Hi Gauthier I like your improvements for the baseline correction very much - very useful!
One thing I noticed is that the TIC plots are now loaded a little at a time instead of everything at once. This makes it a lot slower to open chromatograms compared to the trunk version. For example, overlaying 9 TIC spectra used to take under 3 sec but now it takes about 12 sec. Any reason for this change? Best, Thomas -----Original Message----- From: Gauthier Boaglio [mailto:gauthier.boag...@gmail.com] Sent: 10. november 2014 13:14 To: mzmine-devel@lists.sourceforge.net Subject: Re: [Mzmine-devel] Further developments on the "Baseline Correction" module => BUG FIXES, new testing release Hi Thomas, Thanks for the feedback. Regarding point 1), I'll do it just like you said. For point 2), I went to the same conclusion and already made some changes pointing to that direction (Threading + progress bar + press ESC to cancel preview computing, etc). Please refer to the SVN change log of my testing branch: http://sourceforge.net/p/mzmine/code/3468/log/?path=/branches/gboaglio-experimental If you have time, please give a try to the latest SNAPSHOT: http://sourceforge.net/p/mzmine/code/HEAD/tree/branches/gboaglio-experimental/target/MZmine-2.11-EEE-release-20141109.zip Best Gauthier On 11/10/2014 02:57 AM, Tomas Pluskal wrote: > Hi Gauthier, > > After installing all the prerequsities in R using the below commands, I got > your baseline correction module running: > > install.packages(c("ptw", "baseline", "hyperSpec")) > source("http://bioconductor.org/biocLite.R";) > biocLite("PROcess") > > After brief testing, I like the improvements very much. But I think some > improvements are necessary. > 1) Please clearly state the dependencies of the module, and improve > the error reporting in case the dependencies are not installed > 2) Currently all calculations seem to be done on the Swing thread, which > causes the GUI to freeze while the baseline preview plot is being calculated. > Since this can take a long time, it is not optimal. It would be better to > perform the calculations on a different thread, or (preferably) using a Task. > > If you can address these points, let's move the code to the trunk! > > Cheers, > > Tomas > > > On Nov 9, 2014, at 1:24, Gauthier Boaglio <gauthier.boag...@gmail.com> wrote: > >> Fixed the main (but not the least) bugs: >> >> * Fixed baseline task issues (multi-threading was very sadly handled). >> * Fixed "PeakDetectionCorrector" (R code was leading to failures when using >> bins - "use m/z bins" checked). >> >> >> Here is the new release, available for testing: >> http://sourceforge.net/p/mzmine/code/HEAD/tree/branches/gboaglio-expe >> rimental/target/MZmine-2.11-EEE-release-20141108.zip >> >> Best regards >> Gauthier >> >> >> >> On 11/08/2014 11:12 AM, Gauthier Boaglio wrote: >>> Hi Tomas. >>> >>> I already posted those information on the mailing list but I did not >>> received them, so I believe those mails did not reach the list members as >>> well. That is why I am forwarding the whole stuff to your personal address. >>> >>> Test release download link: >>> >>> http://sourceforge.net/p/mzmine/code/HEAD/tree/branches/gboaglio-exp >>> erimental/target/MZmine-2.11-EEE-release-20141107.zip >>> >>> I'm also aware of some bugs while running the task on several file (not >>> especially the batch mode by itself). I'll keep you in touch as soon as I >>> have fixed it. >>> >>> >>> -------- Forwarded Message -------- >>> Subject: Further developments on the "Baseline Correction" module. >>> Date: Fri, 07 Nov 2014 16:46:55 +0100 >>> From: Gauthier Boaglio <gauthier.boag...@gmail.com> >>> To: mzmine-devel@lists.sourceforge.net >>> 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/introduct >>> ion.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/PR >>> Ocess.pdf >>> ). >>> Preview of what it does: >>> >>> >>> New Baseline correction setup: >>> >>> >>> >>> >>> <Mail Attachment.png> >>> >>> >>> >>> >>> >>> >>> With baseline preview enabled: >>> >>> >>> >>> >>> <Mail Attachment.png> >>> >>> >>> >>> >>> >>>> Regards >>>> 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/gau >>> thier-boaglio >>> >>> >>> http://www.evolepid.org/people.php?name=boaglio >>> >>> >>> >>> >>> >> >> -- >> 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/gaut >> hier-boaglio >> >> >> http://www.evolepid.org/people.php?name=boaglio >> >> >> > =============================================== > Tomas Pluskal > G0 Cell Unit, Okinawa Institute of Science and Technology Graduate > University > 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan > WWW: https://groups.oist.jp/g0 > TEL: +81-98-966-8684 > Fax: +81-98-966-2890 > > > ---------------------------------------------------------------------- > -------- _______________________________________________ > Mzmine-devel mailing list > Mzmine-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mzmine-devel -- 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 ------------------------------------------------------------------------------ _______________________________________________ Mzmine-devel mailing list Mzmine-devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mzmine-devel
