| OpenMS 2.5.0

NoiseFilterSGolay

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

pot. predecessor tools | NoiseFilterSGolay | pot. successor tools
FileConverter | PeakPickerWavelet
Resampler | PeakPickerHiRes
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.

    Full documentation: http://www.openms.de/documentation/TOPP_NoiseFilterSGolay.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    To cite OpenMS:

      Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

    Usage:

      NoiseFilterSGolay <options>

    This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript

    ion or use the --helphelp option.

    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.

    For more information, please consult the online documentation for this tool:

      - http://www.openms.de/documentation/TOPP_NoiseFilterSGolay.html

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+NoiseFilterSGolay Removes noise from profile spectra by using a Savitzky Golay filter. Requires uniform (equidistant) data.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'NoiseFilterSGolay'
in input raw data file input file*.mzML
out output raw data file output file*.mzML
processOption inmemory Whether to load all data and process them in-memory or whether to process the data on the fly (lowmemory) without loading the whole file into memory first inmemory,lowmemory
log Name of log file (created only when specified)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command line true,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false
+++algorithm Algorithm parameters section
frame_length 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 4 Order or the polynomial that is fitted.