[Ifeffit] Athena deglitch problem

Sathish Mayanna satty334 at gmail.com
Fri Jan 3 07:25:05 CST 2014


Dear Matt

After installing Demeter to other than C drive there is no problem with
deglitching. For me its easier to rebin the data points and then deglitch
the terrible glitch in my data. If I don't rebin I need hours to deglitch a
single spectra since the data contains a big glitch. I believe the major
problem is solved for now, thanks a lot for your help.

Regards
Sathish


On Tue, Dec 17, 2013 at 7:00 PM,
<ifeffit-request at millenia.cars.aps.anl.gov>wrote:

> Send Ifeffit mailing list submissions to
>         ifeffit at millenia.cars.aps.anl.gov
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> or, via email, send a message with subject or body 'help' to
>         ifeffit-request at millenia.cars.aps.anl.gov
>
> You can reach the person managing the list at
>         ifeffit-owner at millenia.cars.aps.anl.gov
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Ifeffit digest..."
>
>
> Today's Topics:
>
>    1. Re: Athena deglitch problem (Sathish Mayanna)
>    2. Re: Athena deglitch problem (Matt Newville)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 16 Dec 2013 19:42:25 +0100
> From: Sathish Mayanna <satty334 at gmail.com>
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: Re: [Ifeffit] Athena deglitch problem
> Message-ID:
>         <CABVfawm9mL4XhhvBJoPX2=
> ZZ-MNek5YCkRcTHUP6S1UL6+xcaQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> *Dear Matt*
>
>  >
> > > Now it seems  working well except some minor things, I can remove the
> > points
> > > from the data, the random point selection by software  works better for
> > > rebinned data. I think the only problem I have now is I still cannot
> move
> > > the cursor after double click (I can only remove the points which the
> > > software decides - at least now it choose the points where I double
> > click).
> > > When i move my mouse cursor on the plot, it shows the correct
> > coordinates.
> >
> > I'm still a bit confused about whether this actually working for you.
> >  The data you sent has fairly large arrays (>2400 points), but all the
> > data was well-ordered in energy... I think that should "just work",
> > without needing re-binning.  And it does for me, and I don't see how
> > re-binning would affect this.
>
>
> * If I don't rebin the data, Athena will not choose the point which I am
> intend to remove (I think i have some minor issues here). If I rebin the
> data from ~ 2400 to 350 points, Athena will work correctly.*
>
> >
>
>
> > I think it's always been the case that you double-click near the point
> > to be removed, and hope that Athena does select the one you intended.
> >
>
> *This works perfect for rebinned data. *
>
> >
> > > I have one clarifications, when u choose the option to deglitch the
> data
> > > (rebinned or non rebinned data), does the x(E) data plot looks like in
> > the
> > > attached file (line) or it looks like sets of blue round points same
> > size as
> > > cursor.
> >
> > For me, it looks very much like the image you attached.   I do not see
> > a series of dots.
> >
> > > I think, the issue is solved except that I cannot move the randomly
> > chosen
> > > point.
> >
> > Why can't you remove the point chosen?  That seems like it's not
> > working to me. Wasn't that the problem you were having?
> >
>
> *I mentioned "MOVE" in my above sentence, (Just to be more specific, when I
> double click on the plot to choose a point, sometimes Athena select its own
> random points away from the point where I clicked, when I try to drag that
> randomly chosen cursor to the point of my interest, it will not work), IS
> THIS NORMAL?  *
>
> *I will try to figure out all the possible ways for non-rebinned data, if
> it does not work at least for now rebinned data works.*
>
> *Regards*
> *Sathish*
>
>
>
>
> > Again, it may be that I'm not understanding. Cheers,
> >
> > --Matt
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Mon, 16 Dec 2013 08:30:39 -0500
> > From: Bruce Ravel <bravel at bnl.gov>
> > To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> > Subject: Re: [Ifeffit] Handling time resolved data
> > Message-ID: <52AF007F.4050600 at bnl.gov>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> > On 12/13/2013 09:00 AM, Ditty Dixon wrote:
> > > Dear Bruce,
> > >
> > > Recenetly we  did some time resolved measurements, QEXAFS mode. While
> > > the old Athena arranged the file as we want i.e file 1, 2, 3 etc, the
> > > new did it bit different 1, 11 12  and again 2, 21 etc. Screenshot
> > > attached. Why is it doing diffrently for the two version? Can it be
> > > fixed some how.
> >
> > You haven't explained exactly where these data come from, so I am
> > assuming that each scan was written to its own file and these files were
> > imported into Athena.
> >
> > In Athena, data are imported in "ascii-betical" order, that is, sorted
> > in order of characters in the ASCII chart:
> >
> >     http://en.wikipedia.org/wiki/ASCII#ASCII_printable_characters
> >
> > In that sense, Athena sorted your data as expected.  As Chris pointed
> > out, if you want things like
> >
> >     nr_1.spec
> >     nr_2.spec
> >     ...
> >     nr_10.spec
> >
> > to sort numerically by the number between the _ and the .spec, you need
> > to format the them so that numerical and ascii-ordered sorting come out
> > the same.  This is done as
> >
> >     nr_01.spec
> >     nr_02.spec
> >     ...
> >     nr_10.spec
> >
> > For a quick exafs experiment, two digits is probably not enough, so
> > you'd want something like
> >
> >     nr_00001.spec
> >     nr_00002.spec
> >     ...
> >     nr_00010.spec
> >
> >
> > I don't recall quite how the sorting worked in the old version of Athena
> > (it has been over 5 years since I stopped working on it), but my vague
> > memory is that, on Windows, they were imported in the order that they
> > were clicked upon the file selection dialog.  The way it is currently
> > done is much better in that it is reproducible.
> >
> >
> >
> >
> >
> > --
> >   Bruce Ravel  ------------------------------------ bravel at bnl.gov
> >
> >   National Institute of Standards and Technology
> >   Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
> >   Building 535A
> >   Upton NY, 11973
> >
> >   Homepage:    http://xafs.org/BruceRavel
> >   Software:    https://github.com/bruceravel
> >
> >
> > ------------------------------
> >
> > _______________________________________________
> > Ifeffit mailing list
> > Ifeffit at millenia.cars.aps.anl.gov
> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> >
> >
> > End of Ifeffit Digest, Vol 130, Issue 22
> > ****************************************
> >
>
>
>
> --
> Satty
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: <
> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20131216/a071b83c/attachment.html
> >
>
> ------------------------------
>
> Message: 2
> Date: Mon, 16 Dec 2013 17:02:39 -0600
> From: Matt Newville <newville at cars.uchicago.edu>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Athena deglitch problem
> Message-ID:
>         <CA+7ESbrXBnXtH=
> kHYNqK5dxV1d60mBCT5Edrtx4ACX-sL-8nVA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
>
> On Mon, Dec 16, 2013 at 12:42 PM, Sathish Mayanna <satty334 at gmail.com>
> wrote:
> > Dear Matt
> >
> >> >
> >> > Now it seems  working well except some minor things, I can remove the
> >> > points
> >> > from the data, the random point selection by software  works better
> for
> >> > rebinned data. I think the only problem I have now is I still cannot
> >> > move
> >> > the cursor after double click (I can only remove the points which the
> >> > software decides - at least now it choose the points where I double
> >> > click).
> >> > When i move my mouse cursor on the plot, it shows the correct
> >> > coordinates.
> >>
> >> I'm still a bit confused about whether this actually working for you.
> >>  The data you sent has fairly large arrays (>2400 points), but all the
> >> data was well-ordered in energy... I think that should "just work",
> >> without needing re-binning.  And it does for me, and I don't see how
> >> re-binning would affect this.
> >
> >
> >  If I don't rebin the data, Athena will not choose the point which I am
> > intend to remove (I think i have some minor issues here). If I rebin the
> > data from ~ 2400 to 350 points, Athena will work correctly.
>
> Hmm.  I don't really understand why that would be.  Anybody else see this?
> Do you find that you need to re-bin by a factor of 7?
>
> >> I think it's always been the case that you double-click near the point
> >> to be removed, and hope that Athena does select the one you intended.
> >
> >
> > This works perfect for rebinned data.
> >>
> >>
> >> > I have one clarifications, when u choose the option to deglitch the
> data
> >> > (rebinned or non rebinned data), does the x(E) data plot looks like in
> >> > the
> >> > attached file (line) or it looks like sets of blue round points same
> >> > size as
> >> > cursor.
> >>
> >> For me, it looks very much like the image you attached.   I do not see
> >> a series of dots.
> >>
> >> > I think, the issue is solved except that I cannot move the randomly
> >> > chosen
> >> > point.
> >>
> >> Why can't you remove the point chosen?  That seems like it's not
> >> working to me. Wasn't that the problem you were having?
> >
> >
> > I mentioned "MOVE" in my above sentence, (Just to be more specific, when
> I
> > double click on the plot to choose a point, sometimes Athena select its
> own
> > random points away from the point where I clicked, when I try to drag
> that
> > randomly chosen cursor to the point of my interest, it will not work), IS
> > THIS NORMAL?
>
> It's news to me that you can move a point on the graph at all. I
> thought you could only remove it or not.  Anybody else know anything
> about this?
>
> I'm sort of stumped.  Do you see this behavior with other data sets as
> well or just this particular set?  Is re-binning always the solution?
>
> --Matt
>
>
> ------------------------------
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
> End of Ifeffit Digest, Vol 130, Issue 23
> ****************************************
>



-- 
Satty
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20140103/30d04dfb/attachment.html>


More information about the Ifeffit mailing list