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<h1>Fiji Installation Instructions including TOMCAT plugins<a class="headerlink" href="#fiji-installation-instructions-including-tomcat-plugins" title="Permalink to this headline"></a></h1>
<p>This page explains step by step the instructions for the installation of a new Fiji version from scratch with all relevant TOMCAT plugins.</p>
<ol class="arabic">
<li><p class="first">Download and unpack the relevant Fiji.zip file</p>
</li>
<li><p class="first">Copy the following files to the TOMCAT folder (to be created) in the existing Fiji plugins folder</p>
<ol class="loweralpha simple">
<li>Reco_Manager.py</li>
<li>DMP_Reader.class</li>
<li>centering_overlay.py</li>
<li>_multiscale_coords.txt</li>
<li>ZeroMQ_Viewer-0.5.0.jar</li>
</ol>
</li>
<li><p class="first">DMP viewer (<a class="reference external" href="https://git.psi.ch/tomcat/TOMCAT-DMP-Files/tree/master/ImageJ">https://git.psi.ch/tomcat/TOMCAT-DMP-Files/tree/master/ImageJ</a>)</p>
<ol class="loweralpha simple">
<li>Copy <em>DMP_Reader.class</em> to the plugins/TOMCAT folder</li>
<li>Copy <em>HandleExtraFileTypes.class</em> to the plugins folder</li>
<li>If necessary run<ol class="lowerroman">
<li>cd location/of/Fiji/plugins</li>
<li>jar -uf IO_-2.1.0.jar HandleExtraFileTypes.class</li>
</ol>
</li>
</ol>
</li>
<li><p class="first">HDF5 Viewer (<a class="reference external" href="https://github.com/paulscherrerinstitute/ch.psi.imagej.hdf5">https://github.com/paulscherrerinstitute/ch.psi.imagej.hdf5</a>)</p>
<ol class="loweralpha">
<li><p class="first">Download and unzip plugin</p>
</li>
<li><p class="first">Decompile <em>HandleExtraFileTypes.class</em> to <em>HandleExtraFileTypes.java</em>
(previously done with <a class="reference external" href="http://www.javadecompilers.com/jad">Jad v1.5.8g</a>, but not tried now)</p>
</li>
<li><p class="first">Add the following line to <em>HandleExtraFileTypes.java</em>:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="k">if</span> <span class="p">(</span><span class="n">s1</span><span class="o">.</span><span class="n">endsWith</span><span class="p">(</span><span class="s2">&quot;.h5&quot;</span><span class="p">)</span> <span class="o">||</span> <span class="n">s1</span><span class="o">.</span><span class="n">endsWith</span><span class="p">(</span><span class="s2">&quot;.hdf5&quot;</span><span class="p">))</span> <span class="p">{</span>
<span class="k">return</span> <span class="n">tryPlugIn</span><span class="p">(</span><span class="s2">&quot;ch.psi.imagej.hdf5.HDF5Reader&quot;</span><span class="p">,</span> <span class="n">s2</span><span class="p">);</span>
<span class="p">}</span>
</pre></div>
</div>
</li>
<li><p class="first">Recompile using: javac -classpath ../jars/ij-1.51s.jar HandleExtraFileTypes.java</p>
</li>
<li><p class="first">Run jar -uf IO_-2.1.0.jar HandleExtraFileTypes.class</p>
</li>
</ol>
</li>
<li><p class="first">Jython</p>
<ol class="loweralpha simple">
<li>Jython 2.7 has some problems:<ol class="lowerroman">
<li>The <em>os</em> module is missing some attributes (e.g. getuid)</li>
<li><em>os.path.realpath</em> has a strange behavior</li>
</ol>
</li>
<li>Jython 2.5 should be used instead</li>
<li>Therefore remove <em>jython-shaded-2.7.0.jar</em> from the Fiji jars folder</li>
<li>Substitute it with <em>jython-shaded-2.5.3.jar</em> from an older Fiji distribution (if available) or from <a class="reference external" href="https://jar-download.com/explore-java-source-code.php?a=jython-shaded&amp;g=org.scijava&amp;v=2.5.3&amp;downloadable=1">here</a>.</li>
</ol>
</li>
<li><p class="first">Permissions</p>
<ol class="loweralpha simple">
<li>Group for the personal account is different from the group of the e-account</li>
<li>Therefore, others need to have read permissions for files and directories</li>
<li>For this purpose, run /net/gfa-fs-3/export/tomcat/x86_64/bin/x02da_copy_permissions_fijiInstallation.py</li>
</ol>
</li>
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