(index RANGE ${loop_end})</span></pre>
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<li id="75ed0086b826909d323ef1597bd300ce3f6f10af">
<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#75ed0086b826909d323ef1597bd300ce3f6f10af"><strong>debian/patches/Fix-spelling-errors-reported-by-Lintian.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff">From: Ghislain Antony Vaillant <ghisvail@gmail.com></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff">Date: Tue, 8 Nov 2016 12:41:01 +0000</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff">Subject: Fix spelling errors reported by Lintian.</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">---</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"> src/Cifti/CiftiBrainModelsMap.cxx | 8 ++++----</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"> src/CiftiFile.cxx | 6 +++---</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> 2 files changed, 7 insertions(+), 7 deletions(-)</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/src/Cifti/CiftiBrainModelsMap.cxx b/src/Cifti/CiftiBrainModelsMap.cxx</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gh" style="color: #999;">index 39e65c6..d8c1e54 100644</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/Cifti/CiftiBrainModelsMap.cxx</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/Cifti/CiftiBrainModelsMap.cxx</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -262,7 +262,7 @@ const vector<int64_t>& CiftiBrainModelsMap::getNodeList(const StructureEnum::Enu</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> map<StructureEnum::Enum, int>::const_iterator iter = m_surfUsed.find(structure);</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> if (iter == m_surfUsed.end())</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CiftiException("getNodeList called for nonexistant structure");//throw if it doesn't exist, because we don't have a reference to return - things should identify which structures exist before calling this</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CiftiException("getNodeList called for nonexistent structure");//throw if it doesn't exist, because we don't have a reference to return - things should identify which structures exist before calling this</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> CiftiAssertVectorIndex(m_modelsInfo, iter->second);</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"> return m_modelsInfo[iter->second].m_nodeIndices;</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -274,7 +274,7 @@ vector<CiftiBrainModelsMap::SurfaceMap> CiftiBrainModelsMap::getSurfaceMap(const</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"> map<StructureEnum::Enum, int>::const_iterator iter = m_surfUsed.find(structure);</span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"> if (iter == m_surfUsed.end())</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CiftiException("getSurfaceMap called for nonexistant structure");//also throw, for consistency</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CiftiException("getSurfaceMap called for nonexistent structure");//also throw, for consistency</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> CiftiAssertVectorIndex(m_modelsInfo, iter->second);</span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"> const BrainModelPriv& myModel = m_modelsInfo[iter->second];</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -380,7 +380,7 @@ vector<CiftiBrainModelsMap::VolumeMap> CiftiBrainModelsMap::getVolumeStructureMa</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> map<StructureEnum::Enum, int>::const_iterator iter = m_volUsed.find(structure);</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> if (iter == m_volUsed.end())</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CiftiException("getVolumeStructureMap called for nonexistant structure");//also throw, for consistency</span></span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CiftiException("getVolumeStructureMap called for nonexistent structure");//also throw, for consistency</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"> CiftiAssertVectorIndex(m_modelsInfo, iter->second);</span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"> const BrainModelPriv& myModel = m_modelsInfo[iter->second];</span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -404,7 +404,7 @@ const vector<int64_t>& CiftiBrainModelsMap::getVoxelList(const StructureEnum::En</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"> map<StructureEnum::Enum, int>::const_iterator iter = m_volUsed.find(structure);</span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"> if (iter == m_volUsed.end())</span>
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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw CiftiException("getVoxelList called for nonexistant structure");//throw if it doesn't exist, because we don't have a reference to return - things should identify which structures exist before calling this</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw CiftiException("getVoxelList called for nonexistent structure");//throw if it doesn't exist, because we don't have a reference to return - things should identify which structures exist before calling this</span></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"> CiftiAssertVectorIndex(m_modelsInfo, iter->second);</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"> return m_modelsInfo[iter->second].m_voxelIndicesIJK;</span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/src/CiftiFile.cxx b/src/CiftiFile.cxx</span></span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"><span class="gh" style="color: #999;">index 99dd512..6e768d7 100644</span></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/CiftiFile.cxx</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/CiftiFile.cxx</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -165,11 +165,11 @@ void CiftiFile::writeFile(const AString& fileName, const CiftiVersion& writingVe</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"> if (m_readingImpl == NULL || m_dims.empty()) throw CiftiException("writeFile called on uninitialized CiftiFile");</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"> bool writeSwapped = shouldSwap(endian);</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- AString canonicalFilename = pathToCanonical(fileName);//NOTE: returns EMPTY STRING for nonexistant file</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ AString canonicalFilename = pathToCanonical(fileName);//NOTE: returns EMPTY STRING for nonexistent file</span></span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"> const CiftiOnDiskImpl* testImpl = dynamic_cast<CiftiOnDiskImpl*>(m_readingImpl.get());</span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"> bool collision = false, hadWriter = (m_writingImpl != NULL);</span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"> if (testImpl != NULL && canonicalFilename != "" && pathToCanonical(testImpl->getFilename()) == canonicalFilename)</span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- {//empty string test is so that we don't say collision if both are nonexistant - could happen if file is removed/unlinked while reading on some filesystems</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ {//empty string test is so that we don't say collision if both are nonexistent - could happen if file is removed/unlinked while reading on some filesystems</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"> if (m_onDiskVersion == writingVersion && (dontRewrite(endian) || writeSwapped == testImpl->isSwapped())) return;//don't need to copy to itself</span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"> collision = true;//we need to copy to memory temporarily</span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"> boost::shared_ptr<WriteImplInterface> tempMemory(new CiftiMemoryImpl(m_xml));//because tempRead is a ReadImpl, can't be used to copy to</span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -300,7 +300,7 @@ void CiftiFile::verifyWriteImpl()</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"> CiftiOnDiskImpl* testImpl = dynamic_cast<CiftiOnDiskImpl*>(m_readingImpl.get());</span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"> if (testImpl != NULL)</span>
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71
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"> {</span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- AString canonicalCurrent = pathToCanonical(testImpl->getFilename());//returns "" if nonexistant, if unlinked while open</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ AString canonicalCurrent = pathToCanonical(testImpl->getFilename());//returns "" if nonexistent, if unlinked while open</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"> if (canonicalCurrent != "" && canonicalCurrent == pathToCanonical(m_writingFile))//these were already absolute</span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"> convertToInMemory();//save existing data in memory before we clobber file</span></pre>
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<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">Enable-parallel-execution-of-tests.patch</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">Fix-spelling-errors-reported-by-Lintian.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -25,3 +25,8 @@ override_dh_compress-indep:</td>
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">override_dh_auto_test-indep:</span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> echo "Do not run test suite for arch indep builds"</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">override_dh_auto_test-arch:</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> dh_auto_test --no-parallel</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">endif</span></pre>
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<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#1958a1278fbc887fe31daefcf65a5e57f16807b6"><strong>example/CMakeLists.txt</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cmake"></span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">PROJECT</span><span class="p">(</span>example<span class="p">)</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ADD_EXECUTABLE</span><span class="p">(</span>rewrite</span>
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5
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cmake">rewrite.cxx<span class="p">)</span></span>
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6
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cmake"></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">@@ -15,6 +13,13 @@ TARGET_LINK_LIBRARIES(xmlinfo</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="cmake">Cifti</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="cmake"><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">LIBS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ADD_EXECUTABLE</span><span class="p">(</span>datatype</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cmake">datatype.cxx<span class="p">)</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cmake"></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">TARGET_LINK_LIBRARIES</span><span class="p">(</span>datatype</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cmake">Cifti</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cmake"><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">LIBS</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">INCLUDE_DIRECTORIES</span><span class="p">(</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cmake"><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/example</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cmake"><span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/src</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">@@ -29,7 +34,7 @@ ones.dscalar.nii</td>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="cmake"><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">IF</span><span class="p">(</span>QT_FOUND<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;">#QT4</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;">#QT4<span class="idiff left right"> and QT5</span></span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>cifti_be_md5s</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cmake"> 3ba20f6ef590735c1211991f8e0144e6</span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cmake"> e3a1639ef4b354752b0abb0613eedb73</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">@@ -44,6 +49,13 @@ IF(QT_FOUND)</td>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="cmake"> 32345267599b07083092b7dedfd8796c</span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="cmake"> 512e0359c64d69dde93d605f8797f3a2</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="cmake"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>cifti_datatype_md5s</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cmake"> cca91b955b1134251d62764cb1ebf44c</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cmake"> 6359af74ba6b51357aefab7de7a76097</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="cmake"> 10ee62309850e55936fa9f702df8b4d1</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="cmake"> e4997bdd4b8202ff502a19173693c43f</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cmake"> 870dae2d646cadeed1494f6271433499</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cmake"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ELSE</span><span class="p">(</span>QT_FOUND<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cmake"> <span class="c1" style="color: #998; font-style: italic;">#xml++</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>cifti_be_md5s</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">@@ -60,6 +72,13 @@ ELSE(QT_FOUND)</td>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cmake"> 6fabac021e377efd35dede7198feefd4</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cmake"> fe0cbb768e26aa12a0e03990f4f50a30</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cmake"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>cifti_datatype_md5s</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="cmake"> 794d60d9d397fe341e18313efeeac5ea</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="cmake"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ENDIF</span><span class="p">(</span>QT_FOUND<span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cmake"><span class="c1" style="color: #998; font-style: italic;">#ADD_TEST(timer ${CMAKE_CURRENT_BINARY_DIR}/Tests/test_driver timer)</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">@@ -76,8 +95,16 @@ FOREACH(index RANGE ${loop_end})</td>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">ADD_TEST</span><span class="p">(</span>rewrite-little-<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">testfile</span><span class="si" style="color: #d14;">}</span> rewrite <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/example/data/<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">testfile</span><span class="si" style="color: #d14;">}</span> little-<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">testfile</span><span class="si" style="color: #d14;">}</span> LITTLE<span class="p">)</span></span>
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">LIST</span><span class="p">(</span>GET cifti_le_md5s <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">index</span><span class="si" style="color: #d14;">}</span> goodsum<span class="p">)</span></span>
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78
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">ADD_TEST</span><span class="p">(</span>rewrite-little-md5-<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">testfile</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_COMMAND</span><span class="si" style="color: #d14;">}</span> -Dgood_sum=<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">goodsum</span><span class="si" style="color: #d14;">}</span> -Dcheck_file=little-<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">testfile</span><span class="si" style="color: #d14;">}</span> -P <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/cmake/scripts/testmd5.cmake<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">SET_TESTS_PROPERTIES</span><span class="p">(</span>rewrite-little-md5-<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">testfile</span><span class="si" style="color: #d14;">}</span> PROPERTIES DEPENDS rewrite-little-<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">testfile</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">ADD_TEST</span><span class="p">(</span>rewrite-big-<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">testfile</span><span class="si" style="color: #d14;">}</span> rewrite <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/example/data/<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">testfile</span><span class="si" style="color: #d14;">}</span> big-<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">testfile</span><span class="si" style="color: #d14;">}</span> BIG<span class="p">)</span></span>
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">LIST</span><span class="p">(</span>GET cifti_be_md5s <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">index</span><span class="si" style="color: #d14;">}</span> goodsum<span class="p">)</span></span>
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">ADD_TEST</span><span class="p">(</span>rewrite-big-md5-<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">testfile</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_COMMAND</span><span class="si" style="color: #d14;">}</span> -Dgood_sum=<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">goodsum</span><span class="si" style="color: #d14;">}</span> -Dcheck_file=big-<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">testfile</span><span class="si" style="color: #d14;">}</span> -P <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/cmake/scripts/testmd5.cmake<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">SET_TESTS_PROPERTIES</span><span class="p">(</span>rewrite-big-md5-<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">testfile</span><span class="si" style="color: #d14;">}</span> PROPERTIES DEPENDS rewrite-big-<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">testfile</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="cmake"> </span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">ADD_TEST</span><span class="p">(</span>datatype-<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">testfile</span><span class="si" style="color: #d14;">}</span> datatype <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/example/data/<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">testfile</span><span class="si" style="color: #d14;">}</span> datatype-<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">testfile</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">LIST</span><span class="p">(</span>GET cifti_datatype_md5s <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">index</span><span class="si" style="color: #d14;">}</span> goodsum<span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="107" 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">
107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">ADD_TEST</span><span class="p">(</span>datatype-md5-<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">testfile</span><span class="si" style="color: #d14;">}</span> <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_COMMAND</span><span class="si" style="color: #d14;">}</span> -Dgood_sum=<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">goodsum</span><span class="si" style="color: #d14;">}</span> -Dcheck_file=datatype-<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">testfile</span><span class="si" style="color: #d14;">}</span> -P <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">CMAKE_SOURCE_DIR</span><span class="si" style="color: #d14;">}</span>/cmake/scripts/testmd5.cmake<span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="cmake"> <span class="nf" style="color: #900; font-weight: 600;">SET_TESTS_PROPERTIES</span><span class="p">(</span>rewrite-big-md5-<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">testfile</span><span class="si" style="color: #d14;">}</span> PROPERTIES DEPENDS datatype-<span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">testfile</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="cmake"> </span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">ENDFOREACH</span><span class="p">(</span>index RANGE <span class="si" style="color: #d14;">${</span><span class="nv" style="color: teal;">loop_end</span><span class="si" style="color: #d14;">}</span><span class="p">)</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#4c5c68ad3b75ed24e08ddb5f2ff3720dc14fe5b7"><strong>example/datatype.cxx</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "CiftiFile.h"</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <vector></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">std</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">cifti</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">/**\file datatype.cxx</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">This program reads a Cifti file from argv[1], and writes it out to argv[2] using 8-bit unsigned integer and data scaling.</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">It uses a single CiftiFile object to do this, for simplicity - to see how to do something similar with two objects,</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">which is more relevant for how you would do processing on cifti files, see rewrite.cxx.</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">\include datatype.cxx</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="cpp"><span class="cm" style="color: #998; font-style: italic;">*/</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</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;">argv</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">argc</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"usage: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" <input cifti> <output cifti>"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="cpp"> <span class="n" style="color: #333;">cout</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" rewrite the input cifti file to the output filename, using uint8 and data scaling."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"> <span class="n" style="color: #333;">CiftiFile</span> <span class="n" style="color: #333;">inputFile</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]);</span><span class="c1" style="color: #998; font-style: italic;">//on-disk reading by default</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"> <span class="n" style="color: #333;">inputFile</span><span class="p">.</span><span class="n" style="color: #333;">setWritingDataTypeAndScaling</span><span class="p">(</span><span class="n" style="color: #333;">NIFTI_TYPE_UINT8</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">,</span> <span class="mf" style="color: #099;">6.0</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//tells it to use this datatype to best represent this specified range of values [-1.0, 6.0] whenever this instance is written</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"> <span class="n" style="color: #333;">inputFile</span><span class="p">.</span><span class="n" style="color: #333;">writeFile</span><span class="p">(</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]);</span><span class="c1" style="color: #998; font-style: italic;">//if this is the same filename as the input, CiftiFile actually detects this and reads the input into memory first</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//otherwise, it will read and write one row at a time, using very little memory</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//inputFile.setWritingDataTypeNoScaling(NIFTI_TYPE_FLOAT32);//this is how you would revert back to writing as float32 without rescaling</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">catch</span> <span class="p">(</span><span class="n" style="color: #333;">CiftiException</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"Caught CiftiException: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">AString_to_std_string</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">whatString</span><span class="p">())</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#631c8d07f5ea23b9a9f6c57f5389dfcf94bc33b7"><strong>src/CMakeLists.txt</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">PROJECT</span><span class="p">(</span>src<span class="p">)</span></span>
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2
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cmake"></span>
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3
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>HEADERS</span>
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4
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cmake">CiftiFile.h</span>
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<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#32a152aeda3110adcdbd417db5b1d26f0abecd6b"><strong>src/Cifti/CMakeLists.txt</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">PROJECT</span><span class="p">(</span>Cifti<span class="p">)</span></span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="cmake"></span>
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4
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>HEADERS</span>
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5
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cmake">CiftiXML.h</span>
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6
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cmake">CiftiVersion.h</span>
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<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#0685fd34d9c8da41f7280e865f694d39f40305cb"><strong>src/Cifti/CiftiBrainModelsMap.cxx</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="262" 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">@@ -262,7 +262,7 @@ const vector<int64_t>& CiftiBrainModelsMap::getNodeList(const StructureEnum::Enu</td>
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">StructureEnum</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Enum</span><span class="p">,</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;">const_iterator</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_surfUsed</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">structure</span><span class="p">);</span></span>
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263
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<pre style="margin: 0;"> <span id="LC263" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">m_surfUsed</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span></span>
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264
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<pre style="margin: 0;"> <span id="LC264" class="line" lang="cpp"> <span class="p">{</span></span>
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265
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<pre style="margin: 0;">-<span id="LC265" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"getNodeList called for nonexist<span class="idiff left right">a</span>nt structure"</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//throw if it doesn't exist, because we don't have a reference to return - things should identify which structures exist before calling this</span></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"getNodeList called for nonexist<span class="idiff left right">e</span>nt structure"</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//throw if it doesn't exist, because we don't have a reference to return - things should identify which structures exist before calling this</span></span>
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp"> <span class="p">}</span></span>
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"> <span class="n" style="color: #333;">CiftiAssertVectorIndex</span><span class="p">(</span><span class="n" style="color: #333;">m_modelsInfo</span><span class="p">,</span> <span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_modelsInfo</span><span class="p">[</span><span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">].</span><span class="n" style="color: #333;">m_nodeIndices</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="274" 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="274" 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">@@ -274,7 +274,7 @@ vector<CiftiBrainModelsMap::SurfaceMap> CiftiBrainModelsMap::getSurfaceMap(const</td>
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274
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">StructureEnum</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Enum</span><span class="p">,</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;">const_iterator</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_surfUsed</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">structure</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">m_surfUsed</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span></span>
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<td class="diff-line-num old_line" data-linenumber="276" 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">
276
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp"> <span class="p">{</span></span>
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277
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<pre style="margin: 0;">-<span id="LC277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"getSurfaceMap called for nonexist<span class="idiff left right">a</span>nt structure"</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//also throw, for consistency</span></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"getSurfaceMap called for nonexist<span class="idiff left right">e</span>nt structure"</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//also throw, for consistency</span></span>
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278
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278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp"> <span class="p">}</span></span>
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279
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279
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="cpp"> <span class="n" style="color: #333;">CiftiAssertVectorIndex</span><span class="p">(</span><span class="n" style="color: #333;">m_modelsInfo</span><span class="p">,</span> <span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>
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280
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280
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<pre style="margin: 0;"> <span id="LC280" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BrainModelPriv</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">myModel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_modelsInfo</span><span class="p">[</span><span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="380" 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">@@ -380,7 +380,7 @@ vector<CiftiBrainModelsMap::VolumeMap> CiftiBrainModelsMap::getVolumeStructureMa</td>
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380
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380
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<pre style="margin: 0;"> <span id="LC380" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">StructureEnum</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Enum</span><span class="p">,</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;">const_iterator</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_volUsed</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">structure</span><span class="p">);</span></span>
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381
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381
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<pre style="margin: 0;"> <span id="LC381" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">m_volUsed</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span></span>
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382
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382
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<pre style="margin: 0;"> <span id="LC382" class="line" lang="cpp"> <span class="p">{</span></span>
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383
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<pre style="margin: 0;">-<span id="LC383" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"getVolumeStructureMap called for nonexist<span class="idiff left right">a</span>nt structure"</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//also throw, for consistency</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"getVolumeStructureMap called for nonexist<span class="idiff left right">e</span>nt structure"</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//also throw, for consistency</span></span>
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384
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384
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<pre style="margin: 0;"> <span id="LC384" class="line" lang="cpp"> <span class="p">}</span></span>
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385
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385
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<pre style="margin: 0;"> <span id="LC385" class="line" lang="cpp"> <span class="n" style="color: #333;">CiftiAssertVectorIndex</span><span class="p">(</span><span class="n" style="color: #333;">m_modelsInfo</span><span class="p">,</span> <span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>
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386
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386
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<pre style="margin: 0;"> <span id="LC386" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">BrainModelPriv</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">myModel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_modelsInfo</span><span class="p">[</span><span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="404" 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">@@ -404,7 +404,7 @@ const vector<int64_t>& CiftiBrainModelsMap::getVoxelList(const StructureEnum::En</td>
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404
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404
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<pre style="margin: 0;"> <span id="LC404" class="line" lang="cpp"> <span class="n" style="color: #333;">map</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">StructureEnum</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Enum</span><span class="p">,</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;">const_iterator</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_volUsed</span><span class="p">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="n" style="color: #333;">structure</span><span class="p">);</span></span>
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405
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">m_volUsed</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">())</span></span>
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406
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406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="cpp"> <span class="p">{</span></span>
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407
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<pre style="margin: 0;">-<span id="LC407" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"getVoxelList called for nonexist<span class="idiff left right">a</span>nt structure"</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//throw if it doesn't exist, because we don't have a reference to return - things should identify which structures exist before calling this</span></span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"getVoxelList called for nonexist<span class="idiff left right">e</span>nt structure"</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//throw if it doesn't exist, because we don't have a reference to return - things should identify which structures exist before calling this</span></span>
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408
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408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="cpp"> <span class="n" style="color: #333;">CiftiAssertVectorIndex</span><span class="p">(</span><span class="n" style="color: #333;">m_modelsInfo</span><span class="p">,</span> <span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">);</span></span>
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410
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_modelsInfo</span><span class="p">[</span><span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">].</span><span class="n" style="color: #333;">m_voxelIndicesIJK</span><span class="p">;</span></span>
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<li id="e11a4fe1e7bdb48037a91121d18a2344e323cd1f">
<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#e11a4fe1e7bdb48037a91121d18a2344e323cd1f"><strong>src/CiftiFile.cxx</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">@@ -54,7 +54,8 @@ namespace</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="cpp"> <span class="n" style="color: #333;">CiftiXML</span> <span class="n" style="color: #333;">m_xml</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//because we need to parse it to set up the dimensions anyway</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"> <span class="n" style="color: #333;">CiftiOnDiskImpl</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//read-only</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="cpp"> <span class="n" style="color: #333;">CiftiOnDiskImpl</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CiftiXML</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CiftiVersion</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">version</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">swapEndian</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//make new empty file with read/write</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="cpp"> <span class="n" style="color: #333;">CiftiOnDiskImpl</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CiftiXML</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CiftiVersion</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">version</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">swapEndian</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">datatype</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rescale</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">minval</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">maxval</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//make new empty file with read/write</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">getRow</span><span class="p">(</span><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;">dataOut</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">indexSelect</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">tolerateShortRead</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">getColumn</span><span class="p">(</span><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;">dataOut</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CiftiXML</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">getCiftiXML</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_xml</span><span class="p">;</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">@@ -62,6 +63,7 @@ namespace</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">isSwapped</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_nifti</span><span class="p">.</span><span class="n" style="color: #333;">getHeader</span><span class="p">().</span><span class="n" style="color: #333;">isSwapped</span><span class="p">();</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setRow</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">dataIn</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">indexSelect</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setColumn</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">dataIn</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">index</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> </span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">CiftiMemoryImpl</span> <span class="o" style="font-weight: 600;">:</span> <span class="k" style="font-weight: 600;">public</span> <span class="n" style="color: #333;">CiftiFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">WriteImplInterface</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">@@ -135,17 +137,22 @@ CiftiFile::WriteImplInterface::~WriteImplInterface()</td>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="cpp"><span class="n" style="color: #333;">CiftiFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CiftiFile</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="cpp"> <span class="n" style="color: #333;">m_endianPref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NATIVE</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="cpp"> <span class="n" style="color: #333;">setWritingDataTypeNoScaling</span><span class="p">();</span><span class="c1" style="color: #998; font-style: italic;">//default argument is float32</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC146" class="line" lang="cpp"><span class="n" style="color: #333;">CiftiFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CiftiFile</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fileName</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC147" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">m_endianPref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NATIVE</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="cpp"> <span class="n" style="color: #333;">setWritingDataTypeNoScaling</span><span class="p">();</span><span class="c1" style="color: #998; font-style: italic;">//default argument is float32</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="cpp"> <span class="n" style="color: #333;">openFile</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC151" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC152" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CiftiFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">openFile</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fileName</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC154" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="cpp"> <span class="n" style="color: #333;">m_writingImpl</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="cpp"> <span class="n" style="color: #333;">m_readingImpl</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">();</span><span class="c1" style="color: #998; font-style: italic;">//to make sure it closes everything first, even if the open throws</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="cpp"> <span class="n" style="color: #333;">m_dims</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="cpp"> <span class="n" style="color: #333;">close</span><span class="p">();</span><span class="c1" style="color: #998; font-style: italic;">//to make sure it closes everything first, even if the open throws</span></span>
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149
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp"> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shared_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">CiftiOnDiskImpl</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">newRead</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">CiftiOnDiskImpl</span><span class="p">(</span><span class="n" style="color: #333;">pathToAbsolute</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">)));</span><span class="c1" style="color: #998; font-style: italic;">//this constructor opens existing file read-only</span></span>
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150
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp"> <span class="n" style="color: #333;">m_readingImpl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newRead</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//it should be noted that if the constructor throws (if the file isn't readable), new guarantees the memory allocated for the object will be freed</span></span>
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151
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"> <span class="n" style="color: #333;">m_xml</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newRead</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getCiftiXML</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="161" 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">@@ -161,15 +168,33 @@ void CiftiFile::setWritingFile(const AString& fileName, const CiftiVersion& writ</td>
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161
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="cpp"> <span class="n" style="color: #333;">m_endianPref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">endian</span><span class="p">;</span></span>
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162
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169
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="cpp"><span class="p">}</span></span>
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163
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="cpp"></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CiftiFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setWritingDataTypeNoScaling</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">type</span><span class="p">)</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="cpp"><span class="p">{</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="cpp"> <span class="n" style="color: #333;">m_writingDataType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">type</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//could do some validation here</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="cpp"> <span class="n" style="color: #333;">m_doWriteScaling</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="cpp"> <span class="n" style="color: #333;">m_minScalingVal</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="mf" style="color: #099;">1.0</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//these scaling values should never be used, but don't leave them uninitialized</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="cpp"> <span class="n" style="color: #333;">m_maxScalingVal</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span><span class="p">;</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="cpp"> <span class="n" style="color: #333;">m_writingImpl</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">();</span><span class="c1" style="color: #998; font-style: italic;">//prevent writing to previous writing implementation, let the next set...() set up for writing</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="cpp"><span class="p">}</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="cpp"></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CiftiFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setWritingDataTypeAndScaling</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">type</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">minval</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">maxval</span><span class="p">)</span></span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="cpp"> <span class="n" style="color: #333;">m_writingDataType</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">type</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//could do some validation here</span></span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="cpp"> <span class="n" style="color: #333;">m_doWriteScaling</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="cpp"> <span class="n" style="color: #333;">m_minScalingVal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minval</span><span class="p">;</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="cpp"> <span class="n" style="color: #333;">m_maxScalingVal</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">maxval</span><span class="p">;</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"> <span class="n" style="color: #333;">m_writingImpl</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">();</span><span class="c1" style="color: #998; font-style: italic;">//prevent writing to previous writing implementation, let the next set...() set up for writing</span></span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="cpp"><span class="p">}</span></span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp"></span>
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164
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CiftiFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeFile</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fileName</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CiftiVersion</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">writingVersion</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ENDIAN</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">endian</span><span class="p">)</span></span>
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165
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190
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp"><span class="p">{</span></span>
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166
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">m_readingImpl</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">m_dims</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"writeFile called on uninitialized CiftiFile"</span><span class="p">);</span></span>
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167
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192
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">writeSwapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">shouldSwap</span><span class="p">(</span><span class="n" style="color: #333;">endian</span><span class="p">);</span></span>
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168
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<pre style="margin: 0;">-<span id="LC168" class="line" lang="cpp"> <span class="n" style="color: #333;">AString</span> <span class="n" style="color: #333;">canonicalFilename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pathToCanonical</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//NOTE: returns EMPTY STRING for nonexist<span class="idiff left right">a</span>nt file</span></span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="cpp"> <span class="n" style="color: #333;">AString</span> <span class="n" style="color: #333;">canonicalFilename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pathToCanonical</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//NOTE: returns EMPTY STRING for nonexist<span class="idiff left right">e</span>nt file</span></span>
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169
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194
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CiftiOnDiskImpl</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">testImpl</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">dynamic_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">CiftiOnDiskImpl</span><span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">m_readingImpl</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">());</span></span>
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170
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195
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">collision</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="n" style="color: #333;">hadWriter</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">m_writingImpl</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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171
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196
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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">testImpl</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">canonicalFilename</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">pathToCanonical</span><span class="p">(</span><span class="n" style="color: #333;">testImpl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getFilename</span><span class="p">())</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">canonicalFilename</span><span class="p">)</span></span>
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172
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<pre style="margin: 0;">-<span id="LC172" class="line" lang="cpp"> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//empty string test is so that we don't say collision if both are nonexist<span class="idiff left right">a</span>nt - could happen if file is removed/unlinked while reading on some filesystems</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//empty string test is so that we don't say collision if both are nonexist<span class="idiff left right">e</span>nt - could happen if file is removed/unlinked while reading on some filesystems</span></span>
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173
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198
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<pre style="margin: 0;"> <span id="LC198" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">m_onDiskVersion</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">writingVersion</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">(</span><span class="n" style="color: #333;">dontRewrite</span><span class="p">(</span><span class="n" style="color: #333;">endian</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">writeSwapped</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">testImpl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">isSwapped</span><span class="p">()))</span> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//don't need to copy to itself</span></span>
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174
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<td class="diff-line-num new_line" data-linenumber="199" 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">
199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cpp"> <span class="n" style="color: #333;">collision</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//we need to copy to memory temporarily</span></span>
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<td class="diff-line-num old_line" data-linenumber="175" 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">
175
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200
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp"> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shared_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">WriteImplInterface</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tempMemory</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">CiftiMemoryImpl</span><span class="p">(</span><span class="n" style="color: #333;">m_xml</span><span class="p">));</span><span class="c1" style="color: #998; font-style: italic;">//because tempRead is a ReadImpl, can't be used to copy to</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="177" 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="202" 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">@@ -177,7 +202,8 @@ void CiftiFile::writeFile(const AString& fileName, const CiftiVersion& writingVe</td>
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177
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp"> <span class="n" style="color: #333;">m_readingImpl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tempMemory</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//we are about to make the old reading impl very unhappy, replace it so that if we get an error while writing, we hang onto the memory version</span></span>
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178
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203
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cpp"> <span class="n" style="color: #333;">m_writingImpl</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">();</span><span class="c1" style="color: #998; font-style: italic;">//and make it re-magic the writing implementation again if it tries to write again</span></span>
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179
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="cpp"> <span class="p">}</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="cpp"> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shared_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">WriteImplInterface</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tempWrite</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">CiftiOnDiskImpl</span><span class="p">(</span><span class="n" style="color: #333;">pathToAbsolute</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">),</span> <span class="n" style="color: #333;">m_xml</span><span class="p">,</span> <span class="n" style="color: #333;">writingVersion</span><span class="p">,</span> <span class="n" style="color: #333;">writeSwapped</span><span class="p">));</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="cpp"> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shared_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">WriteImplInterface</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tempWrite</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">CiftiOnDiskImpl</span><span class="p">(</span><span class="n" style="color: #333;">pathToAbsolute</span><span class="p">(</span><span class="n" style="color: #333;">fileName</span><span class="p">),</span> <span class="n" style="color: #333;">m_xml</span><span class="p">,</span> <span class="n" style="color: #333;">writingVersion</span><span class="p">,</span> <span class="n" style="color: #333;">writeSwapped</span><span class="p">,</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="cpp"> <span class="n" style="color: #333;">m_writingDataType</span><span class="p">,</span> <span class="n" style="color: #333;">m_doWriteScaling</span><span class="p">,</span> <span class="n" style="color: #333;">m_minScalingVal</span><span class="p">,</span> <span class="n" style="color: #333;">m_maxScalingVal</span><span class="p">));</span></span>
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181
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="cpp"> <span class="n" style="color: #333;">copyImplData</span><span class="p">(</span><span class="n" style="color: #333;">m_readingImpl</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(),</span> <span class="n" style="color: #333;">tempWrite</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(),</span> <span class="n" style="color: #333;">m_dims</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="182" 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">
182
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">collision</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">//if we rewrote the file, we need the handle to the new file, and to dump the temporary in-memory version</span></span>
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183
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="190" 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="216" 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">@@ -190,6 +216,22 @@ void CiftiFile::writeFile(const AString& fileName, const CiftiVersion& writingVe</td>
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190
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CiftiFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">m_writingImpl</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;">m_writingImpl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">close</span><span class="p">();</span><span class="c1" style="color: #998; font-style: italic;">//only writing implementations should ever throw errors on close, and specifically only on-disk</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"> <span class="p">}</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="cpp"> <span class="n" style="color: #333;">m_writingImpl</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="cpp"> <span class="n" style="color: #333;">m_readingImpl</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="cpp"> <span class="n" style="color: #333;">m_dims</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp"> <span class="n" style="color: #333;">m_xml</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CiftiXML</span><span class="p">();</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"> <span class="n" style="color: #333;">m_writingFile</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="cpp"> <span class="n" style="color: #333;">m_onDiskVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CiftiVersion</span><span class="p">();</span><span class="c1" style="color: #998; font-style: italic;">//for completeness, it gets reset on open anyway</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="cpp"> <span class="n" style="color: #333;">m_endianPref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NATIVE</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//reset things to defaults</span></span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="cpp"> <span class="n" style="color: #333;">setWritingDataTypeNoScaling</span><span class="p">();</span><span class="c1" style="color: #998; font-style: italic;">//default argument is float32</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC235" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CiftiFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">convertToInMemory</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">isInMemory</span><span class="p">())</span> <span class="k" style="font-weight: 600;">return</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">@@ -231,9 +273,14 @@ void CiftiFile::getColumn(float* dataOut, const int64_t& index) const</td>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CiftiFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setCiftiXML</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CiftiXML</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">useOldMetadata</span><span class="p">)</span></span>
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233
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275
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp"><span class="p">{</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">xml</span><span class="p">.</span><span class="n" style="color: #333;">getNumberOfDimensions</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"setCiftiXML called with 0-dimensional CiftiXML"</span><span class="p">);</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">xmlDims</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;">getDimensions</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</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;">xmlDims</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="280" 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">
280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">xmlDims</span><span class="p">[</span><span class="n" style="color: #333;">i</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 class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"cifti xml dimensions must be greater than zero"</span><span class="p">);</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="p">}</span></span>
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234
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282
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="cpp"> <span class="n" style="color: #333;">m_readingImpl</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">();</span><span class="c1" style="color: #998; font-style: italic;">//drop old implementation, as it is now invalid due to XML (and therefore matrix size) change</span></span>
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235
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp"> <span class="n" style="color: #333;">m_writingImpl</span><span class="p">.</span><span class="n" style="color: #333;">reset</span><span class="p">();</span></span>
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236
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<pre style="margin: 0;">-<span id="LC236" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">xml</span><span class="p">.</span><span class="n" style="color: #333;">getNumberOfDimensions</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"setCiftiXML called with 0-dimensional CiftiXML"</span><span class="p">);</span></span>
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237
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">useOldMetadata</span><span class="p">)</span></span>
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285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="cpp"> <span class="p">{</span></span>
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239
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="cpp"> <span class="n" style="color: #333;">MetaData</span> <span class="n" style="color: #333;">newmd</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_xml</span><span class="p">.</span><span class="n" style="color: #333;">getFileMetaData</span><span class="p">();</span><span class="c1" style="color: #998; font-style: italic;">//make a copy</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="242" 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">@@ -242,11 +289,7 @@ void CiftiFile::setCiftiXML(const CiftiXML& xml, const bool useOldMetadata)</td>
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="cpp"> <span class="n" style="color: #333;">m_xml</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xml</span><span class="p">;</span></span>
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244
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC245" class="line" lang="cpp"> <span class="n" style="color: #333;">m_dims</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_xml</span><span class="p">.</span><span class="n" style="color: #333;">getDimensions</span><span class="p">();</span></span>
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246
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<pre style="margin: 0;">-<span id="LC246" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</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;">m_dims</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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247
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<pre style="margin: 0;">-<span id="LC247" class="line" lang="cpp"> <span class="p">{</span></span>
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248
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">m_dims</span><span class="p">[</span><span class="n" style="color: #333;">i</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 class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"cifti xml dimensions must be greater than zero"</span><span class="p">);</span></span>
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249
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<pre style="margin: 0;">-<span id="LC249" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"> <span class="n" style="color: #333;">m_dims</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xmlDims</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC293" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp"></span>
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295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CiftiFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setRow</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">dataIn</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">indexSelect</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">@@ -300,14 +343,15 @@ void CiftiFile::verifyWriteImpl()</td>
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300
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343
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<pre style="margin: 0;"> <span id="LC343" class="line" lang="cpp"> <span class="n" style="color: #333;">CiftiOnDiskImpl</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">testImpl</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">dynamic_cast</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">CiftiOnDiskImpl</span><span class="o" style="font-weight: 600;">*></span><span class="p">(</span><span class="n" style="color: #333;">m_readingImpl</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">());</span></span>
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301
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344
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<pre style="margin: 0;"> <span id="LC344" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">testImpl</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>
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302
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345
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<pre style="margin: 0;"> <span id="LC345" class="line" lang="cpp"> <span class="p">{</span></span>
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303
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<pre style="margin: 0;">-<span id="LC303" class="line" lang="cpp"> <span class="n" style="color: #333;">AString</span> <span class="n" style="color: #333;">canonicalCurrent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pathToCanonical</span><span class="p">(</span><span class="n" style="color: #333;">testImpl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getFilename</span><span class="p">());</span><span class="c1" style="color: #998; font-style: italic;">//returns "" if nonexist<span class="idiff left right">a</span>nt, if unlinked while open</span></span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="cpp"> <span class="n" style="color: #333;">AString</span> <span class="n" style="color: #333;">canonicalCurrent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pathToCanonical</span><span class="p">(</span><span class="n" style="color: #333;">testImpl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">getFilename</span><span class="p">());</span><span class="c1" style="color: #998; font-style: italic;">//returns "" if nonexist<span class="idiff left right">e</span>nt, if unlinked while open</span></span>
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304
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">canonicalCurrent</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">canonicalCurrent</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">pathToCanonical</span><span class="p">(</span><span class="n" style="color: #333;">m_writingFile</span><span class="p">))</span><span class="c1" style="color: #998; font-style: italic;">//these were already absolute</span></span>
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305
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348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp"> <span class="p">{</span></span>
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306
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349
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="cpp"> <span class="n" style="color: #333;">convertToInMemory</span><span class="p">();</span><span class="c1" style="color: #998; font-style: italic;">//save existing data in memory before we clobber file</span></span>
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307
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350
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="cpp"> <span class="p">}</span></span>
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309
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352
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<pre style="margin: 0;"> <span id="LC352" class="line" lang="cpp"> <span class="p">}</span></span>
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310
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<pre style="margin: 0;">-<span id="LC310" class="line" lang="cpp"> <span class="n" style="color: #333;">m_writingImpl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shared_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">CiftiOnDiskImpl</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">CiftiOnDiskImpl</span><span class="p">(</span><span class="n" style="color: #333;">m_writingFile</span><span class="p">,</span> <span class="n" style="color: #333;">m_xml</span><span class="p">,</span> <span class="n" style="color: #333;">m_onDiskVersion</span><span class="p">,</span> <span class="n" style="color: #333;">shouldSwap</span><span class="p">(</span><span class="n" style="color: #333;">m_endianPref</span><span class="p">)));</span><span class="c1" style="color: #998; font-style: italic;">//this constructor makes new file for writing</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="cpp"> <span class="n" style="color: #333;">m_writingImpl</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shared_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">CiftiOnDiskImpl</span><span class="o" style="font-weight: 600;">></span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">CiftiOnDiskImpl</span><span class="p">(</span><span class="n" style="color: #333;">m_writingFile</span><span class="p">,</span> <span class="n" style="color: #333;">m_xml</span><span class="p">,</span> <span class="n" style="color: #333;">m_onDiskVersion</span><span class="p">,</span> <span class="n" style="color: #333;">shouldSwap</span><span class="p">(</span><span class="n" style="color: #333;">m_endianPref</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp"> <span class="n" style="color: #333;">m_writingDataType</span><span class="p">,</span> <span class="n" style="color: #333;">m_doWriteScaling</span><span class="p">,</span> <span class="n" style="color: #333;">m_minScalingVal</span><span class="p">,</span> <span class="n" style="color: #333;">m_maxScalingVal</span><span class="p">));</span><span class="c1" style="color: #998; font-style: italic;">//this constructor makes new file for writing</span></span>
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311
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355
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<pre style="margin: 0;"> <span id="LC355" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">m_readingImpl</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span></span>
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312
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356
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<pre style="margin: 0;"> <span id="LC356" class="line" lang="cpp"> <span class="p">{</span></span>
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313
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="cpp"> <span class="n" style="color: #333;">copyImplData</span><span class="p">(</span><span class="n" style="color: #333;">m_readingImpl</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(),</span> <span class="n" style="color: #333;">m_writingImpl</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(),</span> <span class="n" style="color: #333;">m_dims</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">@@ -412,7 +456,7 @@ CiftiOnDiskImpl::CiftiOnDiskImpl(const AString& filename)</td>
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412
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">m_xml</span><span class="p">.</span><span class="n" style="color: #333;">getNumberOfDimensions</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">4</span> <span class="o" style="font-weight: 600;">!=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">dimCheck</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"XML does not match number of nifti dimensions in file "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"'"</span><span class="p">);</span></span>
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413
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457
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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;">4</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="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">dimCheck</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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414
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458
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<pre style="margin: 0;"> <span id="LC458" class="line" lang="cpp"> <span class="p">{</span></span>
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415
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">m_xml</span><span class="p">.</span><span class="n" style="color: #333;">getDimensionLength</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;"><span class="idiff left right">1</span></span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">//CiftiXML will only let this happen with cifti-1</span></span>
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">m_xml</span><span class="p">.</span><span class="n" style="color: #333;">getDimensionLength</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;"><span class="idiff left right">0</span></span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">//CiftiXML will only let this happen with cifti-1</span></span>
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<pre style="margin: 0;"> <span id="LC460" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC461" class="line" lang="cpp"> <span class="n" style="color: #333;">m_xml</span><span class="p">.</span><span class="n" style="color: #333;">getSeriesMap</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">4</span><span class="p">).</span><span class="n" style="color: #333;">setLength</span><span class="p">(</span><span class="n" style="color: #333;">dimCheck</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]);</span><span class="c1" style="color: #998; font-style: italic;">//and only in a series map</span></span>
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<pre style="margin: 0;"> <span id="LC462" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</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">@@ -424,10 +468,126 @@ CiftiOnDiskImpl::CiftiOnDiskImpl(const AString& filename)</td>
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<pre style="margin: 0;"> <span id="LC468" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC469" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC427" class="line" lang="cpp"><span class="n" style="color: #333;">CiftiOnDiskImpl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CiftiOnDiskImpl</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CiftiXML</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CiftiVersion</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">version</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">swapEndian</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">warnForBadExtension</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CiftiXML</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">myXML</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">junk</span><span class="p">[</span><span class="mi" style="color: #099;">16</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">intent_code</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">myXML</span><span class="p">.</span><span class="n" style="color: #333;">getIntentInfo</span><span class="p">(</span><span class="n" style="color: #333;">CiftiVersion</span><span class="p">(),</span> <span class="n" style="color: #333;">junk</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//use default writing version to check file extension, older version is missing some intent codes</span></span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">intent_code</span><span class="p">)</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="cpp"> <span class="p">{</span></span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3000</span><span class="p">:</span><span class="c1" style="color: #998; font-style: italic;">//unknown</span></span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".nii"</span><span class="p">))</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="cpp"> <span class="p">{</span></span>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"warning: cifti file of nonstandard mapping combination '"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">AString_to_std_string</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"' should be saved ending in .<something>.nii"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="cpp"> <span class="p">}</span></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".dconn.nii"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="cpp"> <span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".dtseries.nii"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="cpp"> <span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".pconn.nii"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="cpp"> <span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".ptseries.nii"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="cpp"> <span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".dscalar.nii"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="cpp"> <span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".dfan.nii"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="cpp"> <span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".fiberTemp.nii"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="cpp"> <span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".dlabel.nii"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="cpp"> <span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".pscalar.nii"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="cpp"> <span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".pdconn.nii"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="cpp"> <span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".dpconn.nii"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="cpp"> <span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".pconnseries.nii"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span></span>
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="cpp"> <span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".pconnscalar.nii"</span><span class="p">))</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="498" 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">
498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"warning: cifti file of nonstandard mapping combination '"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">AString_to_std_string</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"' should NOT be saved using an already-used cifti extension, "</span></span>
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<td class="diff-line-num new new_line" data-linenumber="499" 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">
499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"please choose a different, reasonable cifti extension ending in .<something>.nii"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="cpp"> <span class="p">}</span></span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="502" 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">
502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3001</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="503" 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">
503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".dconn.nii"</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="504" 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">
504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="505" 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">
505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"warning: dense by dense cifti file '"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">AString_to_std_string</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"' should be saved ending in .dconn.nii"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="cpp"> <span class="p">}</span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3002</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="509" 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">
509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".dtseries.nii"</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="510" 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">
510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="511" 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">
511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"warning: series by dense cifti file '"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">AString_to_std_string</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"' should be saved ending in .dtseries.nii"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="cpp"> <span class="p">}</span></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="514" 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">
514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3003</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="515" 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">
515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".pconn.nii"</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="516" 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">
516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="cpp"> <span class="p">{</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"warning: parcels by parcels cifti file '"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">AString_to_std_string</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"' should be saved ending in .pconn.nii"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="cpp"> <span class="p">}</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3004</span><span class="p">:</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".ptseries.nii"</span><span class="p">))</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="cpp"> <span class="p">{</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"warning: series by parcels cifti file '"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">AString_to_std_string</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"' should be saved ending in .ptseries.nii"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="cpp"> <span class="p">}</span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3006</span><span class="p">:</span><span class="c1" style="color: #998; font-style: italic;">//3005 unused in practice</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="p">(</span><span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".dscalar.nii"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".dfan.nii"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".fiberTEMP.nii"</span><span class="p">)))</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="cpp"> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//there are additional special extensions in the standard for this mapping combination (specializations of scalar maps)</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//also include workbench's fiberTEMP special extension</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"warning: scalars by dense cifti file '"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">AString_to_std_string</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"' should be saved ending in .dscalar.nii"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="cpp"> <span class="p">}</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3007</span><span class="p">:</span></span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".dlabel.nii"</span><span class="p">))</span></span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="cpp"> <span class="p">{</span></span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"warning: labels by dense cifti file '"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">AString_to_std_string</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"' should be saved ending in .dlabel.nii"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="cpp"> <span class="p">}</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3008</span><span class="p">:</span></span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".pscalar.nii"</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="541" 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">
541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="542" 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">
542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"warning: scalars by parcels cifti file '"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">AString_to_std_string</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"' should be saved ending in .pscalar.nii"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="cpp"> <span class="p">}</span></span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3009</span><span class="p">:</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".pdconn.nii"</span><span class="p">))</span></span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="548" 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">
548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"warning: dense by parcels cifti file '"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">AString_to_std_string</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"' should be saved ending in .pdconn.nii"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="cpp"> <span class="p">}</span></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="551" 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">
551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3010</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="552" 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">
552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".dpconn.nii"</span><span class="p">))</span></span>
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<td class="diff-line-num new new_line" data-linenumber="553" 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">
553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="554" 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">
554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"warning: parcels by dense cifti file '"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">AString_to_std_string</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"' should be saved ending in .dpconn.nii"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
</pre>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="cpp"> <span class="p">}</span></span>
</pre>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="557" 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">
557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3011</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="558" 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">
558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".pconnseries.nii"</span><span class="p">))</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="cpp"> <span class="p">{</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"warning: parcels by parcels by series cifti file '"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">AString_to_std_string</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"' should be saved ending in .pconnseries.nii"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="cpp"> <span class="p">}</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="mi" style="color: #099;">3012</span><span class="p">:</span></span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="s" style="color: #d14;">".pconnscalar.nii"</span><span class="p">))</span></span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="cpp"> <span class="p">{</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"warning: parcels by parcels by scalar cifti file '"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">AString_to_std_string</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"' should be saved ending in .pconnscalar.nii"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="cpp"> <span class="p">}</span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">default</span><span class="o" style="font-weight: 600;">:</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="cpp"> <span class="n" style="color: #333;">CiftiAssert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"internal error, tell the developers what you just tried to do"</span><span class="p">);</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="cpp"> <span class="p">}</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="cpp"> <span class="p">}</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="cpp"><span class="p">}</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="cpp"></span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="cpp"><span class="n" style="color: #333;">CiftiOnDiskImpl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">CiftiOnDiskImpl</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CiftiXML</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">xml</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CiftiVersion</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">version</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">swapEndian</span><span class="p">,</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">datatype</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rescale</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">minval</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">maxval</span><span class="p">)</span></span>
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428
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578
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="cpp"><span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//starts writing new file</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="cpp"> <span class="n" style="color: #333;">warnForBadExtension</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="n" style="color: #333;">xml</span><span class="p">);</span></span>
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580
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<pre style="margin: 0;"> <span id="LC580" class="line" lang="cpp"> <span class="n" style="color: #333;">NiftiHeader</span> <span class="n" style="color: #333;">outHeader</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC430" class="line" lang="cpp"> <span class="n" style="color: #333;">outHeader</span><span class="p">.</span><span class="n" style="color: #333;">setDataType</span><span class="p">(</span><span class="n" style="color: #333;">NIFTI_TYPE_FLOAT32</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//actually redundant currently, default is float32</span></span>
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">rescale</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="cpp"> <span class="n" style="color: #333;">outHeader</span><span class="p">.</span><span class="n" style="color: #333;">setDataTypeAndScaleRange</span><span class="p">(</span><span class="n" style="color: #333;">datatype</span><span class="p">,</span> <span class="n" style="color: #333;">minval</span><span class="p">,</span> <span class="n" style="color: #333;">maxval</span><span class="p">);</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="cpp"> <span class="n" style="color: #333;">outHeader</span><span class="p">.</span><span class="n" style="color: #333;">setDataType</span><span class="p">(</span><span class="n" style="color: #333;">datatype</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">outHeader</span><span class="p">.</span><span class="n" style="color: #333;">getNumComponents</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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<pre style="margin: 0;">+<span id="LC588" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"cifti cannot be written with multi-component nifti datatypes (i.e., complex, RGB)"</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC591" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">intentName</span><span class="p">[</span><span class="mi" style="color: #099;">16</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC592" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">intentCode</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;">getIntentInfo</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="p">,</span> <span class="n" style="color: #333;">intentName</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC593" class="line" lang="cpp"> <span class="n" style="color: #333;">outHeader</span><span class="p">.</span><span class="n" style="color: #333;">setIntent</span><span class="p">(</span><span class="n" style="color: #333;">intentCode</span><span class="p">,</span> <span class="n" style="color: #333;">intentName</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">@@ -455,6 +615,11 @@ CiftiOnDiskImpl::CiftiOnDiskImpl(const AString& filename, const CiftiXML& xml, c</td>
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<pre style="margin: 0;"> <span id="LC615" class="line" lang="cpp"> <span class="n" style="color: #333;">m_xml</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">xml</span><span class="p">;</span></span>
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616
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<pre style="margin: 0;"> <span id="LC616" class="line" lang="cpp"><span class="p">}</span></span>
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617
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<pre style="margin: 0;"> <span id="LC617" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CiftiOnDiskImpl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>
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619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="cpp"> <span class="n" style="color: #333;">m_nifti</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">();</span><span class="c1" style="color: #998; font-style: italic;">//lets this throw when there is a writing problem</span></span>
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="cpp"><span class="p">}</span><span class="c1" style="color: #998; font-style: italic;">//don't bother resetting m_xml, this instance is about to be destroyed</span></span>
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC623" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">CiftiOnDiskImpl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getRow</span><span class="p">(</span><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;">dataOut</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">indexSelect</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">tolerateShortRead</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span></span>
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624
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<pre style="margin: 0;"> <span id="LC624" class="line" lang="cpp"><span class="p">{</span></span>
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460
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625
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<pre style="margin: 0;"> <span id="LC625" class="line" lang="cpp"> <span class="n" style="color: #333;">m_nifti</span><span class="p">.</span><span class="n" style="color: #333;">readData</span><span class="p">(</span><span class="n" style="color: #333;">dataOut</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">,</span> <span class="n" style="color: #333;">indexSelect</span><span class="p">,</span> <span class="n" style="color: #333;">tolerateShortRead</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//5 means 4 reserved (space and time) plus the first cifti dimension</span></span>
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<li id="1e4dfb5374146c117f65eb7fc0fe28a6f3e2de89">
<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#1e4dfb5374146c117f65eb7fc0fe28a6f3e2de89"><strong>src/CiftiFile.h</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">@@ -32,6 +32,7 @@</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "Common/CiftiException.h"</span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "Common/MultiDimIterator.h"</span></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "Cifti/CiftiXML.h"</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "Nifti/nifti1.h"</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#include "boost/shared_ptr.hpp"</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="c"></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">@@ -53,8 +54,8 @@ namespace cifti</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="c"> <span class="n" style="color: #333;">BIG</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="c"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="c"> </span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="c"> <span class="n" style="color: #333;">CiftiFile</span><span class="p">()</span><span class="idiff left"> </span><span class="p"><span class="idiff">{</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">m_endianPref</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">NATIVE</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="p"><span class="idiff right">}</span></span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="c"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="c"> <span class="n" style="color: #333;">CiftiFile</span><span class="p">()<span class="idiff left right">;</span></span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///starts on-disk reading</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"> <span class="n" style="color: #333;">explicit</span> <span class="n" style="color: #333;">CiftiFile</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AString</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fileName</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="c"> </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">@@ -67,6 +68,9 @@ namespace cifti</td>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///does nothing if filename, version, and effective endianness match file currently open, otherwise writes complete file</span></span>
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68
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">writeFile</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fileName</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">CiftiVersion</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">writingVersion</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CiftiVersion</span><span class="p">(),</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ENDIAN</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">endian</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ANY</span><span class="p">);</span></span>
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69
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="c"> </span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///closes the underlying file to flush it, so that exceptions can be thrown</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///reads file into memory, closes file</span></span>
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71
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">convertToInMemory</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="c"> </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">@@ -97,6 +101,10 @@ namespace cifti</td>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="c"> </span>
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98
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///for 2D only, if you don't want to pass a vector for indexing</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setRow</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">dataIn</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">index</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///data type and scaling options - should be set before setRow, etc, to avoid rewriting of file</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setWritingDataTypeNoScaling</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">type</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NIFTI_TYPE_FLOAT32</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setWritingDataTypeAndScaling</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">type</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">minval</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">maxval</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="c"></span>
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101
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">//implementation details from here down</span></span>
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="c"> <span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">ReadImplInterface</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">@@ -113,6 +121,7 @@ namespace cifti</td>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="c"> <span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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114
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setRow</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">dataIn</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">indexSelect</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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115
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setColumn</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">dataIn</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">index</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">close</span><span class="p">()</span> <span class="p">{}</span></span>
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">WriteImplInterface</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="c"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC127" class="line" lang="c"> <span class="n" style="color: #333;">private</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="123" 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="132" 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">@@ -123,6 +132,9 @@ namespace cifti</td>
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<pre style="margin: 0;"> <span id="LC132" class="line" lang="c"> <span class="n" style="color: #333;">CiftiXML</span> <span class="n" style="color: #333;">m_xml</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC133" class="line" lang="c"> <span class="n" style="color: #333;">CiftiVersion</span> <span class="n" style="color: #333;">m_onDiskVersion</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC134" class="line" lang="c"> <span class="n" style="color: #333;">ENDIAN</span> <span class="n" style="color: #333;">m_endianPref</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">m_doWriteScaling</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="136" 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">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int16_t</span> <span class="n" style="color: #333;">m_writingDataType</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="137" 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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<pre style="margin: 0;">+<span id="LC137" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">m_minScalingVal</span><span class="p">,</span> <span class="n" style="color: #333;">m_maxScalingVal</span><span class="p">;</span></span>
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126
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">verifyWriteImpl</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="128" 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">
128
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<td class="diff-line-num new_line" data-linenumber="140" 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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<pre style="margin: 0;"> <span id="LC140" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">copyImplData</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">ReadImplInterface</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">from</span><span class="p">,</span> <span class="n" style="color: #333;">WriteImplInterface</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">to</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <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="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">dims</span><span class="p">);</span></span>
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<li id="9eac26ae03a8483af4a93893a3a08f87f96e5219">
<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#9eac26ae03a8483af4a93893a3a08f87f96e5219"><strong>src/Common/AString.h</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="58" 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">@@ -58,6 +58,10 @@ namespace cifti</td>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c"> <span class="p">{</span></span>
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mystr</span><span class="p">.</span><span class="n" style="color: #333;">mid</span><span class="p">(</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">count</span><span class="p">);</span></span>
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60
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"> <span class="p">}</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">test</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pattern</span><span class="p">)</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="63" 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">
63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">test</span><span class="p">.</span><span class="n" style="color: #333;">endsWith</span><span class="p">(</span><span class="n" style="color: #333;">pattern</span><span class="p">);</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="c"> <span class="p">}</span></span>
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61
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="kr" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span></span>
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62
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"> <span class="n" style="color: #333;">AString</span> <span class="n" style="color: #333;">AString_number</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">num</span><span class="p">)</span></span>
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63
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"> <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">@@ -93,6 +97,10 @@ namespace cifti</td>
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93
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//HACK: Glib::ustring::npos is undefined at link time with glibmm 2.4 for unknown reasons, but the header says it is equal to std::string's, so use it instead</span></span>
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94
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98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mystr</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">first</span><span class="p">,</span> <span class="n" style="color: #333;">count</span><span class="p">);</span></span>
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95
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99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="c"> <span class="p">}</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="c"> <span class="kr" style="font-weight: 600;">inline</span> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">AString_endsWith</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">test</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">pattern</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="101" 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">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="c"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">test</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">test</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">pattern</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">())</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">pattern</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="c"> <span class="p">}</span></span>
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104
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="c"> <span class="n" style="color: #333;">template</span> <span class="o" style="font-weight: 600;"><</span><span class="kr" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span></span>
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97
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105
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<pre style="margin: 0;"> <span id="LC105" class="line" lang="c"> <span class="n" style="color: #333;">AString</span> <span class="n" style="color: #333;">AString_number</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">num</span><span class="p">)</span></span>
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98
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="c"> <span class="p">{</span></span>
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<li id="410b539d70abfc4648b1b19780a2381b1a9fcbbd">
<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#410b539d70abfc4648b1b19780a2381b1a9fcbbd"><strong>src/Common/BinaryFile.cxx</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">@@ -40,6 +40,8 @@</td>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#include <QFile></span></span>
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41
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#else</span></span>
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42
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#include "stdio.h"</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#include "sys/stat.h"</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#include "sys/types.h"</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#include "errno.h"</span></span>
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#define BOOST_FILESYSTEM_VERSION 3</span></span>
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="cpp"> <span class="cp" style="color: #999; font-weight: 600;">#include "boost/filesystem.hpp"</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="70" 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="72" 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">@@ -70,6 +72,7 @@ namespace cifti</td>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">position</span><span class="p">);</span></span>
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74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">pos</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="nf" style="color: #900; font-weight: 600;">size</span><span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">read</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dataOut</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">numRead</span><span class="p">);</span></span>
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74
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">write</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dataIn</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">count</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">ZFileImpl</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="88" 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="91" 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">@@ -88,6 +91,7 @@ namespace cifti</td>
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88
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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89
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">position</span><span class="p">);</span></span>
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90
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">pos</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="nf" style="color: #900; font-weight: 600;">size</span><span class="p">()</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_file</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="91" 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">
91
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95
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">read</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dataOut</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">numRead</span><span class="p">);</span></span>
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92
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">write</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dataIn</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">count</span><span class="p">);</span></span>
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="p">};</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="104" 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="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">@@ -104,6 +108,7 @@ namespace cifti</td>
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104
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">close</span><span class="p">();</span></span>
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105
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">position</span><span class="p">);</span></span>
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106
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">pos</span><span class="p">();</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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107
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">read</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dataOut</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">numRead</span><span class="p">);</span></span>
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108
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">write</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dataIn</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">count</span><span class="p">);</span></span>
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109
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">StrFileImpl</span><span class="p">();</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="186" 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">@@ -186,6 +191,12 @@ int64_t BinaryFile::pos()</td>
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186
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191
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_impl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">pos</span><span class="p">();</span></span>
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187
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cpp"></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">BinaryFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">size</span><span class="p">()</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="cpp"><span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="196" 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">
196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">m_curMode</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">NONE</span><span class="p">)</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"file is not open, can't report size"</span><span class="p">);</span></span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_impl</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">size</span><span class="p">();</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp"><span class="p">}</span></span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="cpp"></span>
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189
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">BinaryFile</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dataIn</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">count</span><span class="p">)</span></span>
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190
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp"><span class="p">{</span></span>
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191
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp"> <span class="n" style="color: #333;">CiftiAssert</span><span class="p">(</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//not sure about allowing 0</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="394" 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="405" 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">@@ -394,7 +405,7 @@ void QFileImpl::write(const void* dataIn, const int64_t& count)</td>
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394
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405
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<pre style="margin: 0;"> <span id="LC405" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span> <span class="p">(</span><span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">count</span><span class="p">)</span></span>
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395
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406
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<pre style="margin: 0;"> <span id="LC406" class="line" lang="cpp"> <span class="p">{</span></span>
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396
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407
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<pre style="margin: 0;"> <span id="LC407" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">maxToWrite</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min</span><span class="p">(</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">total</span><span class="p">,</span> <span class="n" style="color: #333;">CHUNK_SIZE</span><span class="p">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="397" 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">
397
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<pre style="margin: 0;">-<span id="LC397" class="line" lang="cpp"> <span class="n" style="color: #333;">writeret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">((</span><span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff right">dataIn</span></span><span class="p">,</span> <span class="n" style="color: #333;">maxToWrite</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//QFile probably also chokes on large writes</span></span>
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<td class="diff-line-num new old_line" data-linenumber="398" 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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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="cpp"> <span class="n" style="color: #333;">writeret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_file</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">((<span class="idiff left">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">char</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">dataIn</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">total</span></span><span class="p">,</span> <span class="n" style="color: #333;">maxToWrite</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//QFile probably also chokes on large writes</span></span>
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398
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409
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">writeret</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//0 or -1 means error or eof</span></span>
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399
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410
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="cpp"> <span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">writeret</span><span class="p">;</span></span>
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400
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411
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<pre style="margin: 0;"> <span id="LC411" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="494" 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">@@ -494,6 +505,14 @@ int64_t StrFileImpl::pos()</td>
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494
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505
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<pre style="margin: 0;"> <span id="LC505" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_curPos</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//we can avoid a call here also</span></span>
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495
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506
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<pre style="margin: 0;"> <span id="LC506" class="line" lang="cpp"><span class="p">}</span></span>
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496
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507
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<pre style="margin: 0;"> <span id="LC507" class="line" lang="cpp"></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">StrFileImpl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">size</span><span class="p">()</span></span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="cpp"><span class="p">{</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">stat</span> <span class="n" style="color: #333;">mystat</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="511" 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">
511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fstat</span><span class="p">(</span><span class="n" style="color: #333;">fileno</span><span class="p">(</span><span class="n" style="color: #333;">m_file</span><span class="p">),</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">mystat</span><span class="p">);</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">result</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</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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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mystat</span><span class="p">.</span><span class="n" style="color: #333;">st_size</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="cpp"></span>
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497
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516
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<pre style="margin: 0;"> <span id="LC516" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">StrFileImpl</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dataIn</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">count</span><span class="p">)</span></span>
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498
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517
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<pre style="margin: 0;"> <span id="LC517" class="line" lang="cpp"><span class="p">{</span></span>
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499
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518
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<pre style="margin: 0;"> <span id="LC518" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">m_file</span> <span class="o" style="font-weight: 600;">==</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">)</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"write called on unopened StrFileImpl"</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//shouldn't happen</span></span>
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<li id="7cdad2fbf92f42a516417164e615370fe457ac85">
<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#7cdad2fbf92f42a516417164e615370fe457ac85"><strong>src/Common/BinaryFile.h</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">@@ -62,6 +62,7 @@ namespace cifti {</td>
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62
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">pos</span><span class="p">();</span></span>
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63
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">read</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dataOut</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">numRead</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//throw if numRead is NULL and (error or end of file reached early)</span></span>
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64
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">write</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dataIn</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">count</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//failure to complete write is always an exception</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">size</span><span class="p">();</span><span class="c1" style="color: #998; font-style: italic;">//may return -1 if size cannot be determined efficiently</span></span>
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65
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="c"> <span class="n" style="color: #333;">class</span> <span class="n" style="color: #333;">ImplInterface</span></span>
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"> <span class="p">{</span></span>
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="c"> <span class="n" style="color: #333;">protected</span><span class="o" style="font-weight: 600;">:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="72" 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">@@ -72,6 +73,7 @@ namespace cifti {</td>
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72
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="c"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">getFilename</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_fileName</span><span class="p">;</span> <span class="p">}</span></span>
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73
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<td class="diff-line-num new_line" data-linenumber="74" 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">
74
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">position</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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74
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75
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">pos</span><span class="p">()</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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75
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">read</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dataOut</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">numRead</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">write</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">void</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">dataIn</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">count</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="c"> <span class="k" style="font-weight: 600;">virtual</span> <span class="o" style="font-weight: 600;">~</span><span class="n" style="color: #333;">ImplInterface</span><span class="p">();</span></span>
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<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#0072de496a99688cfe175e9fb52da88c2f89573f"><strong>src/Common/CMakeLists.txt</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">PROJECT</span><span class="p">(</span>Common<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="cmake"></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>HEADERS</span>
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5
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cmake">AString.h</span>
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6
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cmake">ByteSwapping.h</span>
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<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#cef9390bac429a064229b057088c655a78a00305"><strong>src/Nifti/CMakeLists.txt</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="cmake"></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="cmake"><span class="nb" style="color: #0086b3;">project</span> <span class="p">(</span>Nifti<span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="cmake"></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="cmake"><span class="nf" style="color: #900; font-weight: 600;">SET</span><span class="p">(</span>HEADERS</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="cmake">NiftiHeader.h</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cmake"><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#0cd4c140b4e6b79e2c3b2cf44b91861befe56050"><strong>src/Nifti/NiftiHeader.cxx</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">@@ -37,6 +37,7 @@</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <cstring></span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <iostream></span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include <limits></span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "stdint.h"</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">std</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"><span class="k" style="font-weight: 600;">using</span> <span class="k" style="font-weight: 600;">namespace</span> <span class="n" style="color: #333;">boost</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">@@ -219,7 +220,7 @@ vector<vector<float> > NiftiHeader::getSForm() const</td>
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219
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp"> <span class="p">{</span></span>
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220
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221
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span></span>
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221
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222
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"> <span class="p">{</span></span>
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222
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<pre style="margin: 0;">-<span id="LC222" class="line" lang="cpp"> <span class="n" style="color: #333;">rotmat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">pixdim</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">i</span></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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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"> <span class="n" style="color: #333;">rotmat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">pixdim</span><span class="p">[</span><span class="n" style="color: #333;"><span class="idiff left right">j</span></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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224
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<pre style="margin: 0;"> <span id="LC224" class="line" lang="cpp"> <span class="p">}</span></span>
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225
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp"> <span class="p">}</span></span>
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225
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226
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">pixdim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.0</span><span class="n" style="color: #333;">f</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">//left handed coordinate system, flip the kvec</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="239" 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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -239,13 +240,13 @@ vector<vector<float> > NiftiHeader::getSForm() const</td>
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239
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240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">qoffset_y</span><span class="p">;</span></span>
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240
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241
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">qoffset_z</span><span class="p">;</span></span>
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241
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242
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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242
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<pre style="margin: 0;">-<span id="LC242" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"<span class="idiff left right">found quaternion with length greater than 1 in nifti header</span>"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"<span class="idiff left right">warning: found quaternion with length greater than 1 in nifti header, using ANALYZE coordinates!</span>"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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243
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244
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">pixdim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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244
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245
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">pixdim</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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245
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246
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">pixdim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//fall back to analyze and complain</span></span>
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248
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"no sform or qform code found, using ANALYZE coordinates!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"<span class="idiff left right">warning: </span>no sform or qform code found, using ANALYZE coordinates!"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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249
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250
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">pixdim</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">];</span></span>
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250
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">pixdim</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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251
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252
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">pixdim</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="265" 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="266" 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">@@ -265,11 +266,31 @@ vector<vector<float> > NiftiHeader::getSForm() const</td>
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265
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_UNITS_MM</span><span class="p">:</span></span>
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266
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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267
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">default</span><span class="o" style="font-weight: 600;">:</span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"unrecognized spatial unit in nifti header"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"<span class="idiff left right">warning: </span>unrecognized spatial unit in nifti header"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="cpp"> <span class="p">}</span></span>
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270
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">.</span><span class="n" style="color: #333;">getMatrix</span><span class="p">();</span></span>
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271
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="cpp"><span class="p">}</span></span>
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272
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273
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp"></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">NiftiHeader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getTimeStep</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp"><span class="p">{</span></span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">timeUnit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">XYZT_TO_TIME</span><span class="p">(</span><span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">xyzt_units</span><span class="p">);</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">pixdim</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">timeUnit</span><span class="p">)</span></span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="cpp"> <span class="p">{</span></span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_UNITS_USEC</span><span class="p">:</span></span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">/=</span> <span class="mf" style="color: #099;">1000000.0</span><span class="p">;</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_UNITS_MSEC</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="284" 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">
284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">/=</span> <span class="mf" style="color: #099;">1000.0</span><span class="p">;</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">default</span><span class="o" style="font-weight: 600;">:</span></span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">AString_to_std_string</span><span class="p">(</span><span class="s" style="color: #d14;">"warning: non-time units code "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">AString_number</span><span class="p">(</span><span class="n" style="color: #333;">timeUnit</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" used in nifti header, pretending units are seconds"</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_UNITS_SEC</span><span class="p">:</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp"> <span class="p">}</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="cpp"><span class="p">}</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC294" class="line" lang="cpp"><span class="n" style="color: #333;">AString</span> <span class="n" style="color: #333;">NiftiHeader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">toString</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span></span>
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274
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295
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<pre style="margin: 0;"> <span id="LC295" class="line" lang="cpp"><span class="p">{</span></span>
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275
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296
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<pre style="margin: 0;"> <span id="LC296" class="line" lang="cpp"> <span class="n" style="color: #333;">AString</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="325" 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="346" 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">@@ -325,6 +346,16 @@ AString NiftiHeader::toString() const</td>
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325
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346
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<pre style="margin: 0;"> <span id="LC346" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"qoffset_y: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">AString_number</span><span class="p">(</span><span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">qoffset_y</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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326
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347
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<pre style="margin: 0;"> <span id="LC347" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"qoffset_z: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">AString_number</span><span class="p">(</span><span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">qoffset_z</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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327
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348
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<pre style="margin: 0;"> <span id="LC348" class="line" lang="cpp"> <span class="p">}</span></span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"effective sform:</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="cpp"> <span class="n" style="color: #333;">vector</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="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tempSform</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getSForm</span><span class="p">();</span></span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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="mi" style="color: #099;">3</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="cpp"> <span class="p">{</span></span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">j</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;">j</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">j</span><span class="p">)</span></span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="cpp"> <span class="p">{</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">AString_number</span><span class="p">(</span><span class="n" style="color: #333;">tempSform</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">j</span><span class="p">]);</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="cpp"> <span class="p">}</span></span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="cpp"> <span class="p">}</span></span>
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328
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359
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<pre style="margin: 0;"> <span id="LC359" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"xyzt_units: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">AString_number</span><span class="p">(</span><span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">xyzt_units</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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329
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360
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<pre style="margin: 0;"> <span id="LC360" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"intent_code: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">AString_number</span><span class="p">(</span><span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">intent_code</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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330
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361
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<pre style="margin: 0;"> <span id="LC361" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span> <span class="o" style="font-weight: 600;">+=</span> <span class="s" style="color: #d14;">"intent_name: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">AString_from_latin1</span><span class="p">(</span><span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">intent_name</span><span class="p">,</span> <span class="mi" style="color: #099;">16</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="377" 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="408" 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">@@ -377,6 +408,13 @@ void NiftiHeader::setIntent(const int32_t& code, const char name[16])</td>
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377
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408
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<pre style="margin: 0;"> <span id="LC408" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">16</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">intent_name</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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409
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<pre style="margin: 0;"> <span id="LC409" class="line" lang="cpp"><span class="p">}</span></span>
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379
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410
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<pre style="margin: 0;"> <span id="LC410" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">NiftiHeader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setDescription</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="n" style="color: #333;">descrip</span><span class="p">[</span><span class="mi" style="color: #099;">80</span><span class="p">])</span></span>
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="cpp"><span class="p">{</span></span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//custom strncpy-like code to fill nulls to the end</span></span>
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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="mi" style="color: #099;">80</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">descrip</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">descrip</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">descrip</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">80</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">descrip</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="sc" style="color: #d14;">'\0'</span><span class="p">;</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="cpp"><span class="p">}</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="cpp"></span>
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380
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418
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<pre style="margin: 0;"> <span id="LC418" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">NiftiHeader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setSForm</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">vector</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="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">sForm</span><span class="p">)</span></span>
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381
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419
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<pre style="margin: 0;"> <span id="LC419" class="line" lang="cpp"><span class="p">{</span></span>
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382
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420
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<pre style="margin: 0;"> <span id="LC420" class="line" lang="cpp"> <span class="n" style="color: #333;">CiftiAssert</span><span class="p">(</span><span class="n" style="color: #333;">sForm</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">3</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//programmer error to pass badly sized matrix</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="386" 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="424" 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">@@ -386,7 +424,8 @@ void NiftiHeader::setSForm(const vector<vector<float> >& sForm)</td>
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<td class="diff-line-num old_line" data-linenumber="386" 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">
386
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424
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<pre style="margin: 0;"> <span id="LC424" class="line" lang="cpp"> <span class="n" style="color: #333;">CiftiAssert</span><span class="p">(</span><span class="n" style="color: #333;">sForm</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//ditto</span></span>
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387
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425
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<pre style="margin: 0;"> <span id="LC425" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sForm</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">].</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"internal error: setSForm matrix badly sized"</span><span class="p">);</span></span>
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388
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426
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<pre style="margin: 0;"> <span id="LC426" class="line" lang="cpp"> <span class="p">}</span></span>
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389
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<pre style="margin: 0;">-<span id="LC389" class="line" lang="cpp"> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">xyzt_units</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SPACE_TIME_TO_XYZT</span><span class="p">(</span><span class="n" style="color: #333;">NIFTI_UNITS_MM</span><span class="p">,</span> <span class="n" style="color: #333;">NIFTI_UNITS_SEC</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//overwrite whatever units we read in</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">timeUnit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">XYZT_TO_TIME</span><span class="p">(</span><span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">xyzt_units</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="428" 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">
428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="cpp"> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">xyzt_units</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SPACE_TIME_TO_XYZT</span><span class="p">(</span><span class="n" style="color: #333;">NIFTI_UNITS_MM</span><span class="p">,</span> <span class="n" style="color: #333;">timeUnit</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//overwrite whatever spatial unit we read in</span></span>
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390
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429
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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="mi" style="color: #099;">4</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>
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391
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430
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<pre style="margin: 0;"> <span id="LC430" class="line" lang="cpp"> <span class="p">{</span></span>
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392
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431
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="cpp"> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">srow_x</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sForm</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="411" 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="450" 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">@@ -411,9 +450,9 @@ void NiftiHeader::setSForm(const vector<vector<float> >& sForm)</td>
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<td class="diff-line-num old_line" data-linenumber="411" 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">
411
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450
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<pre style="margin: 0;"> <span id="LC450" class="line" lang="cpp"> <span class="n" style="color: #333;">kvec</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">kvec</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//because to nifti, "left handed" apparently means "up is down", not "left is right"</span></span>
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<pre style="margin: 0;"> <span id="LC451" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC452" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">rotmat</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">][</span><span class="mi" style="color: #099;">3</span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC414" class="line" lang="cpp"> <span class="n" style="color: #333;">rotmat</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ivec</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span> <span class="n" style="color: #333;">rotmat</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">jvec</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">];</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rotmat</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">kvec</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff right">0</span></span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC415" class="line" lang="cpp"> <span class="n" style="color: #333;">rotmat</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">ivec</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">];</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rotmat</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">jvec</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">];</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rotmat</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">kvec</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">];</span></span>
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<pre style="margin: 0;">-<span id="LC416" class="line" lang="cpp"> <span class="n" style="color: #333;">rotmat</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">ivec</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">];</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rotmat</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">jvec</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">];</span> <span class="n" style="color: #333;">rotmat</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kvec</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="cpp"> <span class="n" style="color: #333;">rotmat</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ivec</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span> <span class="n" style="color: #333;">rotmat</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">ivec</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">];</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rotmat</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">ivec</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="cpp"> <span class="n" style="color: #333;">rotmat</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">jvec</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">];</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rotmat</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">jvec</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">];</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rotmat</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">jvec</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="cpp"> <span class="n" style="color: #333;">rotmat</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">kvec</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">];</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">rotmat</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">][</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">kvec</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">];</span> <span class="n" style="color: #333;">rotmat</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">][</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kvec</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC456" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">quat</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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<pre style="margin: 0;"> <span id="LC457" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">MathFunctions</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">matrixToQuatern</span><span class="p">(</span><span class="n" style="color: #333;">rotmat</span><span class="p">,</span> <span class="n" style="color: #333;">quat</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC458" 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">@@ -435,6 +474,13 @@ void NiftiHeader::setSForm(const vector<vector<float> >& sForm)</td>
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<pre style="margin: 0;"> <span id="LC474" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC476" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">NiftiHeader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setTimeStep</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seconds</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">spaceUnit</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">XYZT_TO_SPACE</span><span class="p">(</span><span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">xyzt_units</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//save the current space units so we don't clobber it...</span></span>
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="cpp"> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">xyzt_units</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SPACE_TIME_TO_XYZT</span><span class="p">(</span><span class="n" style="color: #333;">spaceUnit</span><span class="p">,</span> <span class="n" style="color: #333;">NIFTI_UNITS_SEC</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//overwrite the time part of the units with seconds</span></span>
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="cpp"> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">pixdim</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seconds</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC484" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">NiftiHeader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">clearDataScaling</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC485" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC486" class="line" lang="cpp"> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">scl_slope</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">1.0</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="447" 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">@@ -447,6 +493,141 @@ void NiftiHeader::setDataScaling(const double& mult, const double& offset)</td>
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<pre style="margin: 0;"> <span id="LC493" class="line" lang="cpp"> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">scl_inter</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">offset</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC494" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC495" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="cpp"><span class="k" style="font-weight: 600;">namespace</span></span>
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="cpp"> <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="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span></span>
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">Scaling</span></span>
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mult</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="cpp"> <span class="n" style="color: #333;">Scaling</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">minval</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">maxval</span><span class="p">)</span></span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="cpp"> <span class="p">{</span></span>
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504
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<pre style="margin: 0;">+<span id="LC504" 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;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">T</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">mylimits</span><span class="p">;</span></span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mymin</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mylimits</span><span class="p">.</span><span class="n" style="color: #333;">min</span><span class="p">();</span></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">mylimits</span><span class="p">.</span><span class="n" style="color: #333;">is_integer</span><span class="p">)</span> <span class="n" style="color: #333;">mymin</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">mylimits</span><span class="p">.</span><span class="n" style="color: #333;">max</span><span class="p">();</span><span class="c1" style="color: #998; font-style: italic;">//again, c++11 can use lowest() instead of these lines</span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="cpp"> <span class="n" style="color: #333;">mult</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">maxval</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">minval</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="p">)</span><span class="n" style="color: #333;">mylimits</span><span class="p">.</span><span class="n" style="color: #333;">max</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">mymin</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//multiplying is the first step of decoding (after byteswap), so start with the range</span></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="cpp"> <span class="n" style="color: #333;">offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">minval</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">mymin</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">mult</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//offset is added after multiplying the encoded value by mult</span></span>
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="cpp"> <span class="p">}</span></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="cpp"> <span class="p">};</span></span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="cpp"><span class="p">}</span></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="cpp"></span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">NiftiHeader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setDataTypeAndScaleRange</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">type</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">minval</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">maxval</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="cpp"><span class="p">{</span></span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="cpp"> <span class="n" style="color: #333;">setDataType</span><span class="p">(</span><span class="n" style="color: #333;">type</span><span class="p">);</span></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">type</span><span class="p">)</span></span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="cpp"> <span class="p">{</span></span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_RGB24</span><span class="p">:</span></span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="cpp"> <span class="n" style="color: #333;">clearDataScaling</span><span class="p">();</span><span class="c1" style="color: #998; font-style: italic;">//RGB ignores scaling fields</span></span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">DT_BINARY</span><span class="p">:</span><span class="c1" style="color: #998; font-style: italic;">//currently not supported in read/write functions anyway</span></span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="cpp"> <span class="n" style="color: #333;">setDataScaling</span><span class="p">(</span><span class="n" style="color: #333;">maxval</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">minval</span><span class="p">,</span> <span class="n" style="color: #333;">minval</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//make the two possible decoded values equal to the min and max</span></span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_INT8</span><span class="p">:</span></span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="cpp"> <span class="p">{</span></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="cpp"> <span class="n" style="color: #333;">Scaling</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int8_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">myscale</span><span class="p">(</span><span class="n" style="color: #333;">minval</span><span class="p">,</span> <span class="n" style="color: #333;">maxval</span><span class="p">);</span></span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="cpp"> <span class="n" style="color: #333;">setDataScaling</span><span class="p">(</span><span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">mult</span><span class="p">,</span> <span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">offset</span><span class="p">);</span></span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="cpp"> <span class="p">}</span></span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_UINT8</span><span class="p">:</span></span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="cpp"> <span class="p">{</span></span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="cpp"> <span class="n" style="color: #333;">Scaling</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint8_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">myscale</span><span class="p">(</span><span class="n" style="color: #333;">minval</span><span class="p">,</span> <span class="n" style="color: #333;">maxval</span><span class="p">);</span></span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="cpp"> <span class="n" style="color: #333;">setDataScaling</span><span class="p">(</span><span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">mult</span><span class="p">,</span> <span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">offset</span><span class="p">);</span></span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="cpp"> <span class="p">}</span></span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_INT16</span><span class="p">:</span></span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="cpp"> <span class="p">{</span></span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="cpp"> <span class="n" style="color: #333;">Scaling</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">myscale</span><span class="p">(</span><span class="n" style="color: #333;">minval</span><span class="p">,</span> <span class="n" style="color: #333;">maxval</span><span class="p">);</span></span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="cpp"> <span class="n" style="color: #333;">setDataScaling</span><span class="p">(</span><span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">mult</span><span class="p">,</span> <span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">offset</span><span class="p">);</span></span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="cpp"> <span class="p">}</span></span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_UINT16</span><span class="p">:</span></span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="cpp"> <span class="n" style="color: #333;">Scaling</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint16_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">myscale</span><span class="p">(</span><span class="n" style="color: #333;">minval</span><span class="p">,</span> <span class="n" style="color: #333;">maxval</span><span class="p">);</span></span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="cpp"> <span class="n" style="color: #333;">setDataScaling</span><span class="p">(</span><span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">mult</span><span class="p">,</span> <span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">offset</span><span class="p">);</span></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="cpp"> <span class="p">}</span></span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_INT32</span><span class="p">:</span></span>
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549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="cpp"> <span class="p">{</span></span>
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550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="cpp"> <span class="n" style="color: #333;">Scaling</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">myscale</span><span class="p">(</span><span class="n" style="color: #333;">minval</span><span class="p">,</span> <span class="n" style="color: #333;">maxval</span><span class="p">);</span></span>
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551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="cpp"> <span class="n" style="color: #333;">setDataScaling</span><span class="p">(</span><span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">mult</span><span class="p">,</span> <span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">offset</span><span class="p">);</span></span>
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552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="cpp"> <span class="p">}</span></span>
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554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_UINT32</span><span class="p">:</span></span>
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555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="cpp"> <span class="p">{</span></span>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="cpp"> <span class="n" style="color: #333;">Scaling</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">myscale</span><span class="p">(</span><span class="n" style="color: #333;">minval</span><span class="p">,</span> <span class="n" style="color: #333;">maxval</span><span class="p">);</span></span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="cpp"> <span class="n" style="color: #333;">setDataScaling</span><span class="p">(</span><span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">mult</span><span class="p">,</span> <span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">offset</span><span class="p">);</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="cpp"> <span class="p">}</span></span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_INT64</span><span class="p">:</span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="cpp"> <span class="p">{</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="cpp"> <span class="n" style="color: #333;">Scaling</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">myscale</span><span class="p">(</span><span class="n" style="color: #333;">minval</span><span class="p">,</span> <span class="n" style="color: #333;">maxval</span><span class="p">);</span></span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="cpp"> <span class="n" style="color: #333;">setDataScaling</span><span class="p">(</span><span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">mult</span><span class="p">,</span> <span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">offset</span><span class="p">);</span></span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="cpp"> <span class="p">}</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_UINT64</span><span class="p">:</span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="568" 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">
568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="cpp"> <span class="n" style="color: #333;">Scaling</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">uint64_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">myscale</span><span class="p">(</span><span class="n" style="color: #333;">minval</span><span class="p">,</span> <span class="n" style="color: #333;">maxval</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="569" 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">
569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="cpp"> <span class="n" style="color: #333;">setDataScaling</span><span class="p">(</span><span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">mult</span><span class="p">,</span> <span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">offset</span><span class="p">);</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="572" 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">
572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_FLOAT32</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="573" 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">
573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_COMPLEX64</span><span class="p">:</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num new old_line" data-linenumber="450" 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="diff-line-num new new_line" data-linenumber="575" 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">
575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="cpp"> <span class="n" style="color: #333;">Scaling</span><span class="o" style="font-weight: 600;"><</span><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;">myscale</span><span class="p">(</span><span class="n" style="color: #333;">minval</span><span class="p">,</span> <span class="n" style="color: #333;">maxval</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="576" 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">
576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="cpp"> <span class="n" style="color: #333;">setDataScaling</span><span class="p">(</span><span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">mult</span><span class="p">,</span> <span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">offset</span><span class="p">);</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="579" 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">
579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_FLOAT64</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="580" 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">
580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_COMPLEX128</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="581" 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">
581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="582" 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">
582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="cpp"> <span class="n" style="color: #333;">Scaling</span><span class="o" style="font-weight: 600;"><</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">myscale</span><span class="p">(</span><span class="n" style="color: #333;">minval</span><span class="p">,</span> <span class="n" style="color: #333;">maxval</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="583" 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">
583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="cpp"> <span class="n" style="color: #333;">setDataScaling</span><span class="p">(</span><span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">mult</span><span class="p">,</span> <span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">offset</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="584" 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">
584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="586" 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">
586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_FLOAT128</span><span class="p">:</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="587" 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">
587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_COMPLEX256</span><span class="p">:</span></span>
</pre>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="cpp"> <span class="p">{</span></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="cpp"> <span class="n" style="color: #333;">Scaling</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;">double</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">myscale</span><span class="p">(</span><span class="n" style="color: #333;">minval</span><span class="p">,</span> <span class="n" style="color: #333;">maxval</span><span class="p">);</span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="cpp"> <span class="n" style="color: #333;">setDataScaling</span><span class="p">(</span><span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">mult</span><span class="p">,</span> <span class="n" style="color: #333;">myscale</span><span class="p">.</span><span class="n" style="color: #333;">offset</span><span class="p">);</span></span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="cpp"> <span class="p">}</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">default</span><span class="o" style="font-weight: 600;">:</span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="cpp"> <span class="n" style="color: #333;">CiftiAssert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"internal error, report what you did to the developers"</span><span class="p">);</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="cpp"> <span class="p">}</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="cpp"><span class="p">}</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="cpp"></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">NiftiHeader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getNumComponents</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="cpp"><span class="p">{</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">getDataType</span><span class="p">())</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="603" 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">
603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_RGB24</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="604" 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">
604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="606" 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">
606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_COMPLEX64</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="607" 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">
607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_COMPLEX128</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="608" 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">
608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_COMPLEX256</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="609" 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">
609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="610" 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">
610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="611" 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">
611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">DT_BINARY</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="612" 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">
612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_INT8</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="613" 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">
613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_UINT8</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="614" 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">
614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_INT16</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="615" 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">
615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_UINT16</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="616" 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">
616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_INT32</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="617" 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">
617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_UINT32</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="618" 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">
618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_FLOAT32</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="619" 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">
619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_INT64</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="620" 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">
620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_UINT64</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC621" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_FLOAT64</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="622" 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">
622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_FLOAT128</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC623" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">default</span><span class="o" style="font-weight: 600;">:</span></span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="cpp"> <span class="n" style="color: #333;">CiftiAssert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"internal error, report what you did to the developers"</span><span class="p">);</span></span>
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628
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<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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<pre style="margin: 0;">+<span id="LC629" class="line" lang="cpp"><span class="p">}</span></span>
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630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="cpp"></span>
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450
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<td class="diff-line-num new_line" data-linenumber="631" 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">
631
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<pre style="margin: 0;"> <span id="LC631" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">NiftiHeader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">BinaryFile</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">inFile</span><span class="p">)</span></span>
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451
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632
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<pre style="margin: 0;"> <span id="LC632" class="line" lang="cpp"><span class="p">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="452" 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">
452
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<td class="diff-line-num new_line" data-linenumber="633" 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">
633
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<pre style="margin: 0;"> <span id="LC633" class="line" lang="cpp"> <span class="n" style="color: #333;">nifti_1_header</span> <span class="n" style="color: #333;">buffer1</span><span class="p">;</span></span>
</pre>
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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">@@ -454,6 +635,7 @@ void NiftiHeader::read(BinaryFile& inFile)</td>
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<pre style="margin: 0;"> <span id="LC635" class="line" lang="cpp"> <span class="n" style="color: #333;">inFile</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">buffer1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">nifti_1_header</span><span class="p">));</span></span>
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<pre style="margin: 0;"> <span id="LC636" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">NIFTI2_VERSION</span><span class="p">(</span><span class="n" style="color: #333;">buffer1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC637" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">swapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="cpp"> <span class="n" style="color: #333;">Quirks</span> <span class="n" style="color: #333;">myquirks</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC639" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</span></span>
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<pre style="margin: 0;"> <span id="LC640" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC641" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="465" 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="647" 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">@@ -465,14 +647,14 @@ void NiftiHeader::read(BinaryFile& inFile)</td>
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<pre style="margin: 0;"> <span id="LC647" class="line" lang="cpp"> <span class="n" style="color: #333;">swapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC648" class="line" lang="cpp"> <span class="n" style="color: #333;">swapHeaderBytes</span><span class="p">(</span><span class="n" style="color: #333;">buffer2</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC649" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC468" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">setupFrom</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">buffer2</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">myquirks</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">setupFrom</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">buffer2</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">inFile</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getFilename</span></span><span class="p"><span class="idiff right">()</span>);</span></span>
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<pre style="margin: 0;"> <span id="LC651" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC652" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">NIFTI2_NEEDS_SWAP</span><span class="p">(</span><span class="n" style="color: #333;">buffer1</span><span class="p">))</span><span class="c1" style="color: #998; font-style: italic;">//yes, this works on nifti-1 also</span></span>
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<pre style="margin: 0;"> <span id="LC653" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC654" class="line" lang="cpp"> <span class="n" style="color: #333;">swapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC655" class="line" lang="cpp"> <span class="n" style="color: #333;">swapHeaderBytes</span><span class="p">(</span><span class="n" style="color: #333;">buffer1</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC656" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC475" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">setupFrom</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff right">buffer1</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left">myquirks</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">setupFrom</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">buffer1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">inFile</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">getFilename</span></span><span class="p"><span class="idiff right">()</span>);</span></span>
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658
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<pre style="margin: 0;"> <span id="LC658" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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659
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<pre style="margin: 0;"> <span id="LC659" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="n" style="color: #333;">inFile</span><span class="p">.</span><span class="n" style="color: #333;">getFilename</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" is not a valid NIfTI file"</span><span class="p">);</span></span>
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478
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660
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<pre style="margin: 0;"> <span id="LC660" 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">@@ -480,58 +662,74 @@ void NiftiHeader::read(BinaryFile& inFile)</td>
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480
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662
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<pre style="margin: 0;"> <span id="LC662" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"error reading NIfTI file "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">inFile</span><span class="p">.</span><span class="n" style="color: #333;">getFilename</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">": "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">e</span><span class="p">.</span><span class="n" style="color: #333;">whatString</span><span class="p">());</span></span>
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481
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663
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<pre style="margin: 0;"> <span id="LC663" class="line" lang="cpp"> <span class="p">}</span></span>
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482
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664
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<pre style="margin: 0;"> <span id="LC664" class="line" lang="cpp"> <span class="n" style="color: #333;">m_extensions</span><span class="p">.</span><span class="n" style="color: #333;">clear</span><span class="p">();</span></span>
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483
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<pre style="margin: 0;">-<span id="LC483" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">extender</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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484
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<pre style="margin: 0;">-<span id="LC484" class="line" lang="cpp"> <span class="n" style="color: #333;">inFile</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">extender</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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485
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<pre style="margin: 0;">-<span id="LC485" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//if it has extensions in a format we don't know about, don't try to read them</span></span>
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486
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<pre style="margin: 0;">-<span id="LC486" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">extender</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</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;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//sadly, this is the only thing nifti-1 says about the extender bytes</span></span>
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487
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<pre style="margin: 0;">-<span id="LC487" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">extender</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">extender</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">extender</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">extender</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</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;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//from http://nifti.nimh.nih.gov/nifti-2 as of 4/4/2014:</span></span>
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488
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<pre style="margin: 0;">-<span id="LC488" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">extensions</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">//"extentions match those of NIfTI-1.1 when the extender bytes are 1 0 0 0"</span></span>
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489
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<pre style="margin: 0;">-<span id="LC489" class="line" lang="cpp"> <span class="p">{</span></span>
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490
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<pre style="margin: 0;">-<span id="LC490" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">extStart</span><span class="p">;</span></span>
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491
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<pre style="margin: 0;">-<span id="LC491" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">version</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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492
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<pre style="margin: 0;">-<span id="LC492" class="line" lang="cpp"> <span class="p">{</span></span>
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493
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<pre style="margin: 0;">-<span id="LC493" class="line" lang="cpp"> <span class="n" style="color: #333;">extStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">352</span><span class="p">;</span></span>
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494
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<pre style="margin: 0;">-<span id="LC494" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC495" class="line" lang="cpp"> <span class="n" style="color: #333;">CiftiAssert</span><span class="p">(</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC496" class="line" lang="cpp"> <span class="n" style="color: #333;">extStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">544</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC497" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC498" class="line" lang="cpp"> <span class="n" style="color: #333;">CiftiAssert</span><span class="p">(</span><span class="n" style="color: #333;">inFile</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">extStart</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC499" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">extStart</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">vox_offset</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">myquirks</span><span class="p">.</span><span class="n" style="color: #333;">no_extender</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC666" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC667" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">min_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">352</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC668" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="n" style="color: #333;">min_offset</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">544</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">AString_to_std_string</span><span class="p">(</span><span class="s" style="color: #d14;">"warning: in file '"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">inFile</span><span class="p">.</span><span class="n" style="color: #333;">getFilename</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"', vox_offset is "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">AString_number</span><span class="p">(</span><span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">vox_offset</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="cpp"> <span class="s" style="color: #d14;">", nifti standard specifies that it should be at least "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">AString_number</span><span class="p">(</span><span class="n" style="color: #333;">min_offset</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">", assuming malformed file with no extender"</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC672" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">extender</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC673" class="line" lang="cpp"> <span class="n" style="color: #333;">inFile</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">extender</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//if it has extensions in a format we don't know about, don't try to read them</span></span>
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675
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">extender</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</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;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//sadly, this is the only thing nifti-1 says about the extender bytes</span></span>
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676
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">extender</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">extender</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">extender</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">extender</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</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;">extensions</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//from http://nifti.nimh.nih.gov/nifti-2 as of 4/4/2014:</span></span>
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">extensions</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">//"extentions match those of NIfTI-1.1 when the extender bytes are 1 0 0 0"</span></span>
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<pre style="margin: 0;"> <span id="LC678" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC501" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">esize</span><span class="p">,</span> <span class="n" style="color: #333;">ecode</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC502" class="line" lang="cpp"> <span class="n" style="color: #333;">inFile</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">esize</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">));</span></span>
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503
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<pre style="margin: 0;">-<span id="LC503" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">swapped</span><span class="p">)</span> <span class="n" style="color: #333;">ByteSwapping</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">swap</span><span class="p">(</span><span class="n" style="color: #333;">esize</span><span class="p">);</span></span>
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504
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<pre style="margin: 0;">-<span id="LC504" class="line" lang="cpp"> <span class="n" style="color: #333;">inFile</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ecode</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">));</span></span>
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505
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<pre style="margin: 0;">-<span id="LC505" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">swapped</span><span class="p">)</span> <span class="n" style="color: #333;">ByteSwapping</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">swap</span><span class="p">(</span><span class="n" style="color: #333;">ecode</span><span class="p">);</span></span>
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506
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<pre style="margin: 0;">-<span id="LC506" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">esize</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">esize</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">extStart</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">vox_offset</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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507
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<pre style="margin: 0;">-<span id="LC507" class="line" lang="cpp"> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shared_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">NiftiExtension</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tempExtension</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">NiftiExtension</span><span class="p">());</span></span>
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508
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<pre style="margin: 0;">-<span id="LC508" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="n" style="color: #333;">esize</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">))</span><span class="c1" style="color: #998; font-style: italic;">//don't try to read 0 bytes</span></span>
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">extStart</span><span class="p">;</span></span>
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680
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">version</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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509
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681
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<pre style="margin: 0;"> <span id="LC681" class="line" lang="cpp"> <span class="p">{</span></span>
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510
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="cpp"> <span class="n" style="color: #333;">tempExtension</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m_bytes</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">esize</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">));</span></span>
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511
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<pre style="margin: 0;">-<span id="LC511" class="line" lang="cpp"> <span class="n" style="color: #333;">inFile</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">tempExtension</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m_bytes</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">(),</span> <span class="n" style="color: #333;">esize</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">));</span></span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="cpp"> <span class="n" style="color: #333;">extStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">352</span><span class="p">;</span></span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="cpp"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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684
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="cpp"> <span class="n" style="color: #333;">CiftiAssert</span><span class="p">(</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">);</span></span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="cpp"> <span class="n" style="color: #333;">extStart</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">544</span><span class="p">;</span></span>
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686
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="cpp"> <span class="p">}</span></span>
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687
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="cpp"> <span class="n" style="color: #333;">CiftiAssert</span><span class="p">(</span><span class="n" style="color: #333;">inFile</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">()</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">extStart</span><span class="p">);</span></span>
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688
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">while</span><span class="p">(</span><span class="n" style="color: #333;">extStart</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">vox_offset</span><span class="p">)</span></span>
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689
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="cpp"> <span class="p">{</span></span>
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690
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">esize</span><span class="p">,</span> <span class="n" style="color: #333;">ecode</span><span class="p">;</span></span>
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691
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="cpp"> <span class="n" style="color: #333;">inFile</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">esize</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">));</span></span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">swapped</span><span class="p">)</span> <span class="n" style="color: #333;">ByteSwapping</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">swap</span><span class="p">(</span><span class="n" style="color: #333;">esize</span><span class="p">);</span></span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="cpp"> <span class="n" style="color: #333;">inFile</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">ecode</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">));</span></span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">swapped</span><span class="p">)</span> <span class="n" style="color: #333;">ByteSwapping</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">swap</span><span class="p">(</span><span class="n" style="color: #333;">ecode</span><span class="p">);</span></span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">esize</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">8</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">esize</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">extStart</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">vox_offset</span><span class="p">)</span> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="cpp"> <span class="n" style="color: #333;">boost</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">shared_ptr</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">NiftiExtension</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">tempExtension</span><span class="p">(</span><span class="k" style="font-weight: 600;">new</span> <span class="n" style="color: #333;">NiftiExtension</span><span class="p">());</span></span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="kt" style="color: #458; font-weight: 600;">size_t</span><span class="p">)</span><span class="n" style="color: #333;">esize</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">))</span><span class="c1" style="color: #998; font-style: italic;">//don't try to read 0 bytes</span></span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="cpp"> <span class="p">{</span></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="cpp"> <span class="n" style="color: #333;">tempExtension</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m_bytes</span><span class="p">.</span><span class="n" style="color: #333;">resize</span><span class="p">(</span><span class="n" style="color: #333;">esize</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">));</span></span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="cpp"> <span class="n" style="color: #333;">inFile</span><span class="p">.</span><span class="n" style="color: #333;">read</span><span class="p">(</span><span class="n" style="color: #333;">tempExtension</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m_bytes</span><span class="p">.</span><span class="n" style="color: #333;">data</span><span class="p">(),</span> <span class="n" style="color: #333;">esize</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">2</span> <span class="o" style="font-weight: 600;">*</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="p">));</span></span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="cpp"> <span class="p">}</span></span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="cpp"> <span class="n" style="color: #333;">tempExtension</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m_ecode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ecode</span><span class="p">;</span></span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="cpp"> <span class="n" style="color: #333;">m_extensions</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">tempExtension</span><span class="p">);</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="cpp"> <span class="n" style="color: #333;">extStart</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">esize</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//esize includes the two int32_ts</span></span>
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<pre style="margin: 0;"> <span id="LC705" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC513" class="line" lang="cpp"> <span class="n" style="color: #333;">tempExtension</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">m_ecode</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ecode</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC514" class="line" lang="cpp"> <span class="n" style="color: #333;">m_extensions</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">tempExtension</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC515" class="line" lang="cpp"> <span class="n" style="color: #333;">extStart</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">esize</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//esize includes the two int32_ts</span></span>
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<pre style="margin: 0;"> <span id="LC706" class="line" lang="cpp"> <span class="p">}</span></span>
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707
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<pre style="margin: 0;"> <span id="LC707" class="line" lang="cpp"> <span class="p">}</span></span>
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708
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<pre style="margin: 0;"> <span id="LC708" class="line" lang="cpp"> <span class="n" style="color: #333;">m_isSwapped</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">swapped</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//now that we know there were no errors (because they throw), complete the internal state</span></span>
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<pre style="margin: 0;"> <span id="LC709" class="line" lang="cpp"> <span class="n" style="color: #333;">m_version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">version</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC710" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC711" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC522" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">void</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">NiftiHeader</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">setupFrom</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nifti_1_header</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">header</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="cpp"><span class="n" style="color: #333;"><span class="idiff left">NiftiHeader</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">Quirks</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">NiftiHeader</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">setupFrom</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nifti_1_header</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">header</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">AString</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">filename</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC713" class="line" lang="cpp"><span class="p">{</span></span>
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524
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<pre style="margin: 0;">-<span id="LC524" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">sizeof_hdr</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">nifti_1_header</span><span class="p">))</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"incorrect sizeof_hdr"</span><span class="p">);</span></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="cpp"> <span class="n" style="color: #333;">Quirks</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">sizeof_hdr</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">nifti_1_header</span><span class="p">))</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"incorrect sizeof_hdr in file '"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"'"</span><span class="p">);</span></span>
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525
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716
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<pre style="margin: 0;"> <span id="LC716" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">magic</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"n+1</span><span class="se" style="color: #d14;">\0</span><span class="s" style="color: #d14;">"</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//only support single-file nifti</span></span>
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526
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<pre style="margin: 0;">-<span id="LC526" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">magic</span><span class="p">,</span> <span class="n" style="color: #333;">magic</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"incorrect magic"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC527" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">dim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">dim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">7</span><span class="p">)</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"incorrect dim[0]"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="717" 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">
717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">strncmp</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">magic</span><span class="p">,</span> <span class="n" style="color: #333;">magic</span><span class="p">,</span> <span class="mi" style="color: #099;">4</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"incorrect magic<span class="idiff left"> in file '"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"'</span>"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="718" 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">
718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">dim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">dim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">7</span><span class="p">)</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"incorrect dim[0]<span class="idiff left"> in file '"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"'</span>"</span><span class="p">);</span></span>
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528
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<td class="diff-line-num new_line" data-linenumber="719" 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">
719
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<pre style="margin: 0;"> <span id="LC719" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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;">header</span><span class="p">.</span><span class="n" style="color: #333;">dim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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529
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720
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<pre style="margin: 0;"> <span id="LC720" class="line" lang="cpp"> <span class="p">{</span></span>
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530
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<pre style="margin: 0;">-<span id="LC530" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">dim</span><span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</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 class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"dim["</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">AString_number</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"] < 1"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="531" 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="diff-line-num new new_line" data-linenumber="721" 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">
721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">dim</span><span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</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 class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"dim["</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">AString_number</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"] < 1 in file '"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"'"</span><span class="p">);</span></span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="cpp"> <span class="p">}</span></span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">vox_offset</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">352</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC724" class="line" lang="cpp"> <span class="p">{</span></span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">vox_offset</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">348</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="726" 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">
726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="727" 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">
727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"file '"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"' has invalid vox_offset: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">AString_number</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">vox_offset</span><span class="p">));</span></span>
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728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="729" 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">
729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="cpp"> <span class="n" style="color: #333;">ret</span><span class="p">.</span><span class="n" style="color: #333;">no_extender</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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531
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730
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<pre style="margin: 0;"> <span id="LC730" class="line" lang="cpp"> <span class="p">}</span></span>
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532
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<td class="diff-line-num new_line old" data-linenumber="731" 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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<pre style="margin: 0;">-<span id="LC532" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">vox_offset</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">352</span><span class="p">)</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"incorrect vox_offset"</span><span class="p">);</span></span>
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533
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731
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<pre style="margin: 0;"> <span id="LC731" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">numBits</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">typeToNumBits</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">datatype</span><span class="p">);</span></span>
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534
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<pre style="margin: 0;">-<span id="LC534" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">bitpix</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">numBits</span><span class="p">)</span> <span class="k" style="font-weight: 600;"><span class="idiff left">throw</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">CiftiException</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"datatype disagrees with bitpix"</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">bitpix</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">numBits</span><span class="p">)</span> <span class="n" style="color: #333;"><span class="idiff left">cerr</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">AString_to_std_string</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"warning: datatype disagrees with bitpix in file '"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"'"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">endl</span></span><span class="p">;</span></span>
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535
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733
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<pre style="margin: 0;"> <span id="LC733" class="line" lang="cpp"> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">sizeof_hdr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">sizeof_hdr</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//copy in everything, so we don't have to fake anything to print the header as read</span></span>
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536
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734
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<pre style="margin: 0;"> <span id="LC734" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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="mi" style="color: #099;">4</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">//mostly using nifti-2 field order to make it easier to find if things are missed</span></span>
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537
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735
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<pre style="margin: 0;"> <span id="LC735" class="line" lang="cpp"> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="574" 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">@@ -574,24 +772,27 @@ void NiftiHeader::setupFrom(const nifti_1_header& header)</td>
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574
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772
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<pre style="margin: 0;"> <span id="LC772" class="line" lang="cpp"> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">intent_code</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">intent_code</span><span class="p">;</span></span>
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575
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773
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<pre style="margin: 0;"> <span id="LC773" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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="mi" style="color: #099;">16</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">intent_name</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">intent_name</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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576
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774
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<pre style="margin: 0;"> <span id="LC774" class="line" lang="cpp"> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">dim_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">dim_info</span><span class="p">;</span></span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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577
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776
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<pre style="margin: 0;"> <span id="LC776" class="line" lang="cpp"><span class="p">}</span></span>
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777
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<pre style="margin: 0;"> <span id="LC777" class="line" lang="cpp"></span>
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579
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">void</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">NiftiHeader</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">setupFrom</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nifti_2_header</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">header</span></span><span class="p">)</span></span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="cpp"><span class="n" style="color: #333;"><span class="idiff left">NiftiHeader</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">Quirks</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">NiftiHeader</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">setupFrom</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nifti_2_header</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">header</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">AString</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">filename</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC779" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC581" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">sizeof_hdr</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">nifti_2_header</span><span class="p">))</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"incorrect sizeof_hdr"</span><span class="p">);</span></span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="cpp"> <span class="n" style="color: #333;">Quirks</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">sizeof_hdr</span> <span class="o" style="font-weight: 600;">!=</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">nifti_2_header</span><span class="p">))</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"incorrect sizeof_hdr in file '"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filename</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"'"</span><span class="p">);</span></span>
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582
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<td class="diff-line-num new_line" data-linenumber="782" 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">
782
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<pre style="margin: 0;"> <span id="LC782" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">magic</span><span class="p">[]</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"n+2</span><span class="se" style="color: #d14;">\0\r\n\032\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//only support single-file nifti</span></span>
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<td class="diff-line-num old_line" data-linenumber="583" 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">
583
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<td class="diff-line-num new_line" data-linenumber="783" 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">
783
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<pre style="margin: 0;"> <span id="LC783" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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="mi" style="color: #099;">8</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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584
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784
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<pre style="margin: 0;"> <span id="LC784" class="line" lang="cpp"> <span class="p">{</span></span>
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585
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<td class="diff-line-num new_line old" data-linenumber="785" 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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<pre style="margin: 0;">-<span id="LC585" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">magic</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">magic</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"incorrect magic"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="785" 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">
785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">magic</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">magic</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"incorrect magic<span class="idiff left"> in file '"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"'</span>"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="586" 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">
586
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786
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<pre style="margin: 0;"> <span id="LC786" class="line" lang="cpp"> <span class="p">}</span></span>
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587
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<pre style="margin: 0;">-<span id="LC587" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">dim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">dim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">7</span><span class="p">)</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"incorrect dim[0]"</span><span class="p">);</span></span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">dim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">dim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">7</span><span class="p">)</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"incorrect dim[0]<span class="idiff left"> in file '"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"'</span>"</span><span class="p">);</span></span>
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588
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788
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<pre style="margin: 0;"> <span id="LC788" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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;">header</span><span class="p">.</span><span class="n" style="color: #333;">dim</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">];</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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589
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<td class="diff-line-num new_line" data-linenumber="789" 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">
789
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<pre style="margin: 0;"> <span id="LC789" class="line" lang="cpp"> <span class="p">{</span></span>
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590
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<td class="diff-line-num new_line old" data-linenumber="790" 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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<pre style="margin: 0;">-<span id="LC590" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">dim</span><span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</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 class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"dim["</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">AString_number</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"] < 1"</span><span class="p">);</span></span>
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<td class="diff-line-num new old_line" data-linenumber="591" 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="diff-line-num new new_line" data-linenumber="790" 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">
790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">dim</span><span class="p">[</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</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 class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"dim["</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">AString_number</span><span class="p">(</span><span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"] < 1<span class="idiff left"> in file '"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">"'</span>"</span><span class="p">);</span></span>
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<td class="diff-line-num old_line" data-linenumber="591" 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">
591
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791
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<pre style="margin: 0;"> <span id="LC791" class="line" lang="cpp"> <span class="p">}</span></span>
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592
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<pre style="margin: 0;">-<span id="LC592" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">vox_offset</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;"><span class="idiff left">352</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">throw</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">CiftiException</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"incorrect vox_offset"</span></span><span class="p"><span class="idiff right">);</span></span></span>
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593
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<pre style="margin: 0;">-<span id="LC593" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">bitpix</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">typeToNumBits</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">datatype</span><span class="p">))</span> <span class="k" style="font-weight: 600;"><span class="idiff left">throw</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">CiftiException</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"datatype disagrees with bitpix"</span></span><span class="p"><span class="idiff right">)</span>;</span></span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">vox_offset</span> <span class="o" style="font-weight: 600;"><</span> <span class="mi" style="color: #099;"><span class="idiff left">544</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">throw</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">CiftiException</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"file '"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"' has invalid vox_offset: "</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">AString_number</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">header</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">vox_offset</span></span><span class="p"><span class="idiff">));</span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">//haven't noticed any nifti-2 with bad vox_offset yet, and all cifti files have a big extension, so they have to have used it correctly</span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="793" 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">
793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">bitpix</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">typeToNumBits</span><span class="p">(</span><span class="n" style="color: #333;">header</span><span class="p">.</span><span class="n" style="color: #333;">datatype</span><span class="p">))</span> <span class="n" style="color: #333;"><span class="idiff left">cerr</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">AString_to_std_string</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"warning: datatype disagrees with bitpix in file '"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">"'"</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><<</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">endl</span></span><span class="p">;</span></span>
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594
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794
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<pre style="margin: 0;"> <span id="LC794" class="line" lang="cpp"> <span class="n" style="color: #333;">memcpy</span><span class="p">(</span><span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">m_header</span><span class="p">,</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="k" style="font-weight: 600;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">nifti_2_header</span><span class="p">));</span></span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ret</span><span class="p">;</span></span>
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595
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796
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<pre style="margin: 0;"> <span id="LC796" class="line" lang="cpp"><span class="p">}</span></span>
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596
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797
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<pre style="margin: 0;"> <span id="LC797" class="line" lang="cpp"></span>
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798
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<pre style="margin: 0;"> <span id="LC798" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">NiftiHeader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">typeToNumBits</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">type</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="631" 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">@@ -631,7 +832,7 @@ int NiftiHeader::typeToNumBits(const int64_t& type)</td>
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631
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832
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<pre style="margin: 0;"> <span id="LC832" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">256</span><span class="p">;</span></span>
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632
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833
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<pre style="margin: 0;"> <span id="LC833" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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633
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834
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<pre style="margin: 0;"> <span id="LC834" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">default</span><span class="o" style="font-weight: 600;">:</span></span>
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634
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<pre style="margin: 0;">-<span id="LC634" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"incorrect datatype code"</span><span class="p">);</span></span>
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835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"incorrect <span class="idiff left right">nifti </span>datatype code"</span><span class="p">);</span></span>
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635
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836
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<pre style="margin: 0;"> <span id="LC836" class="line" lang="cpp"> <span class="p">}</span></span>
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636
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837
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<pre style="margin: 0;"> <span id="LC837" class="line" lang="cpp"><span class="p">}</span></span>
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637
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838
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<pre style="margin: 0;"> <span id="LC838" class="line" lang="cpp"></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">@@ -706,6 +907,12 @@ void NiftiHeader::swapHeaderBytes(nifti_2_header& header)</td>
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706
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907
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<pre style="margin: 0;"> <span id="LC907" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">NiftiHeader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">BinaryFile</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">outFile</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</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;">version</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">swapEndian</span><span class="p">)</span></span>
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908
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<pre style="margin: 0;"> <span id="LC908" class="line" lang="cpp"><span class="p">{</span></span>
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708
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909
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<pre style="margin: 0;"> <span id="LC909" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">canWriteVersion</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="p">))</span> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"unable to write NIfTI version "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">AString_number</span><span class="p">(</span><span class="n" style="color: #333;">version</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" for file "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">outFile</span><span class="p">.</span><span class="n" style="color: #333;">getFilename</span><span class="p">());</span></span>
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910
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<pre style="margin: 0;">+<span id="LC910" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">junk1</span><span class="p">,</span> <span class="n" style="color: #333;">junk2</span><span class="p">;</span></span>
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911
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<pre style="margin: 0;">+<span id="LC911" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int16_t</span> <span class="n" style="color: #333;">datatype</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getDataType</span><span class="p">();</span></span>
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912
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<pre style="margin: 0;">+<span id="LC912" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">getDataScaling</span><span class="p">(</span><span class="n" style="color: #333;">junk1</span><span class="p">,</span> <span class="n" style="color: #333;">junk2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">&&</span> <span class="p">((</span><span class="n" style="color: #333;">datatype</span> <span class="o" style="font-weight: 600;">&</span> <span class="mh" style="color: #099;">0x70</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">datatype</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">1536</span><span class="p">))</span></span>
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913
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<pre style="margin: 0;">+<span id="LC913" class="line" lang="cpp"> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;">//that hacky expression is to detect 16, 32, 64, 1536, 1792, and 2048</span></span>
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914
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<pre style="margin: 0;">+<span id="LC914" class="line" lang="cpp"> <span class="n" style="color: #333;">cerr</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"warning: writing nifti file with scaling factor and floating point datatype"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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915
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<pre style="margin: 0;">+<span id="LC915" class="line" lang="cpp"> <span class="p">}</span></span>
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709
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916
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<pre style="margin: 0;"> <span id="LC916" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="n" style="color: #333;">padding</span><span class="p">[</span><span class="mi" style="color: #099;">16</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span> <span class="p">};</span></span>
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710
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917
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<pre style="margin: 0;"> <span id="LC917" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">voxOffset</span><span class="p">;</span></span>
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711
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918
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<pre style="margin: 0;"> <span id="LC918" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span></span>
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<li id="c8d9666779c52ffe39b1b01c4c06b8285258f0cf">
<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#c8d9666779c52ffe39b1b01c4c06b8285258f0cf"><strong>src/Nifti/NiftiHeader.h</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="58" 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">@@ -58,25 +58,36 @@ namespace cifti</td>
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58
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c"> </span>
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59
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c"> <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="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">getDimensions</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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60
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"> <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;">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="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">getSForm</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">getTimeStep</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//seconds</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">getDataOffset</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">vox_offset</span><span class="p">;</span> <span class="p">}</span></span>
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63
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int16_t</span> <span class="n" style="color: #333;">getDataType</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">datatype</span><span class="p">;</span> <span class="p">}</span></span>
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span> <span class="n" style="color: #333;">getIntentCode</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">intent_code</span><span class="p">;</span> <span class="p">}</span></span>
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64
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c"> <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;">getIntentName</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">intent_name</span><span class="p">;</span> <span class="p">}</span><span class="c1" style="color: #998; font-style: italic;">//NOTE: 16 BYTES, MAY NOT HAVE A NULL TERMINATOR</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="c"> <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;">getDescription</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">descrip</span><span class="p">;</span> <span class="p">}</span><span class="c1" style="color: #998; font-style: italic;">//NOTE: 80 BYTES, MAY NOT HAVE A NULL TERMINATOR</span></span>
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">getDataScaling</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">mult</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">offset</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//returns false if scaling not needed</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">getNumComponents</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="c"> <span class="n" style="color: #333;">AString</span> <span class="n" style="color: #333;">toString</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setDimensions</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">dimsIn</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setSForm</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <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;">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="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">sForm</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setTimeStep</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">seconds</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setIntent</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int32_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">code</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="n" style="color: #333;">name</span><span class="p">[</span><span class="mi" style="color: #099;">16</span><span class="p">]);</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setDescription</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="n" style="color: #333;">descrip</span><span class="p">[</span><span class="mi" style="color: #099;">80</span><span class="p">]);</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setDataType</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">type</span><span class="p">);</span></span>
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77
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">clearDataScaling</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setDataScaling</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">mult</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">offset</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">setDataTypeAndScaleRange</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int16_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">type</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">minval</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">maxval</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="c"> <span class="c1" style="color: #998; font-style: italic;">///get the FSL "scale" space</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="c"> <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;">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="kt" style="color: #458; font-weight: 600;">float</span><span class="o" style="font-weight: 600;">></span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">getFSLSpace</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="c"> </span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">operator</span><span class="o" style="font-weight: 600;">==</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">NiftiHeader</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rhs</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//for testing purposes</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">operator</span><span class="o" style="font-weight: 600;">!=</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">NiftiHeader</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rhs</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span> <span class="p">{</span> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">!</span><span class="p">((</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">this</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">rhs</span><span class="p">);</span> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="c"> <span class="n" style="color: #333;">private</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="c"> <span class="k" style="font-weight: 600;">struct</span> <span class="n" style="color: #333;">Quirks</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">no_extender</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="c"> <span class="n" style="color: #333;">Quirks</span><span class="p">()</span> <span class="p">{</span> <span class="n" style="color: #333;">no_extender</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="c"> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="c"> <span class="n" style="color: #333;">nifti_2_header</span> <span class="n" style="color: #333;">m_header</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//storage for header values regardless of version</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">m_version</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">m_isSwapped</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">@@ -84,8 +95,8 @@ namespace cifti</td>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">swapHeaderBytes</span><span class="p">(</span><span class="n" style="color: #333;">nifti_2_header</span> <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">header</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">prepareHeader</span><span class="p">(</span><span class="n" style="color: #333;">nifti_1_header</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">header</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span><span class="c1" style="color: #998; font-style: italic;">//transform internal state into ready to write header struct</span></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">prepareHeader</span><span class="p">(</span><span class="n" style="color: #333;">nifti_2_header</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">header</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">void</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">setupFrom</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nifti_1_header</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">header</span></span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//error check provided header, and populate members from it</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;"><span class="idiff left">void</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">setupFrom</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nifti_2_header</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">header</span></span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">Quirks</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">setupFrom</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nifti_1_header</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">header</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">AString</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">filename</span></span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//error check provided header, and populate members from it</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="c"> <span class="n" style="color: #333;"><span class="idiff left">Quirks</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">setupFrom</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">nifti_2_header</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">header</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">AString</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">filename</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">typeToNumBits</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">type</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">computeVoxOffset</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</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;">version</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="c"> <span class="p">};</span></span>
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<li id="7d2ec12a9cdd93000c8f8714368517127db5b64b">
<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#7d2ec12a9cdd93000c8f8714368517127db5b64b"><strong>src/NiftiIO.cxx</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">@@ -42,6 +42,16 @@ void NiftiIO::openRead(const AString& filename)</td>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"file uses the binary datatype, which is unsupported: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">m_dims</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">getDimensions</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">filesize</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_file</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span><span class="c1" style="color: #998; font-style: italic;">//returns -1 if it can't efficiently determine size</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span> <span class="n" style="color: #333;">elemCount</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">getNumComponents</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</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="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span><span class="p">)</span><span class="n" style="color: #333;">m_dims</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">();</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="cpp"> <span class="n" style="color: #333;">elemCount</span> <span class="o" style="font-weight: 600;">*=</span> <span class="n" style="color: #333;">m_dims</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">];</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">filesize</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">0</span> <span class="o" style="font-weight: 600;">&&</span> <span class="n" style="color: #333;">filesize</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">getDataOffset</span><span class="p">()</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">numBytesPerElem</span><span class="p">()</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">elemCount</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="cpp"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"nifti file is truncated: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"><span class="p">}</span></span>
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46
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">NiftiIO</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">writeNew</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">NiftiHeader</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</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;">version</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">withRead</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">bool</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">swapEndian</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">@@ -69,33 +79,7 @@ void NiftiIO::close()</td>
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69
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79
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"></span>
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70
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">NiftiIO</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getNumComponents</span><span class="p">()</span> <span class="k" style="font-weight: 600;">const</span></span>
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71
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="cpp"><span class="p">{</span></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">switch</span> <span class="p">(</span><span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">getDataType</span><span class="p">())</span></span>
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73
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="cpp"> <span class="p">{</span></span>
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74
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_RGB24</span><span class="p">:</span></span>
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75
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">3</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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77
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_COMPLEX64</span><span class="p">:</span></span>
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78
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_COMPLEX128</span><span class="p">:</span></span>
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79
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_COMPLEX256</span><span class="p">:</span></span>
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80
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">2</span><span class="p">;</span></span>
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81
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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82
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_INT8</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="83" 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">
83
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_UINT8</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="84" 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">
84
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_INT16</span><span class="p">:</span></span>
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<td class="diff-line-num old old_line" data-linenumber="85" 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">
85
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_UINT16</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_INT32</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_UINT32</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_FLOAT32</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_INT64</span><span class="p">:</span></span>
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90
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_UINT64</span><span class="p">:</span></span>
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91
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_FLOAT64</span><span class="p">:</span></span>
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92
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">NIFTI_TYPE_FLOAT128</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">default</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="cpp"> <span class="n" style="color: #333;">CiftiAssert</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">throw</span> <span class="n" style="color: #333;">CiftiException</span><span class="p">(</span><span class="s" style="color: #d14;">"internal error, report what you did to the developers"</span><span class="p">);</span></span>
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98
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">getNumComponents</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC85" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">NiftiIO</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numBytesPerElem</span><span class="p">()</span></span>
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<li id="e1bc753f66e97e3c73bc3ba07e7931c56b13526c">
<a href="https://salsa.debian.org/med-team/ciftilib/compare/43f1c8290a71d5994542d813582501057c778346...7404c968411b750315bcfa5dfc882faf771474c2#e1bc753f66e97e3c73bc3ba07e7931c56b13526c"><strong>src/NiftiIO.h</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="58" 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">@@ -58,6 +58,8 @@ namespace cifti</td>
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58
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">convertRead</span><span class="p">(</span><span class="n" style="color: #333;">TO</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">FROM</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">count</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//for reading from file</span></span>
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59
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="c"> <span class="n" style="color: #333;">template</span><span class="o" style="font-weight: 600;"><</span><span class="kr" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TO</span><span class="p">,</span> <span class="kr" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">FROM</span><span class="o" style="font-weight: 600;">></span></span>
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60
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60
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">convertWrite</span><span class="p">(</span><span class="n" style="color: #333;">TO</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">FROM</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">in</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int64_t</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">count</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//for writing to file</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="c"> <span class="n" style="color: #333;">template</span><span class="o" style="font-weight: 600;"><</span><span class="kr" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TO</span><span class="p">,</span> <span class="kr" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">FROM</span><span class="o" style="font-weight: 600;">></span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="c"> <span class="k" style="font-weight: 600;">static</span> <span class="n" style="color: #333;">TO</span> <span class="n" style="color: #333;">clamp</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">FROM</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">in</span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//deal with integer cast being undefined when converting from outside range</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="c"> <span class="n" style="color: #333;">public</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">openRead</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="n" style="color: #333;">writeNew</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">AString</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">NiftiHeader</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">header</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</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;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">bool</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">withRead</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">bool</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">swapEndian</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</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">@@ -240,12 +242,12 @@ namespace cifti</td>
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<pre style="margin: 0;"> <span id="LC242" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</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;">count</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC243" class="line" lang="c"> <span class="n" style="color: #333;">out</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">TO</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">floor</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">5</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">offset</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mult</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">in</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">]</span>);</span><span class="c1" style="color: #998; font-style: italic;">//we don't always need that much precision, but it will still be faster than hard drives</span></span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="c"> <span class="n" style="color: #333;">out</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">clamp</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">TO</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">floor</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">5l</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">offset</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mult</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="idiff"> </span><span class="p"><span class="idiff">(</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">in</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">])</span>);</span><span class="c1" style="color: #998; font-style: italic;">//we don't always need that much precision, but it will still be faster than hard drives</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</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;">count</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC248" class="line" lang="c"> <span class="n" style="color: #333;">out</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">TO</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">floor</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">5</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">in</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">]</span>);</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="c"> <span class="n" style="color: #333;">out</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">clamp</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">TO</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">floor</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">5</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">in</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">])</span>);</span></span>
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</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">@@ -270,17 +272,17 @@ namespace cifti</td>
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="c"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">mult</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="c"> <span class="n" style="color: #333;">bool</span> <span class="n" style="color: #333;">doScale</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">getDataScaling</span><span class="p">(</span><span class="n" style="color: #333;">mult</span><span class="p">,</span> <span class="n" style="color: #333;">offset</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC274" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</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;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TO</span><span class="o" style="font-weight: 600;">>::</span><span class="n" style="color: #333;">is_integer</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">//do round to nearest when integer output type</span></span>
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<pre style="margin: 0;">-<span id="LC273" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="c"> <span class="p">{</span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">//TODO: what about NaN?</span></span></span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">doScale</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</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;">count</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="c"> <span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC278" class="line" lang="c"> <span class="n" style="color: #333;">out</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">TO</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">floor</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">5</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="p"><span class="idiff">((</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">in</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">offset</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">mult</span></span><span class="p">);</span><span class="c1" style="color: #998; font-style: italic;">//we don't always need that much precision, but it will still be faster than hard drives</span></span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="c"> <span class="n" style="color: #333;">out</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">clamp</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">TO</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">floor</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">5l</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="p"><span class="idiff">((</span></span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">long</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">in</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">offset</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">mult</span></span><span class="p"><span class="idiff right">)</span>);</span><span class="c1" style="color: #998; font-style: italic;">//we don't always need that much precision, but it will still be faster than hard drives</span></span>
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<pre style="margin: 0;"> <span id="LC281" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC282" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="c"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int64_t</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;">count</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span></span>
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282
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284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="c"> <span class="p">{</span></span>
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283
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<pre style="margin: 0;">-<span id="LC283" class="line" lang="c"> <span class="n" style="color: #333;">out</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">TO</span></span><span class="p"><span class="idiff">)</span></span><span class="n" style="color: #333;"><span class="idiff">floor</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">5</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">in</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">]</span>);</span></span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="c"> <span class="n" style="color: #333;">out</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">clamp</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">TO</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="kt" style="color: #458; font-weight: 600;"><span class="idiff">double</span></span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">floor</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">.</span></span><span class="mi" style="color: #099;"><span class="idiff">5</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">in</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">])</span>);</span></span>
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</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">@@ -300,6 +302,19 @@ namespace cifti</td>
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<pre style="margin: 0;"> <span id="LC302" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">m_header</span><span class="p">.</span><span class="n" style="color: #333;">isSwapped</span><span class="p">())</span> <span class="n" style="color: #333;">ByteSwapping</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">swapArray</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">,</span> <span class="n" style="color: #333;">count</span><span class="p">);</span></span>
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301
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC304" class="line" lang="c"> </span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="c"> <span class="n" style="color: #333;">template</span><span class="o" style="font-weight: 600;"><</span><span class="kr" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">TO</span><span class="p">,</span> <span class="kr" style="font-weight: 600;">typename</span> <span class="n" style="color: #333;">FROM</span><span class="o" style="font-weight: 600;">></span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="c"> <span class="n" style="color: #333;">TO</span> <span class="n" style="color: #333;">NiftiIO</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">clamp</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">FROM</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">in</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="c"> <span class="p">{</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="c"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">numeric_limits</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">TO</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">mylimits</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="309" 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">
309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mylimits</span><span class="p">.</span><span class="n" style="color: #333;">max</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">in</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mylimits</span><span class="p">.</span><span class="n" style="color: #333;">max</span><span class="p">();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="310" 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">
310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mylimits</span><span class="p">.</span><span class="n" style="color: #333;">is_integer</span><span class="p">)</span><span class="c1" style="color: #998; font-style: italic;">//c++11 can use lowest() instead of this mess</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="c"> <span class="p">{</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">mylimits</span><span class="p">.</span><span class="n" style="color: #333;">min</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">in</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">mylimits</span><span class="p">.</span><span class="n" style="color: #333;">min</span><span class="p">();</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="c"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="c"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">mylimits</span><span class="p">.</span><span class="n" style="color: #333;">max</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">in</span><span class="p">)</span> <span class="k" style="font-weight: 600;">return</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">mylimits</span><span class="p">.</span><span class="n" style="color: #333;">max</span><span class="p">();</span></span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="c"> <span class="p">}</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="c"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">TO</span><span class="p">)</span><span class="n" style="color: #333;">in</span><span class="p">;</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="c"> <span class="p">}</span></span>
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303
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<pre style="margin: 0;"> <span id="LC318" class="line" lang="c"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="c"></span>
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#endif //__NIFTI_IO_H__</span></span></pre>
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