(Re-)Hi Tomas, Could you send me one of the samples (a not confidential one, if applicable) you've been using to obtain those display increased time (and may be, also, the exact suite of actions you did to get this result), because, with my own samples (maybe they're not huge enough), I cannot really see where the issue occurs. Thanks a lot by advance.
Cheers Gaut On 11/12/2014 10:03 AM, Gauthier Boaglio wrote: > Hi Thomas, > > Thanks for testing. I'm about to go into that. This behavior is not > something I did on purpose; I mean: the only goal of the "TIC View" > checkbox was to provide a possibility to visualize the corrected files > with summed m/z rather than base peak intensity. So it shouldn't have > affected the way the things are calculated (at least regarding the > Asymmetry algorithm - which remains exactly the same as before), but > the previewing feature. Your remark is very helpful and I suppose I am > doing something wrong in some place. > Well, checking TIC for baseline computing, also checks, by default, > the "TIC view" one (which feature I added to the preview's left side > parameters). Theoretically, I should have let the preview mode to > "Base Peak Intensity", I suppose. > > On the other hand, the "TIC view" option, is not something I wanted to > commit to the trunk (I found it necessary to serve my own purpose), > but it is not necessarily something most of the people would need. > > It makes me ask myself, and maybe you and others can give me answers, > about the following: > > 1/ Is this "TIC preview" option useful (in which case, I should merge > it to trunk, as well as the alternative baselining algorithms) ? > 2/ If yes, should I let it UNCHECKED by default (that is "Base peak > intensity" view), to faster the preview in the first place ? > > I'll let you know as soon as I have figured out what is going on there > (and fixed it). > > Best > Gaut > > > On 11/10/2014 03:41 PM, TFRD (Thomas Franck Dyrlund) wrote: >> 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 > > -- 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 ------------------------------------------------------------------------------ Comprehensive Server Monitoring with Site24x7. 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