Algorithms

Most signal processing algorithms follow a similar pattern in OpenMS.

filter = FilterObject()
exp = MSExperiment()
# populate exp
filter.filterExperiment(exp)

Since they work on a single MSExperiment object, little input is needed to execute a filter directly on the data. Examples of filters that follow this pattern are GaussFilter, SavitzkyGolayFilter as well as the spectral filters BernNorm, MarkerMower, NLargest, Normalizer, ParentPeakMower, Scaler, SpectraMerger, SqrtMower, ThresholdMower, WindowMower.

using the same example file as before in

from pyopenms import *
exp = MSExperiment()
gf = GaussFilter()
MzMLFile().load("test.mzML", exp)
gf.filterExperiment(exp)
MzMLFile().store("test.filtered.mzML", exp)