OpenMS: NoiseFilterGaussian

Executes a Gaussian filter to reduce the noise in an MS experiment.

pot. predecessor tools	$\longrightarrow$ NoiseFilterGaussian $\longrightarrow$	pot. successor tools
FileConverter		PeakPickerWavelet
Resampler		PeakPickerHiRes
Resampler		BaselineFilter

The Gaussian filter is a peak area preserving low-pass filter and is characterized by narrow bandwidths, sharp cutoffs, and low passband ripple.

Note:: The Gaussian filter works for uniform as well as for non-uniform data.

The command line parameters of this tool are:

NoiseFilterGaussian -- Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).
Version: 1.10.0 Mar  7 2013, 08:30:22, Revision: unknown

Usage:
  NoiseFilterGaussian <options>

This tool has algoritm parameters which can only be used via an INI file and are not accessible from the command line!

Options (mandatory options marked with '*'):
  -in <file>*        Input raw data file  (valid formats: 'mzML')
  -out <file>*       Output raw data file  (valid formats: 'mzML')
                     
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)

The following configuration subsections are valid:
 - algorithm   Algorithm parameters section

You can write an example INI file using the '-write_ini' option.
Documentation of subsection parameters can be found in the
doxygen documentation or the INIFileEditor.
Have a look at OpenMS documentation for more information.

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+NoiseFilterGaussianRemoves noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).

version1.10.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'NoiseFilterGaussian'

in input raw data file input file*.mzML

out output raw data file output file*.mzML

log Name of log file (created only when specified)

debug0 Sets the debug level

threads1 Sets the number of threads allowed to be used by the TOPP tool

no_progressfalse Disables progress logging to command linetrue,false

testfalse Enables the test mode (needed for internal use only)true,false

+++algorithmAlgorithm parameters section

gaussian_width0.2 Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z).

ppm_tolerance10 Gaussian width, depending on the m/z position.
The higher the value, the wider the peak and therefore the wider the gaussian.

use_ppm_tolerancefalse If true, instead of the gaussian_width value, the ppm_tolerance is used. The gaussian is calculated in each step anew, so this is much slower.true,false

The algorithm parameters for the Gaussian filter are: Parameters of this class are:

Name Type Default Restrictions Description

gaussian_width float 0.2 Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z).

ppm_tolerance float 10 Gaussian width, depending on the m/z position.
The higher the value, the wider the peak and therefore the wider the gaussian.

use_ppm_tolerance string false true, false If true, instead of the gaussian_width value, the ppm_tolerance is used. The gaussian is calculated in each step anew, so this is much slower.

Note:

Name	Type	Default	Restrictions	Description
gaussian_width	float	0.2		Use a gaussian filter width which has approximately the same width as your mass peaks (FWHM in m/z).
ppm_tolerance	float	10		Gaussian width, depending on the m/z position. The higher the value, the wider the peak and therefore the wider the gaussian.
use_ppm_tolerance	string	false	true, false	If true, instead of the gaussian_width value, the ppm_tolerance is used. The gaussian is calculated in each step anew, so this is much slower.

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.