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<div class="title">BaselineFilter </div> </div>
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<div class="textblock"><p>Executes the top-hat filter to remove the baseline of an MS experiment.</p>
<center> <table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="2"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> BaselineFilter <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">pot. successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_NoiseFilterSGolay.html">NoiseFilterSGolay</a>, <br/>
<a class="el" href="TOPP_NoiseFilterGaussian.html">NoiseFilterGaussian</a> </td><td valign="middle" align="center" rowspan="1"><a class="el" href="TOPP_PeakPickerWavelet.html">PeakPickerWavelet</a>, <br/>
<a class="el" href="TOPP_PeakPickerHiRes.html">PeakPickerHiRes</a> <br/>
(or ID engines on MS/MS data) </td></tr>
</table>
</center><p>This nonlinear filter, known as the top-hat operator in morphological mathematics (see Soille, ''Morphological Image Analysis''), is independent of the underlying baseline shape. It is able to detect an over brightness even if the environment is not uniform. The principle is based on the subtraction of a signal from its opening (erosion followed by a dilation). The size the structuring element (here a flat line) being conditioned by the width of the lineament (in our case the maximum width of a mass spectrometric peak) to be detected.</p>
<dl class="section note"><dt>Note</dt><dd>The top-hat filter works only on roughly uniform data! To generate equally-spaced data you can use the <a class="el" href="TOPP_Resampler.html">Resampler</a>.</dd>
<dd>
The length (given in Thomson) of the structuring element should be wider than the maximum peak width in the raw data.</dd></dl>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
BaselineFilter -- Removes the baseline from profile spectra using a top-hat filter.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
BaselineFilter <options>
Options (mandatory options marked with '*'):
-in <file>* Input raw data file (valid formats: 'mzML')
-out <file>* Output raw data file (valid formats: 'mzML')
-struc_elem_length <size> Length of the structuring element (should be wider than maximal peak width -
see documentation). (default: '3')
-struc_elem_unit <unit> Unit of 'struc_elem_length' parameter. (default: 'Thomson' valid: 'Thomson',
'DataPoints')
-method <string> The name of the morphological filter to be applied. If you are unsure, use the
default. (default: 'tophat' valid: 'identity', 'erosion', 'dilation', 'opening',
'closing', 'gradient', 'tophat', 'bothat', 'erosion_simple', 'dilation_simple')
Common TOPP options:
-ini <file> Use the given TOPP INI file
-threads <n> Sets the number of threads allowed to be used by the TOPP tool (default: '1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
</pre><p> <b>INI file documentation of this tool:</b> <div class="ini_global">
<div class="legend">
<b>Legend:</b><br>
<div class="item item_required">required parameter</div>
<div class="item item_advanced">advanced parameter</div>
</div>
<div class="node"><span class="node_name">+BaselineFilter</span><span class="node_description">Removes the baseline from profile spectra using a top-hat filter.</span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:16px;">version</span><span class="item_value">1.11.1</span>
<span class="item_description">Version of the tool that generated this parameters file.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="node"><span class="node_name">++1</span><span class="node_description">Instance '1' section for 'BaselineFilter'</span></div>
<div class="item"><span class="item_name item_required" style="padding-left:24px;">in</span><span class="item_value"></span>
<span class="item_description">input raw data file </span><span class="item_tags">input file</span><span class="item_restrictions">*.mzML</span></div> <div class="item"><span class="item_name item_required" style="padding-left:24px;">out</span><span class="item_value"></span>
<span class="item_description">output raw data file </span><span class="item_tags">output file</span><span class="item_restrictions">*.mzML</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">struc_elem_length</span><span class="item_value">3</span>
<span class="item_description">Length of the structuring element (should be wider than maximal peak width - see documentation).</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">struc_elem_unit</span><span class="item_value">Thomson</span>
<span class="item_description">Unit of 'struc_elem_length' parameter.</span><span class="item_tags"></span><span class="item_restrictions">Thomson,DataPoints</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">method</span><span class="item_value">tophat</span>
<span class="item_description">The name of the morphological filter to be applied. If you are unsure, use the default.</span><span class="item_tags"></span><span class="item_restrictions">identity,erosion,dilation,opening,closing,gradient,tophat,bothat,erosion_simple,dilation_simple</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">log</span><span class="item_value"></span>
<span class="item_description">Name of log file (created only when specified)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">debug</span><span class="item_value">0</span>
<span class="item_description">Sets the debug level</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">threads</span><span class="item_value">1</span>
<span class="item_description">Sets the number of threads allowed to be used by the TOPP tool</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">no_progress</span><span class="item_value">false</span>
<span class="item_description">Disables progress logging to command line</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">test</span><span class="item_value">false</span>
<span class="item_description">Enables the test mode (needed for internal use only)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5</font></TD>
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