OpenMS: NoiseFilterSGolay

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

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

The idea of the Savitzky Golay filter is to find filter-coefficients that preserve higher moments, which means to approximate the underlying function within the moving window by a polynomial of higher order (typically quadratic or quartic) (see A. Savitzky and M. J. E. Golay, ''Smoothing and Differentiation of Data by Simplified Least Squares Procedures'').

Note:: The Savitzky Golay filter works only on uniform data (to generate equally spaced data use the Resampler tool).

The command line parameters of this tool are:

NoiseFilterSGolay -- Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.
Version: 1.10.0 Mar  7 2013, 08:30:22, Revision: unknown

Usage:
  NoiseFilterSGolay <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

+NoiseFilterSGolayRemoves noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.

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

++1Instance '1' section for 'NoiseFilterSGolay'

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

frame_length11 The number of subsequent data points used for smoothing.
This number has to be uneven. If it is not, 1 will be added.

polynomial_order4 Order or the polynomial that is fitted.

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

Name Type Default Restrictions Description

frame_length int 11 The number of subsequent data points used for smoothing.
This number has to be uneven. If it is not, 1 will be added.

polynomial_order int 4 Order or the polynomial that is fitted.

Note:

Name	Type	Default	Restrictions	Description
frame_length	int	11		The number of subsequent data points used for smoothing. This number has to be uneven. If it is not, 1 will be added.
polynomial_order	int	4		Order or the polynomial that is fitted.

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