Hello Mark,

Would it be a problem for your application if the baseline correction was 
performed on detected chromatograms, instead of on the raw data?
Currently, the smoothing module works that way.

Note that peak detection (=chromatogram deconvolution) would still be performed 
after baseline correction.

Best,

Tomas


On Nov 17, 2014, at 20:06, Earll Mark GBJH 
<mark.ea...@syngenta.com<mailto:mark.ea...@syngenta.com>> wrote:

Dear All,

As Chris says it’s a long time ago for us but maybe I can explain a bit..

The reason for the baseline correction was because we had some rally horrible 
baseline shifts (I’ve since found out due to the analytical chemist putting a 
flow-ramp into the method). I seem to remember it had a bandwidth setting so 
that you could baseline correct finite sized strips in the M/Z dimension.  
Selecting a smaller width below 0.1 was impractically slow.

I guess it’s not the most elegant of solution but if you have a flat baseline 
it makes peak picking a hell of a lot easier later on.

Another general comment that I’ve had from new users of MZmine is that you seem 
to have to select the same things over and over again in the workflows such as 
Min Height and Mass resolution. It might make it a bit easier to use if the 
choices were reduced a bit (i.e. parameters inherited from a previous 
operation),also a bit more of a linear layout of the menus in order of 
operation, or maybe a wizard would help new users.

Anyway really great to see there is continuing development of MZ mine.

I should send you the Thermo RAW files I’ve had trouble with at some point

Cheers,

Mark

From: Pudney Chris (ext) GBJH
Sent: 17 November 2014 09:22
To: Tomas Pluskal; Developer discussion
Cc: Earll Mark GBJH
Subject: RE: [Mzmine-devel] Further developments on the "Baseline Correction" 
module => Question I have...

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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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<mailto: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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--
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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/gauthier-boaglio
        http://www.evolepid.org/people.php?name=boaglio


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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/gauthier-boaglio
       http://www.evolepid.org/people.php?name=boaglio




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===============================================
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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
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--

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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/gauthier-boaglio

       http://www.evolepid.org/people.php?name=boaglio



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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
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--

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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/gauthier-boaglio

       http://www.evolepid.org/people.php?name=boaglio



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===============================================
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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===============================================
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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