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1 2 3 | <html><head><meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"><title>mia-3dimagestatistics-in-mask</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="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html" title="Analysis, filtering, combining, and segmentation of 3D images"><link rel="prev" href="Secmia3dimagefilterstack.html" title="mia-3dimagefilterstack"><link rel="next" href="Secmia3dimagestats.html" title="mia-3dimagestats"></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-3dimagestatistics-in-mask</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="Secmia3dimagefilterstack.html">Prev</a> </td><th width="60%" align="center">Analysis, filtering, combining, and segmentation of 3D images</th><td width="20%" align="right"> <a accesskey="n" href="Secmia3dimagestats.html">Next</a></td></tr></table><hr></div><div class="section"><div class="titlepage"><div><div><h3 class="title"><a name="Secmia3dimagestatisticsinmask"></a>mia-3dimagestatistics-in-mask</h3></div></div></div><h4><a name="idp10156"></a>Sysnopis:</h4><div class="cmdsynopsis"><p><code class="command">mia-3dimagestatistics-in-mask</code> {-i <em class="replaceable"><code>io</code></em>} {-m <em class="replaceable"><code>io</code></em>} [
<em class="replaceable"><code>options</code></em>
...]</p></div><h4><a name="idp10165"></a>Description:</h4><p>This program evaluates the statistics of an image within a masked region of the image. Possible outputs are a summary statistics and a histogram of the values.</p><h4><a name="idp10167"></a>Options:</h4><h4><a name="idp10168"></a>File-IO</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-i, --image=(input, required); io</span></dt><dd><p>input image to be analyzed. For supported file types see <a class="xref" href="SecPlugintype3dimageio.html" title="Plugin type: 3dimage/io">Plugin type: 3dimage/io</a></p></dd><dt><span class="term">-m, --mask=(input, required); io</span></dt><dd><p>mask image to use to restrict the analysis. For supported file types see <a class="xref" href="SecPlugintype3dimageio.html" title="Plugin type: 3dimage/io">Plugin type: 3dimage/io</a></p></dd><dt><span class="term">-s, --summary=(output); string</span></dt><dd><p>File to write the summary statistics to as plain text.</p></dd><dt><span class="term">-H, --histogram=(output); string</span></dt><dd><p>File to write the histogram to</p></dd></dl></div><h4><a name="idp10188"></a>Help & 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="idp10239"></a>Parameters</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">--struct-name=undefined; stringSTRING</span></dt><dd><p>Name of the structure the statistics are evaluated for</p></dd><dt><span class="term">-l, --limit=20; uint in [20, inf)</span></dt><dd><p>Number of pixels the mask should at least contain.</p></dd><dt><span class="term">-b, --bins=8; ulong in [4, inf)</span></dt><dd><p>number of histogram bins to be used</p></dd><dt><span class="term">--hmin=0; float</span></dt><dd><p>lower bound for the histogram mapping. All values below this value will be mapped into the lowest bin. If this parameter is equal or larger than hmax, the histogram range is evaluated automatically.lower bound for the histogram mapping. All values below this value will be mapped into the lowest bin. If this parameter is equal or larger than hmax, the histogram range is evaluated automatically.</p></dd><dt><span class="term">--hmax=0; float</span></dt><dd><p>hpper bound for the histogram mapping. All values above this valuewill be mapped into the highest bin. If this parameter is equal or smaller than hmin, the histogram range is evaluated automatically.hpper bound for the histogram mapping. All values above this valuewill be mapped into the highest bin. If this parameter is equal or smaller than hmin, the histogram range is evaluated automatically.</p></dd></dl></div><h4><a name="idp10261"></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="idp10267"></a>Example:</h4><p>evaluate the summary statistics on the input and a histogram with 10 bins and automtically evaluated boundaries. Save summary in summary.txt and the histogram in hist.txt</p><pre class="screen">mia-3dimagestatistics-in-mask --image image.v.gz --mask mask.v.gz --summary summary.txt --histogram hist.txt</pre><h4><a name="idp10270"></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="Secmia3dimagefilterstack.html">Prev</a> </td><td width="20%" align="center"><a accesskey="u" href="SecAnalysisfilteringcombiningandsegmentationof3Dimages.html">Up</a></td><td width="40%" align="right"> <a accesskey="n" href="Secmia3dimagestats.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">mia-3dimagefilterstack </td><td width="20%" align="center"><a accesskey="h" href="index.html">Home</a></td><td width="40%" align="right" valign="top"> mia-3dimagestats</td></tr></table></div></body></html>
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