Re: [Ifeffit] Ifeffit Digest, Vol 137, Issue 5
Thanks everyone for the suggestions! I will give Six pack a go first since I have that software. If that doesn't work, I'll send another message. I wish you all a pleasant day. Teck Kwang Choo PhD Candidate Department of Chemical Engineering Room 225, Building 36 Monash University Mobile No.: 04-11489904 On 3 July 2014 01:33, ifeffit-requ...@millenia.cars.aps.anl.gov wrote: Send Ifeffit mailing list submissions to ifeffit@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-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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: Principal Component Analysis (PCA) for XANES (fred.mosselm...@diamond.ac.uk) 2. Re: Principal Component Analysis (PCA) for XANES (Matthew Marcus) 3. Re: Ifeffit Digest, Vol 137, Issue 4 (Abhijeet Gaur) -- Message: 1 Date: Wed, 2 Jul 2014 07:48:29 + From: fred.mosselm...@diamond.ac.uk To: ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES Message-ID: cf65047c5b0562499eaff9fbbc542d6475785...@exchmbx01.fed.cclrc.ac.uk Content-Type: text/plain; charset=us-ascii Dear Teck, ITFA does transformation factor analysis as well, if you just want to do PCA, the PCA module in Sam Webb's sixpack is quite intuitive to use. https://home.comcast.net/~sam_webb/sixpack.html cheers Fred -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom -- Message: 2 Date: Wed, 02 Jul 2014 08:33:25 -0700 From: Matthew Marcus mamar...@lbl.gov To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES Message-ID: 53b42645.5040...@lbl.gov Content-Type: text/plain; charset=ISO-8859-1; format=flowed Athena (IFEFFIT package) does it. So does the ALS Beamline 10.3.2 software package at https://sites.google.com/a/lbl.gov/microxas-lbl-gov/software . If you can't get at it there, I can send the executable and manual. mam On 7/1/2014 10:59 PM, Teck Kwang Choo wrote: Hi Everyone, Does anyone know what software I should use to perform a Principal Component Analysis (PCA) on my K-edge XANES spectra (for sulfur)? The reason I need to use this technique is because I have a couple of reference compound spectra but am not sure which of those I should use to fit my unknown sample spectrum. Any help is appreciated. Thanks and kind regards. Teck Kwang Choo PhD Candidate Department of Chemical Engineering Room 225, Building 36 Monash University Mobile No.: 04-11489904 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Message: 3 Date: Wed, 2 Jul 2014 21:03:17 +0530 From: Abhijeet Gaur abhijeetga...@gmail.com To: ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Ifeffit Digest, Vol 137, Issue 4 Message-ID: CAEq27Q2UkMuFScofU8w20jO= 7a34mkykkimsgy5+h+7b_nc...@mail.gmail.com Content-Type: text/plain; charset=utf-8 Hi Teck Kwang Choo, For PCA analysis you can use SixPack data analysis package by Dr. Sam Webb available at https://home.comcast.net/~sam_webb/sixpack.html. Also you can use Dmeter by Dr Bruce Ravel available at http://bruceravel.github.io/demeter/. With best wishes Dr Abhijeet Gaur On Wed, Jul 2, 2014 at 12:52 PM, ifeffit-requ...@millenia.cars.aps.anl.gov wrote: Send Ifeffit mailing list submissions to
Re: [Ifeffit] Matthew Marcus Ifeffit Digest, Vol 137, Issue 5
To: Matthew Marcus Hi Matthew, would you be able to send me the executable file and manual for PCA? My spectra files are in .dat form . Thanks and kind regards. Teck Kwang Choo PhD Candidate Department of Chemical Engineering Room 225, Building 36 Monash University Mobile No.: 04-11489904 On 3 July 2014 16:19, Teck Kwang Choo teck.kwang.c...@monash.edu wrote: Thanks everyone for the suggestions! I will give Six pack a go first since I have that software. If that doesn't work, I'll send another message. I wish you all a pleasant day. Teck Kwang Choo PhD Candidate Department of Chemical Engineering Room 225, Building 36 Monash University Mobile No.: 04-11489904 On 3 July 2014 01:33, ifeffit-requ...@millenia.cars.aps.anl.gov wrote: Send Ifeffit mailing list submissions to ifeffit@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-requ...@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-ow...@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: Principal Component Analysis (PCA) for XANES (fred.mosselm...@diamond.ac.uk) 2. Re: Principal Component Analysis (PCA) for XANES (Matthew Marcus) 3. Re: Ifeffit Digest, Vol 137, Issue 4 (Abhijeet Gaur) -- Message: 1 Date: Wed, 2 Jul 2014 07:48:29 + From: fred.mosselm...@diamond.ac.uk To: ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES Message-ID: cf65047c5b0562499eaff9fbbc542d6475785...@exchmbx01.fed.cclrc.ac.uk Content-Type: text/plain; charset=us-ascii Dear Teck, ITFA does transformation factor analysis as well, if you just want to do PCA, the PCA module in Sam Webb's sixpack is quite intuitive to use. https://home.comcast.net/~sam_webb/sixpack.html cheers Fred -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom -- Message: 2 Date: Wed, 02 Jul 2014 08:33:25 -0700 From: Matthew Marcus mamar...@lbl.gov To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES Message-ID: 53b42645.5040...@lbl.gov Content-Type: text/plain; charset=ISO-8859-1; format=flowed Athena (IFEFFIT package) does it. So does the ALS Beamline 10.3.2 software package at https://sites.google.com/a/lbl.gov/microxas-lbl-gov/software . If you can't get at it there, I can send the executable and manual. mam On 7/1/2014 10:59 PM, Teck Kwang Choo wrote: Hi Everyone, Does anyone know what software I should use to perform a Principal Component Analysis (PCA) on my K-edge XANES spectra (for sulfur)? The reason I need to use this technique is because I have a couple of reference compound spectra but am not sure which of those I should use to fit my unknown sample spectrum. Any help is appreciated. Thanks and kind regards. Teck Kwang Choo PhD Candidate Department of Chemical Engineering Room 225, Building 36 Monash University Mobile No.: 04-11489904 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Message: 3 Date: Wed, 2 Jul 2014 21:03:17 +0530 From: Abhijeet Gaur abhijeetga...@gmail.com To: ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Ifeffit Digest, Vol 137, Issue 4 Message-ID: CAEq27Q2UkMuFScofU8w20jO= 7a34mkykkimsgy5+h+7b_nc...@mail.gmail.com Content-Type: text/plain; charset=utf-8 Hi Teck Kwang Choo, For PCA analysis you can use SixPack data analysis package
[Ifeffit] Demeter-devel MacPorts Athena issues work-around
Dear OS X Users,
First let me thank Frank Schima for fixing the issues with Artemis and
ATOMS with his new demeter-devel Macports download -- I (and all Mac users)
greatly appreciate it!
I thought I would bring two issues with Macports Athena to your attention...
FYI, I am using Mac OS X Mavericks v. 10.9.4, with an Intel processor. I
followed the directions found here today to delete the old version of
demeter and download the new one:
http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04404.html
Issue 1. With the new demeter-devel Macports download, Athena freezes upon
opening. Opening up Athena via Terminal brought up perl5.16 -- I could see
the GUI, the Tip of the Day, and the Athena startup box, but the system
just froze. I had to force quit every time, getting the following notice in
my Terminal: 'Terminated: 15'. I had a feeling it was an issue with the Tip
of the Day popping up, so I edited the Athena.pm file (in the UI folder),
and edited line 197 from
‘$app-show_tip if Demeter-co-default('athena', 'tips');’ TO
‘$app-show_tip if Demeter-co-default('athena', 'tip');’
(honestly, I don't know enough about this code to be able to give it a real
option that would turn off the Tip of the Day as the default, so I just
hoped this would make the program give me general error in the GUI but that
Athena could still load). Luckily, my not-fix fix worked. I get an error
every time I open it, but after clicking 'OK', Athena behaves just like
normal. I hope you can use this information to provide a real fix to the
problem!
Issue 2. I can only load data files into Athena if there are no headers of
any sort -- commenting out each header line with a # or % does not work.
When I try to load in a .dat file with a commented-out header, I get the
following error message in Terminal:
'At line 436 of file iff_show.f
Fortran runtime error: End of record'
followed by Athena quitting itself.
This is an issue with both the regular Macports demeter download and the
demeter-devel download. These data files loaded in just fine to the old
iXAFS version of Athena, and on a PC. Is there a plugin I should be using
in the Demeter versions? If I delete the header, or load it in from a .prj
file, everything works just fine. So it is not huge issue, as I do have a
work around.
Thank you, Frank, for the new version of Demeter, and thank you all for any
thoughts you have on Issue 2.
Best regards,
Margaret Anne
Margaret Anne G. Hinkle
Ph.D. Candidate
Earth and Planetary Sciences
Washington University in St. Louis
Rudolph Hall
Campus Box 1169
1 Brookings Drive
St. Louis, MO 63130
email: mhin...@eps.wustl.edu
website: aqgeochem.wustl.edu
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