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

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

stty: 'standard input': Inappropriate ioctl for device

NoiseFilterGaussian -- Removes noise from profile spectra by using Gaussian filter (on uniform as well as non-uniform data).
Full documentation: http://www.openms.de/doxygen/nightly/html/TOPP_NoiseFilterGaussian.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:
  NoiseFilterGaussian <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_NoiseFilterGaussian.html

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).

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

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

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

ppm_tolerance10.0 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

write_log_messagesfalse true: Warn if no signal was found by the Gauss filter algorithm.true, false