Sorry. Forgot to give the release download link, as well as changing the subject.
Release here: http://sourceforge.net/p/mzmine/code/HEAD/tree/branches/gboaglio-experimental/target/MZmine-2.11-EEE-release-20141107.zip On 11/07/2014 04:42 PM, Gauthier Boaglio wrote: > Hi all, > > I did some further developments on the "Baseline Correction" module. > This is not yet completely "crash tested" (specially regarding the > compatibility of what I made with the "batch mode" system). But still > working quite well. And it might be a good candidate for integration > in the trunk. Perhaps... I let you judges on this, but I'd be glad to > help with this task if applicable. > > Here's the change log. If any of you has the irreducible need to see > and test it, any comment or bug report would be greatly appreciated! > Thanks. > > MZmine2 change log for "Baseline corrector module": > > -------------------------------------------------- > >>> Modified files (package >>> "net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection"): > > * ParameterSetupDialogWithChromatogramPreview: > > => Slightly modified to add the possibility for switching > to TIC (versus Base Peak) preview. > > > * TICPlot: > > => Added the possibility to switch to TIC plot type from a > "non-TICVisualizerWindow" context. > > > * TICDataSet: > > => Added the possibility to switch to TIC plot type from a > "non-TICVisualizerWindow" context. > > > * BaselineCorrectionTask: > > => Adding more baseline algorithms. > > Deeply modified to delegate baseline correction to > various correctors (whose implement specific methods by them-selves). > > Those correctors all share a common behavior by > inheriting from the base class "BaselineCorrector", and apply there > specific way of building the baselines via the various algorithms > implemented in the sub-package > "net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.correctors". > > > * BaselineCorrectionParameters: > > => Adding more baseline algorithms. > > Holds baseline correction module COMMON parameters. > > Reduced strictly to the parameters common to all the > BaselineCorrectors. > > See > "net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.correctors" > > sub-package for method specific parameters. > > >>> Added files (package >>> "net.sf.mzmine.modules.rawdatamethods.filtering.baselinecorrection.correctors"): > > > Adding more baseline algorithms. Deeply refactored the baseline > correction module design. Added preview feature. > > * BaselineCorrector > > * BaselineCorrectorSetupDialog > > * BaselineProvider > > * InstantUpdateSetupDialog > > > Correctors: > > * AsymmetryCorrector / AsymmetryCorrectorParameters: > > => Adding more baseline algorithms. > > Asymmetric baseline corrector (same as before). > Estimates a trend based on asymmetric least squares. > > Uses "asysm" feature from "ptw" R-package > (http://cran.r-project.org/web/packages/ptw/ptw.pdf). > > > * RollingBallCorrector / RollingBallCorrectorParameters: > > => Adding more baseline algorithms. > > Rolling Ball baseline corrector. Estimates a trend > based on Rolling Ball algorithm. > > Uses "rollingBall" feature from "baseline" > R-package (http://cran.r-project.org/web/packages/baseline/baseline.pdf). > > (Ideas from Rolling Ball algorithm for X-ray > spectra by M.A.Kneen and H.J. Annegarn. Variable window width has been > left out). > > > * PeakDetectionCorrector / PeakDetectionCorrectorParameters: > > => Adding more baseline algorithms. > > Peak detection is done in several steps sorting > out real peaks through different criteria. Peaks are removed from > > spectra and minimums and medians are used to > smooth the remaining parts of the spectra. > > Uses "peakDetection" feature from "baseline" > R-package (http://cran.r-project.org/web/packages/baseline/baseline.pdf). > > (A translation from Kevin R. Coombes et al.'s > MATLAB code for detecting peaks and removing baselines). > > > * RubberBandCorrector / RubberBandCorrectorParameters: > > => Adding more baseline algorithms. > > Rubber Band baseline corrector. > > Estimates a trend based on Rubber Band algorithm > (which determines a convex envelope for the spectra). > > Uses "spc.rubberband" feature from "hyperSpec" > R-package > (http://cran.r-project.org/web/packages/hyperSpec/vignettes/introduction.pdf). > > > * LocMinLoessCorrector / LocMinLoessCorrectorParameters: > > => Adding more baseline algorithms. > > Local Minima + LOESS (smoothed low-percentile > intensity) baseline corrector. > > Uses "bslnoff" feature from "PROcess" > R/Bioconductor package > (http://bioconductor.org/packages/release/bioc/manuals/PROcess/man/PROcess.pdf). > > > > Cheers > Gauthier > -- Gauthier BOAGLIO CEFE - UMR 5175 1919 route de Mende F-34293 Montpellier cedex 5 Tel: +33/0 4 67 61 32 15 Fax: +33/0 4 67 61 33 36 email: gauthier.boag...@cefe.cnrs.fr www: http://www.cefe.cnrs.fr/en/evolutionary-ecology-and-epidemiology/gauthier-boaglio http://www.evolepid.org/people.php?name=boaglio ------------------------------------------------------------------------------ _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
