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-experimental/target/MZmine-2.11-EEE-release-20141108.zip
<http://sourceforge.net/p/mzmine/code/HEAD/tree/branches/gboaglio-experimental/target/MZmine-2.11-EEE-release-20141107.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-experimental/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/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).
>
Preview of what it does:
New Baseline correction setup:
With baseline preview enabled:
>
> 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/gauthier-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/gauthier-boaglio
http://www.evolepid.org/people.php?name=boaglio
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