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<html><head><meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"><title>mia-2dimagestats</title><link rel="stylesheet" type="text/css" href="progref.css"><meta name="generator" content="DocBook XSL Stylesheets V1.79.1"><link rel="home" href="index.html" title="Mia Program Reference"><link rel="up" href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html" title="Analysis, filtering, combining, and segmentation of 2D images"><link rel="prev" href="Secmia2dimageseriesmaximumintensityprojection.html" title="mia-2dimageseries-maximum-intensity-projection"><link rel="next" href="Secmia2dlerp.html" title="mia-2dlerp"></head><body bgcolor="white" text="black" link="#0000FF" vlink="#840084" alink="#0000FF"><div class="navheader"><table width="100%" summary="Navigation header"><tr><th colspan="3" align="center">mia-2dimagestats</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="Secmia2dimageseriesmaximumintensityprojection.html">Prev</a> </td><th width="60%" align="center">Analysis, filtering, combining, and segmentation of 2D images</th><td width="20%" align="right"> <a accesskey="n" href="Secmia2dlerp.html">Next</a></td></tr></table><hr></div><div class="section"><div class="titlepage"><div><div><h3 class="title"><a name="Secmia2dimagestats"></a>mia-2dimagestats</h3></div></div></div><h4><a name="idp2190"></a>Sysnopis:</h4><div class="cmdsynopsis"><p><code class="command">mia-2dimagestats</code>  {-i <em class="replaceable"><code>io</code></em>} [
          <em class="replaceable"><code>options</code></em>
        ...]</p></div><h4><a name="idp2197"></a>Description:</h4><p>This progranm is used to evaluate some statistics of an image. Output is Mean, Variation, Median, and Median Average Distance of the intensity values. The program allows one to set a lower threshold and to cut off a percentage of the high intensity pixels</p><h4><a name="idp2199"></a>Options:</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-i, --in-file=(input, required); io</span></dt><dd><p>input image to be analyzed. For supported file types see <a class="xref" href="SecPlugintype2dimageio.html" title="Plugin type: 2dimage/io">Plugin type: 2dimage/io</a></p></dd><dt><span class="term">-t, --thresh=10; float</span></dt><dd><p>intensity thresh to ignoreintensity thresh to ignore</p></dd><dt><span class="term">-g, --high-thresh=0.05; float</span></dt><dd><p>upper histogram percentage to ignoreupper histogram percentage to ignore</p></dd><dt><span class="term">--use-histogram</span></dt><dd><p>Use a histogram to accumulate statistics</p></dd></dl></div><h4><a name="idp2218"></a>Help &amp; Info</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-V, --verbose=warning; dict</span></dt><dd><p>verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:</p><div class="informaltable"><table class="informaltable" border="0"><colgroup><col class="c1"><col class="c2"></colgroup><tbody><tr><td align="left" valign="top">info:</td><td align="left" valign="top">Low level messages</td></tr><tr><td align="left" valign="top">trace:</td><td align="left" valign="top">Function call trace</td></tr><tr><td align="left" valign="top">fail:</td><td align="left" valign="top">Report test failures</td></tr><tr><td align="left" valign="top">warning:</td><td align="left" valign="top">Warnings</td></tr><tr><td align="left" valign="top">error:</td><td align="left" valign="top">Report errors</td></tr><tr><td align="left" valign="top">debug:</td><td align="left" valign="top">Debug output</td></tr><tr><td align="left" valign="top">message:</td><td align="left" valign="top">Normal messages</td></tr><tr><td align="left" valign="top">fatal:</td><td align="left" valign="top">Report only fatal errors</td></tr></tbody></table></div></dd><dt><span class="term">--copyright=(); bool</span></dt><dd><p>print copyright information</p></dd><dt><span class="term">-h, --help=(); bool</span></dt><dd><p>print this help</p></dd><dt><span class="term">-?, --usage=(); bool</span></dt><dd><p>print a short help</p></dd><dt><span class="term">--version=(); bool</span></dt><dd><p>print the version number and exit</p></dd></dl></div><h4><a name="idp2269"></a>Processing</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">--threads=-1; int</span></dt><dd><p>Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (-1: automatic estimation).</p></dd></dl></div><h4><a name="idp2275"></a>Example:</h4><p>Evaluate the statistics of image input.png. Don't include the upper 1% of intensities in the statistics. The result is written to stdout</p><pre class="screen">mia-2dimagestats -i input.png -g 1</pre><h4><a name="idp2278"></a>Author(s):</h4><p>Gert Wollny</p></div><div class="navfooter"><hr><table width="100%" summary="Navigation footer"><tr><td width="40%" align="left"><a accesskey="p" href="Secmia2dimageseriesmaximumintensityprojection.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="SecAnalysisfilteringcombiningandsegmentationof2Dimages.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="Secmia2dlerp.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">mia-2dimageseries-maximum-intensity-projection </td><td width="20%" align="center"><a accesskey="h" href="index.html">Home</a></td><td width="40%" align="right" valign="top"> mia-2dlerp</td></tr></table></div></body></html>

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