To everyone (who tested the "baseliner" - mainly Tomas P. and Thomas FRD, I guess):
Is this "TIC (Total ion intensity) view" option (checkbox available in preview mode) useful (in which case, I should merge it to trunk, at the same time as the alternative baselining algorithms), or not? At first, I did not planned to reflect this (small feature) to the trunk - it was only a convenience serving my own purpose - but Thomas (FRD) made me doubt. So guys, do you think this is a plus, or useless, or too minor? Thanks for your lights on this point. Best Gauthier To Thomas (FRD), I know you are not Tomas (P) and sorry for having removed (unintentionally) the "h" in your first name ? ;) People often do the same with this same letter in my own first name ;) OK, I wasn't able to see were the problem was. Thanks to let me know if you find anything more about this issue. Also, for the record, the "Local Minima + LOESS Corrector" was badly and sadly buggy, and I don't have published the fix (even if it is fixed) yet. So better do not use it before my next commit. Gauthier On 11/12/2014 03:33 PM, TFRD (Thomas Franck Dyrlund) wrote: > I just tried to reproduce the slower load but this time there was no problem. > It might have been due to low memory or something. I'll let you know if I > experience it again and then try to look at my settings. > > And just to reduce the confusion then Tomas Pluskal <plus...@oist.jp> and > Thomas Dyrlund (t...@steno.dk) are not the same person :-) > > /Thomas > > -----Original Message----- > From: Gauthier Boaglio [mailto:gauthier.boag...@gmail.com] > Sent: 12. november 2014 10:52 > To: Developer discussion > Subject: Re: [Mzmine-devel] Further developments on the "Baseline Correction" > module => BUG FIXES, new testing release > > (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/gboagli >>> o-experimental >>> >>> >>> If you have time, please give a try to the latest SNAPSHOT: >>> >>> http://sourceforge.net/p/mzmine/code/HEAD/tree/branches/gboaglio-expe >>> rimental/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-ex >>>>> pe 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-e >>>>>> xp 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/introdu >>>>>> ct >>>>>> 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/g >>>>>> au >>>>>> 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/ga >>>>> ut >>>>> 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. > Monitor 10 servers for $9/Month. > Get alerted through email, SMS, voice calls or mobile push notifications. > Take corrective actions from your mobile device. > http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk > _______________________________________________ > Mzmine-devel mailing list > Mzmine-devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/mzmine-devel -- Gauthier BOAGLIO CEFE - 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