Hi Tomas,OK, I haven't thought about that button (clicking on it should cancel the "Running Preview Task"). But it is one problem among plenty (related) others. I completely reviewed the way I was handling the tasks and threads (and, in this case, how we terminate them). Theoretically, the case of the OK button should be easy to fix with the new implementation. But, I am currently fighting against the fact that an rEngine.eval("some R instructions") can be very painful to stop (and maybe impossible), as it is looping in R features side, not in java side. Hardly interruptible then.
Ex. Asymetric Corrector with smoothing=10 and asym=0.0 takes forever in R (it is extreme as a case, but I'd like to avoid blocking the whole application in that case too). And doesn't throw any error. I'm trying to find out a solution for that. And we have the same problem while running it as a Task (not from preview), if we try to "Cancel Task" from the TaskTable. So it really has to be fixed.
Note that this "long R instruction run" issue is applicable to all the features of MZmine that rely on R. Not really having a good time ;) At worst, I suppose, we can brute force kill the Rengine in those cases, but that is a bit violent, and this would probably mean having one instance of R for each task instead of a Singleton...
Well, I'm thinking hard on it, but, if you have ideas, they're very welcome. Cheers Gauthier On 11/14/2014 05:21 AM, Tomas Pluskal wrote:
Hi Gauthier,I noticed that if you close the preview windows (by clicking the OK button) while the preview is being generated, the preview function stops working completely.TomasOn Nov 13, 2014, at 15:59, Gauthier Boaglio <gauthier.boag...@gmail.com <mailto:gauthier.boag...@gmail.com>> wrote:Hi Tomas,Yep, I got it. I hesitated at first and chose the other one. But your remark makes completely sense. I'll turn it into a combobox. I made some changes and fixes yesterday - errors visual feedback (missing required packages) and bug fixes : if some of you guys have time to look into it for potential remaining issues, that would be cool. If no dramatic issue is discovered, I'll merge the feature with the trunk as soon as I can.Current test release is: http://sourceforge.net/p/mzmine/code/HEAD/tree/branches/gboaglio-experimental/target/MZmine-2.11-EEE-release-20141113.zipCheers Gaut On 11/13/2014 04:35 AM, Tomas Pluskal wrote:Hi Gauthier,I think the switch between base peak plot and TIC plot is useful to keep in the trunk, but I would prefer to have a combo box (with two options) rather than a checkbox. From the checkbox it is not clear what is displayed if it is unchecked.E.g., the combo can be (Title) Plot: (Option 1) Base peak intensity (Option 2) Total ion current (TIC) Cheers, TomasOn Nov 13, 2014, at 3:24, Gauthier Boaglio <gauthier.boag...@gmail.com <mailto:gauthier.boag...@gmail.com>> wrote:To everyone (who tested the "baseliner" - mainly Tomas P. and Thomas FRD, I guess): Is this "TIC (Total ion intensity) view" option (checkbox available inpreview mode) useful (in which case, I should merge it to trunk, at thesame 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 toominor? 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 sadlybuggy, 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 <mailto:plus...@oist.jp>> and Thomas Dyrlund (t...@steno.dk <mailto: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 discussionSubject: 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, ifapplicable) 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 fileswith 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), butthe previewing feature. Your remark is very helpful and I suppose I amdoing 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 tocommit 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 GauthierI like your improvements for the baseline correction very much - veryuseful! 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 13:14To: mzmine-devel@lists.sourceforge.net <mailto: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 yousaid. 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 didnot received them, so I believe those mails did not reach the listmembers 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.zipI'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 typefrom a "non-TICVisualizerWindow" context. * TICDataSet:=> Added the possibility to switch to TIC plot typefrom a "non-TICVisualizerWindow" context. * BaselineCorrectionTask: => Adding more baseline algorithms.Deeply modified to delegate baseline correctionto various correctors (whose implement specific methods by them-selves).Those correctors all share a common behavior byinheriting 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 thebaseline correction module design. Added preview feature. * BaselineCorrector * BaselineCorrectorSetupDialog * BaselineProvider * InstantUpdateSetupDialogCorrectors:* 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 36email: gauthier.boag...@cefe.cnrs.fr <mailto:gauthier.boag...@cefe.cnrs.fr> www: http://www.cefe.cnrs.fr/en/evolutionary-ecology-and-epidemiology/gauthier-boagliohttp://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 - 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 36email: gauthier.boag...@cefe.cnrs.fr <mailto:gauthier.boag...@cefe.cnrs.fr> www: http://www.cefe.cnrs.fr/en/evolutionary-ecology-and-epidemiology/gauthier-boagliohttp://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=============================================== Tomas PluskalG0 Cell Unit, Okinawa Institute of Science and Technology Graduate University1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan WWW: https://groups.oist.jp/g0 TEL: +81-98-966-8684 Fax: +81-98-966-2890 ------------------------------------------------------------------------------ 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 - 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=============================================== Tomas PluskalG0 Cell Unit, Okinawa Institute of Science and Technology Graduate University1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan WWW: https://groups.oist.jp/g0 TEL: +81-98-966-8684 Fax: +81-98-966-2890 ------------------------------------------------------------------------------ Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. 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-- 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
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