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

pot. predecessor tools	→ NoiseFilterSGolay →	pot. successor tools
FileConverter		PeakPickerHiRes
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:

stty: 'standard input': Inappropriate ioctl for device

NoiseFilterSGolay -- Removes noise from profile spectra by using a Savitzky Golay filter (on uniform (equidistant) data).
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_NoiseFilterSGolay.html
Version: 3.4.0-pre-nightly-2024-12-16 Dec 17 2024, 02:41:12, Revision: 96ad74c
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

Usage:
  NoiseFilterSGolay <options>

This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed description 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/doxygen/nightly/html/TOPP_NoiseFilterSGolay.html

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

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

version3.4.0-pre-nightly-2024-12-16 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

processOptioninmemory 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 firstinmemory, lowmemory

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

forcefalse Overrides tool-specific checkstrue, 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.