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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | <html><head><meta http-equiv="Content-Type" content="text/html; charset=ISO-8859-1"><title>mia-3ddistance-stats</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="Secmia3dcrispsegment.html" title="mia-3dcrispsegment"><link rel="next" href="Secmia3dfuzzysegment.html" title="mia-3dfuzzysegment"></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-3ddistance-stats</th></tr><tr><td width="20%" align="left"><a accesskey="p" href="Secmia3dcrispsegment.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="Secmia3dfuzzysegment.html">Next</a></td></tr></table><hr></div><div class="section"><div class="titlepage"><div><div><h3 class="title"><a name="Secmia3ddistancestats"></a>mia-3ddistance-stats</h3></div></div></div><h4><a name="idp9458"></a>Sysnopis:</h4><div class="cmdsynopsis"><p><code class="command">mia-3ddistance-stats</code> {-i <em class="replaceable"><code>io</code></em>} {-r <em class="replaceable"><code>io</code></em>} {-o <em class="replaceable"><code>string</code></em>} [
<em class="replaceable"><code>options</code></em>
...]</p></div><h4><a name="idp9469"></a>Description:</h4><p>This program is used to evaluate the distance between equally labelled areas in two images. The output file is a csv file containing the distances for each labeled coordinate in the test image in the following form:
label,n-samples,distance,distance,...
A simple R program to get some per label statistics from this data would look like
args <- commandArgs(TRUE)
data <- read.csv(args[1], header=FALSE)
for ( i in 1:dim(data)[1] ) {
line <- data[i,]
label <- as.integer(line[1])
end_range <- 2 + as.numeric(line[2])
s <- as.numeric(line[3:end_range])
result <- sprintf("%d %8.4f %8.4f %8.4f %8.4f\n"
label, mean(s), sqrt(var(s)), median(s), max(s))
cat(result)
}
</p><h4><a name="idp9471"></a>Options:</h4><h4><a name="idp9472"></a>File-IO</h4><div class="variablelist"><dl class="variablelist compact"><dt><span class="term">-i, --in-labels=(input, required); io</span></dt><dd><p>input label image. 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">-r, --ref-labels=(input, required); io</span></dt><dd><p>reference label image. 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">-l, --label-map=(input); string</span></dt><dd><p>optional mapping of label numbers</p></dd><dt><span class="term">-o, --out-file=(output, required); string</span></dt><dd><p>output file name to write the distances to. The output file is a csv file, containing distances listed for each label.</p></dd></dl></div><h4><a name="idp9492"></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="idp9543"></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="idp9549"></a>Example:</h4><p>Evaluate the distances for each label available in image.v to the corresponding labels in the image reference.v ans store the result a coma separated list of values, i.e. distances.csv.</p><pre class="screen">mia-3ddistance-stats -i image.v -r reference.v -o distances.csv</pre><h4><a name="idp9552"></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="Secmia3dcrispsegment.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="Secmia3dfuzzysegment.html">Next</a></td></tr><tr><td width="40%" align="left" valign="top">mia-3dcrispsegment </td><td width="20%" align="center"><a accesskey="h" href="index.html">Home</a></td><td width="40%" align="right" valign="top"> mia-3dfuzzysegment</td></tr></table></div></body></html>
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