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<div class="section" id="building">
<h1>Building<a class="headerlink" href="#building" title="Permalink to this headline">¶</a></h1>
<div class="contents local topic" id="table-of-contents">
<p class="topic-title first">Table of Contents</p>
<ul class="simple">
<li><a class="reference internal" href="#matlab-codes" id="id1">Matlab codes</a></li>
<li><a class="reference internal" href="#dependent-packages" id="id2">Dependent Packages</a><ul>
<li><a class="reference internal" href="#required-packages" id="id3">Required Packages</a></li>
<li><a class="reference internal" href="#optional-packages" id="id4">Optional Packages</a></li>
<li><a class="reference internal" href="#third-party-packages-included-in-dmritool" id="id5">Third Party Packages (included in dmritool)</a></li>
</ul>
</li>
<li><a class="reference internal" href="#build-souce-code" id="id6">Build Souce Code</a><ul>
<li><a class="reference internal" href="#linux-and-mac" id="id7">Linux and Mac</a></li>
<li><a class="reference internal" href="#windows" id="id8">Windows</a></li>
</ul>
</li>
</ul>
</div>
<a class="reference external image-reference" href="https://travis-ci.org/DiffusionMRITool/dmritool"><img alt="https://travis-ci.org/DiffusionMRITool/dmritool.svg?branch=master" src="https://travis-ci.org/DiffusionMRITool/dmritool.svg?branch=master" /></a>
<div class="section" id="matlab-codes">
<h2><a class="toc-backref" href="#id1">Matlab codes</a><a class="headerlink" href="#matlab-codes" title="Permalink to this headline">¶</a></h2>
<p>The codes in folder <code class="docutils literal"><span class="pre">${DMRITOOL_SOURCE_DIR}/Matlab</span></code> are purely in matlab.
Thus you do not need to build c++ codes to run codes in that folder.
The codes in folder <code class="docutils literal"><span class="pre">${DMRITOOL_SOURCE_DIR}/Wrapping/Matlab</span></code> are matlab mex files, which depend on the c++ codes.</p>
<p>See <a class="reference internal" href="matlabfiles/matlabfunctions.html"><span class="doc">the matlab function list</span></a>,
where these functions starting with mex prefix need to be built using cmake.</p>
</div>
<div class="section" id="dependent-packages">
<h2><a class="toc-backref" href="#id2">Dependent Packages</a><a class="headerlink" href="#dependent-packages" title="Permalink to this headline">¶</a></h2>
<div class="section" id="required-packages">
<h3><a class="toc-backref" href="#id3">Required Packages</a><a class="headerlink" href="#required-packages" title="Permalink to this headline">¶</a></h3>
<ul class="simple">
<li><a class="reference external" href="http://www.cmake.org">CMake</a> (Version 2.8 or newer)</li>
<li><a class="reference external" href="https://gcc.gnu.org">GCC</a> (4.8 or newer. DMRITool uses C++11, thus it cannot work for old gcc)</li>
<li><a class="reference external" href="http://www.itk.org">Insight Toolkit</a> (ITK, version 4.9 or newer)</li>
<li><a class="reference external" href="http://www.vtk.org">Visualization Toolkit</a> (VTK, version 6 or newer)</li>
<li><a class="reference external" href="https://github.com/Slicer/SlicerExecutionModel">SlicerExecutionModel</a> (GenerateCLP, for command line interface):</li>
<li><a class="reference external" href="https://github.com/xianyi/OpenBLAS">OpenBLAS</a> + <a class="reference external" href="https://www.netlib.org/lapack">Lapack</a> or <a class="reference external" href="https://software.intel.com/en-us/intel-mkl">MKL</a> (at least one is required)</li>
<li><a class="reference external" href="http://www.gnu.org/software/gsl">GNU Scientific Library</a> (GSL, for special functions)</li>
</ul>
</div>
<div class="section" id="optional-packages">
<h3><a class="toc-backref" href="#id4">Optional Packages</a><a class="headerlink" href="#optional-packages" title="Permalink to this headline">¶</a></h3>
<ul class="simple">
<li><a class="reference external" href="http://www.qt-project.org">Qt</a>: needed for building <code class="docutils literal"><span class="pre">QTApplications</span></code>.</li>
<li><a class="reference external" href="http://www.doxygen.org">Doxygen</a>: needed when building doxygen documents.</li>
</ul>
</div>
<div class="section" id="third-party-packages-included-in-dmritool">
<h3><a class="toc-backref" href="#id5">Third Party Packages (included in dmritool)</a><a class="headerlink" href="#third-party-packages-included-in-dmritool" title="Permalink to this headline">¶</a></h3>
<ul class="simple">
<li><a class="reference external" href="https://github.com/google/googletest">GTest</a>: GTest can be automatically downloaded and built when building tests.</li>
<li><a class="reference external" href="http://spams-devel.gforge.inria.fr">SPAMS</a>: included in <code class="docutils literal"><span class="pre">ThirdParty/Spams</span></code></li>
</ul>
</div>
</div>
<div class="section" id="build-souce-code">
<h2><a class="toc-backref" href="#id6">Build Souce Code</a><a class="headerlink" href="#build-souce-code" title="Permalink to this headline">¶</a></h2>
<div class="section" id="linux-and-mac">
<h3><a class="toc-backref" href="#id7">Linux and Mac</a><a class="headerlink" href="#linux-and-mac" title="Permalink to this headline">¶</a></h3>
<ol class="arabic">
<li><p class="first">build/install <a class="reference external" href="http://www.cmake.org">CMake</a>, <a class="reference external" href="https://gcc.gnu.org">GCC</a>, <a class="reference external" href="http://git-scm.com">Git</a>, <a class="reference external" href="http://www.gnu.org/software/gsl">GSL</a>, <a class="reference external" href="http://www.vtk.org">VTK</a>, <a class="reference external" href="http://www.itk.org">ITK</a>, <a class="reference external" href="http://www.qt-project.org">Qt</a> (optional), <a class="reference external" href="http://www.doxygen.org">Doxygen</a> (optional).</p>
</li>
<li><p class="first">build/install <a class="reference external" href="https://github.com/xianyi/OpenBLAS">OpenBlas</a> + <a class="reference external" href="https://www.netlib.org/lapack">Lapack</a> or <a class="reference external" href="https://software.intel.com/en-us/intel-mkl">MKL</a> .</p>
<p><a class="reference external" href="https://software.intel.com/en-us/intel-mkl">MKL</a> is free for students, educators, academic researchers and open source contributors.
See <a class="reference external" href="https://software.intel.com/en-us/qualify-for-free-software">the free download link</a>.
<a class="reference external" href="https://github.com/xianyi/OpenBLAS">OpenBlas</a> and <a class="reference external" href="https://www.netlib.org/lapack">Lapack</a> are always free and easy to use.</p>
<p>If you choose <a class="reference external" href="https://github.com/xianyi/OpenBLAS">OpenBlas</a> + <a class="reference external" href="https://www.netlib.org/lapack">Lapack</a>, you can use them from system repositories.
In this case, you need to set environment variables correctly.
See <a class="reference external" href="https://github.com/xianyi/OpenBLAS/wiki/faq#multi-threaded">FAQ of OpenBlas</a>.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">export</span> <span class="n">OPENBLAS_NUM_THREADS</span><span class="o">=</span><span class="mi">1</span>
</pre></div>
</div>
<p>We suggest that you build <a class="reference external" href="https://github.com/xianyi/OpenBLAS">OpenBlas</a> from its source codes.
Suggested building command for <a class="reference external" href="https://github.com/xianyi/OpenBLAS">OpenBlas</a> used in <a class="reference external" href="https://diffusionmritool.github.io">dmritool</a> is:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">git</span> <span class="n">clone</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">xianyi</span><span class="o">/</span><span class="n">OpenBLAS</span><span class="o">.</span><span class="n">git</span>
<span class="n">cd</span> <span class="n">OpenBlas</span>
<span class="n">git</span> <span class="n">checkout</span> <span class="n">v0</span><span class="o">.</span><span class="mf">2.13</span>
<span class="n">make</span> <span class="n">BINARY</span><span class="o">=</span><span class="mi">64</span> <span class="n">USE_THREAD</span><span class="o">=</span><span class="mi">0</span> <span class="n">USE_OPENMP</span><span class="o">=</span><span class="mi">1</span> <span class="n">cc</span><span class="o">=</span><span class="n">gcc</span> <span class="n">FC</span><span class="o">=</span><span class="n">gfortran</span>
<span class="n">make</span> <span class="n">install</span>
</pre></div>
</div>
</li>
<li><p class="first">build <a class="reference external" href="https://github.com/Slicer/SlicerExecutionModel">SlicerExecutionModel</a></p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">git</span> <span class="n">clone</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">Slicer</span><span class="o">/</span><span class="n">SlicerExecutionModel</span><span class="o">.</span><span class="n">git</span>
<span class="n">mkdir</span> <span class="n">SlicerExecutionModel</span><span class="o">-</span><span class="n">build</span>
<span class="n">cd</span> <span class="n">SlicerExecutionModel</span><span class="o">-</span><span class="n">build</span>
<span class="n">ccmake</span> <span class="o">../</span><span class="n">SlicerExecutionModel</span>
<span class="n">make</span>
</pre></div>
</div>
</li>
<li><p class="first">build <a class="reference external" href="https://diffusionmritool.github.io">DMRITool</a> source</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">git</span> <span class="n">clone</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">DiffusionMRITool</span><span class="o">/</span><span class="n">dmritool</span>
<span class="n">mkdir</span> <span class="n">dmritool</span><span class="o">-</span><span class="n">build</span>
<span class="n">cd</span> <span class="n">dmritool</span><span class="o">-</span><span class="n">build</span>
<span class="n">ccmake</span> <span class="o">../</span><span class="n">dmritool</span>
<span class="n">make</span>
</pre></div>
</div>
</li>
</ol>
<blockquote>
<div><ul class="simple">
<li>When building <a class="reference external" href="https://diffusionmritool.github.io">DMRITool</a> with <code class="docutils literal"><span class="pre">ccmake</span></code>, <code class="docutils literal"><span class="pre">GenerateCLP_DIR</span></code> needs to be set as <code class="docutils literal"><span class="pre">SlicerExecutionModel-build/GenerateCLP</span></code>.</li>
<li>The code uses <a class="reference external" href="https://github.com/xianyi/OpenBLAS">OpenBlas</a> + <a class="reference external" href="https://www.netlib.org/lapack">Lapack</a> if <code class="docutils literal"><span class="pre">DMRITOOL_USE_MKL</span></code> is set <code class="docutils literal"><span class="pre">OFF</span></code>, it uses <a class="reference external" href="https://software.intel.com/en-us/intel-mkl">MKL</a> if <code class="docutils literal"><span class="pre">DMRITOOL_USE_MKL</span></code> is <code class="docutils literal"><span class="pre">ON</span></code>.</li>
<li>If <code class="docutils literal"><span class="pre">DMRITOOL_USE_FASTLAPACK=ON</span></code>, then the codes use fast versions for SVD and eigen-decomposition,
but it may have errors for <a class="reference external" href="https://github.com/xianyi/OpenBLAS">openblas</a>.
You can check whether <code class="docutils literal"><span class="pre">utlVNLLapackGTest</span></code> and <code class="docutils literal"><span class="pre">utlVNLBlasGTest</span></code> can successfully pass.
If these two tests do not passed, you may need to build <a class="reference external" href="https://github.com/xianyi/OpenBLAS">OpenBlas</a> manually or build <a class="reference external" href="https://diffusionmritool.github.io">DMRITool</a> with <code class="docutils literal"><span class="pre">DMRITOOL_USE_FASTLAPACK=OFF</span></code></li>
<li>If you want to build <a class="reference external" href="http://www.mathworks.com">matlab</a> mex files, please set <code class="docutils literal"><span class="pre">DMRITOOL_WRAP_MATLAB=ON</span></code>.</li>
<li>If <code class="docutils literal"><span class="pre">BUILD_TESTING</span></code> is set <code class="docutils literal"><span class="pre">ON</span></code>, some tests based on <a class="reference external" href="https://github.com/google/googletest">GTest</a> will be built.
We suggest you set it <code class="docutils literal"><span class="pre">ON</span></code>. <a class="reference external" href="https://github.com/google/googletest">GTest</a> will be automatically downloaded and built if you do not have it in system.</li>
<li><a class="reference external" href="http://www.qt-project.org">Qt</a> is needed if <code class="docutils literal"><span class="pre">BUILD_QT_APPLICATIONS</span></code> is set <code class="docutils literal"><span class="pre">ON</span></code>.</li>
<li><code class="docutils literal"><span class="pre">VERBOSITY_LEVEL</span></code> is used for debug. The default value is 0.
If you set it as 1, the routines can provide more logging information and perform more condition checking,
but it may make the built executables a little bit slower.</li>
<li>If you use an old version of ITK (<4.9), you may have to set <code class="docutils literal"><span class="pre">CMAKE_CXX_FLAGS=-fpermissive</span></code> to build the codes.
That is <a class="reference external" href="https://itk.org/pipermail/insight-developers/2015-December/024705.html">a known issue of ITK with c++11 support</a>, which is solved after ITK 4.9.</li>
</ul>
</div></blockquote>
<ol class="arabic" start="5">
<li><p class="first">build <a class="reference external" href="http://www.doxygen.org">doxygen</a> document (optional)</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">doxygen</span>
</pre></div>
</div>
</li>
<li><p class="first">Set environments.</p>
</li>
</ol>
<blockquote>
<div><ul>
<li><p class="first">You can add <code class="docutils literal"><span class="pre">dmritool-build/bin</span></code> into your <code class="docutils literal"><span class="pre">PATH</span></code> to use the binary executables easily.</p>
</li>
<li><p class="first">When <code class="docutils literal"><span class="pre">DMRITOOL_WRAP_MATLAB</span></code> is set <code class="docutils literal"><span class="pre">ON</span></code>, the built mex executables are in <code class="docutils literal"><span class="pre">dmritool-build/Wrapping/Matlab/bin</span></code>.
Then to use these mex executables in matlab, you need to put the folder into matlab path.</p>
</li>
<li><p class="first">For matlab mex files, you also need to set <code class="docutils literal"><span class="pre">BLAS_VERSION</span></code> as the openblas lib or mkl lib.
If you use <a class="reference external" href="https://software.intel.com/en-us/intel-mkl">mkl</a>, then set <code class="docutils literal"><span class="pre">blas_version</span></code> as</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">export</span> <span class="n">BLAS_VERSION</span><span class="o">=</span><span class="s2">"MKL_DIR/lib/intel64/libmkl_rt.so"</span>
</pre></div>
</div>
<p>If you use <a class="reference external" href="https://github.com/xianyi/OpenBLAS">openblas</a>, then set <code class="docutils literal"><span class="pre">blas_version</span></code> as</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">export</span> <span class="n">BLAS_VERSION</span><span class="o">=</span><span class="s2">"/usr/local/lib/libopenblas.so"</span>
</pre></div>
</div>
</li>
</ul>
</div></blockquote>
<ol class="arabic" start="7">
<li><p class="first">build tests (optional, but suggested)</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">test</span>
</pre></div>
</div>
</li>
</ol>
<blockquote>
<div><ul class="simple">
<li>Set <code class="docutils literal"><span class="pre">BUILD_TESTING</span></code> <code class="docutils literal"><span class="pre">ON</span></code> to build tests.</li>
<li>Make sure all tests are successfully passed. Otherwise the routines may not run correctly.</li>
</ul>
</div></blockquote>
</div>
<div class="section" id="windows">
<h3><a class="toc-backref" href="#id8">Windows</a><a class="headerlink" href="#windows" title="Permalink to this headline">¶</a></h3>
<p>We did not test the building of <a class="reference external" href="https://diffusionmritool.github.io">DMRITool</a> in windows.
You can try it by yourself.</p>
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