G’day,
Tomas, it’s so long ago that I can’t recall for sure whether multiple
REngine instances are possible. However, a bit of Googling suggests
not <http://comments.gmane.org/gmane.comp.lang.r.rosuda.devel/321>,
and that if you want that sort of thing then RServe
<http://www.rforge.net/Rserve/> is the way to go.
As for why baseline correction is done before generating chromatograms
I’ll defer to Mark Earll on that one…
Regards,
*Chris Pudney *| /Data Visualization Specialist/
R&D IS Data Sciences <http://teamspace/sites/DataSciences> |
chris.pud...@syngenta.com <mailto:chris.pud...@syngenta.com>| R&D Blog
<http://blog.pro.intra/cpudney>
+61 8 9383 1278 | Datacraft Technologies, Perth, Australia (GMT+8hrs
<http://www.timeanddate.com/worldclock/australia/perth>)
*From:*Tomas Pluskal [mailto:plus...@oist.jp]
*Sent:* 14 November 2014 12:59
*To:* Developer discussion
*Cc:* Pudney Chris (ext) GBJH
*Subject:* Re: [Mzmine-devel] Further developments on the "Baseline
Correction" module => Question I have...
Hi Gauthier,
I am not sure how this is internally implemented in the rJava library,
but would it be possible to create a new REngine instance for each R
task that is being executed?
That way, even if one REngine is blocked by long computation, the
others would stay uneffected - note I'm just guessing here, I haven't
actually tested it.
I will cc this email to Chris, who originally developed the R support
in MZmine. He might have a better idea.
Best regards,
Tomas
On Nov 14, 2014, at 13:47, Gauthier Boaglio
<gauthier.boag...@gmail.com <mailto:gauthier.boag...@gmail.com>> wrote:
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.
Tomas
On 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.zip
Cheers
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,
Tomas
On 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 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 <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 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
<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 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";
<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>
<mailto: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>
<mailto:gauthier.boag...@gmail.com>
To: mzmine-devel@lists.sourceforge.net
<mailto: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
<mailto: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
<mailto: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
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www:
http://www.cefe.cnrs.fr/en/evolutionary-ecology-and-epidemiology/gauthier-boaglio
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Fax: +33/0 4 67 61 33 36
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