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 +0000 >> 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 >> > 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. spam on our mailing list (Bruce Ravel) >> > 2. Re: to use scattering path in different model or to construct >> > a new model which is the combination of different simple compound >> > (Bruce Ravel) >> > 3. Principal Component Analysis (PCA) for XANES (Teck Kwang Choo) >> > 4. Re: Principal Component Analysis (PCA) for XANES >> > (Amayri, Dr. Samer) >> > >> > >> > ---------------------------------------------------------------------- >> > >> > Message: 1 >> > Date: Tue, 01 Jul 2014 13:31:59 -0400 >> > From: Bruce Ravel <bra...@bnl.gov> >> > To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> >> > Subject: [Ifeffit] spam on our mailing list >> > Message-ID: <53b2f08f.7000...@bnl.gov> >> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> > >> > >> > Hi all, >> > >> > Over the years we've done a pretty good job of keeping spam off this >> > mailing list. As you saw, one slipped through this afternoon. Hopefully >> > it was a one-time event and it will not be necessary to change the >> > friendly nature of security on the list. >> > >> > B >> > >> > -- >> > Bruce Ravel ------------------------------------ bra...@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 >> > >> > >> > ------------------------------ >> > >> > Message: 2 >> > Date: Tue, 01 Jul 2014 15:16:20 -0400 >> > From: Bruce Ravel <bra...@bnl.gov> >> > To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> >> > Subject: Re: [Ifeffit] to use scattering path in different model or to >> > construct a new model which is the combination of different >> simple >> > compound >> > Message-ID: <53b30904.5030...@bnl.gov> >> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> > >> > On 07/01/2014 10:43 AM, ZHAN Fei wrote: >> > > 1 In the example,multiplet scattering path comes from two model >> > > respectively,if use path from different model in different shell's >> > > fit,there is risk of ignore important multiple path across >> models.Should >> > > construct a cluster ,run feff to ensure? >> > >> > I don't completely understand the question, but I'll give it a try. >> > >> > In the example of Shelly's paper, she had a situation where she >> > *couldn't* write a single feff.inp file. Her local environment was the >> > average of all possible ways that the uranyl ion could bond to biomass. >> > The uranyl binding disproportionated into a pH-dependent mixture of >> > carboxyl, phosphoryl, and hydroxyl sites. There was simply no way to >> > write a feff.inp file for that. So her solution was to run Feff more >> > than once, picking and choosing paths that represented her best guess >> > for modeling the average bonding environment. >> > >> > I think what you are really getting at, though, is whether it was right >> > for Shelly to use parts of Feff calculations on a crystals to model >> > something else. If you were to read up on the theory used in Feff, you >> > would find that the important thing is that the muffin tin radii of the >> > scatterers get calculated reasonably. Unless Shelly had a reason to >> > think that the interatomic distances in her biomass sample were VERY >> > different than in the crystals she used to run Feff, then the scattering >> > amplitudes and phase shifts were almost certainly computed quite well >> > enough. >> > >> > > 2 I have confusion of the relationship pf N between single path and >> > > multiple path,for example I think U-Oe-C U-Oe-Pshould be 1 2 >> > > respectively,instead 2 4 in paper. >> > >> > I think Scott's explanation is correct. In real-space, >> > multiple-scattering theory, both ways around a three-legged path have to >> > be counted. >> > >> > B >> > >> > >> > -- >> > Bruce Ravel ------------------------------------ bra...@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 >> > >> > >> > ------------------------------ >> > >> > Message: 3 >> > Date: Wed, 2 Jul 2014 15:59:25 +1000 >> > From: Teck Kwang Choo <teck.kwang.c...@monash.edu> >> > To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> >> > Subject: [Ifeffit] Principal Component Analysis (PCA) for XANES >> > Message-ID: >> > < >> > cahxrqwdt2lvasbvbuu7hmag0owcc9u8fkbchzdamyw14-uy...@mail.gmail.com> >> > Content-Type: text/plain; charset="utf-8" >> > >> > 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 >> > -------------- next part -------------- >> > An HTML attachment was scrubbed... >> > URL: < >> > >> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20140702/afc4cff2/attachment-0001.htm >> > > >> > >> > ------------------------------ >> > >> > Message: 4 >> > Date: Wed, 2 Jul 2014 07:22:08 +0000 >> > From: "Amayri, Dr. Samer" <ama...@uni-mainz.de> >> > To: "'XAFS Analysis using Ifeffit'" >> > <ifeffit@millenia.cars.aps.anl.gov> >> > Subject: Re: [Ifeffit] Principal Component Analysis (PCA) for XANES >> > Message-ID: >> > < >> > ab4ba6d33c596041b4d27dc9ffd88f2d5b6e9...@e14mdb-01.zdv.uni-mainz.de> >> > Content-Type: text/plain; charset="utf-8" >> > >> > Hallo Teck, >> > >> > To get the Principal Component Analysis (PCA) program you can contact >> Dr. >> > Andr? Ro?berg (rossb...@esrf.fr). >> > >> > Heir some references related to ITFA: >> > Rossberg, A., Reich, T. & Bernhard, G. (2003). Analytical and >> > Bioanalytical Chemistry 376, 631-638. >> > Scheinost, A. C., Rossberg, A., Marcus, M., Pfister, S. & Kretzschmar, >> R. >> > (2005). Physica Scripta T115, 1038-1040. >> > Ikeda, A., Hennig, C., Rossberg, A., Tsushima, S., Scheinost, A. C. & >> > Bernhard, G. (2008). Analytical Chemistry 80, 1102-1110. >> > Rossberg, A., Ulrich, K. U., Weiss, S., Tsushima, S., Hiemstra, T. & >> > Scheinost, A. C. (2009). Environmental Science & >> > Technology 43, 1400-1406. >> > Breynaert, E., Scheinost, A. C., Dom, D., Rossberg, A., Vancluysen, J., >> > Gobechiya, E., Kirschhock, C. E. A. & Maes, A. (2010). >> > Environmental Science & Technology 44, 6649-6655. >> > >> > With best regards >> > >> > Dr. Samer Amayri >> > >> > >> > >> > From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto: >> > ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Teck Kwang Choo >> > Sent: Wednesday, July 02, 2014 7:59 AM >> > To: XAFS Analysis using Ifeffit >> > Subject: [Ifeffit] Principal Component Analysis (PCA) for XANES >> > >> > 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 >> > -------------- next part -------------- >> > An HTML attachment was scrubbed... >> > URL: < >> > >> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20140702/41d07580/attachment.htm >> > > >> > >> > ------------------------------ >> > >> > _______________________________________________ >> > Ifeffit mailing list >> > Ifeffit@millenia.cars.aps.anl.gov >> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> > >> > >> > End of Ifeffit Digest, Vol 137, Issue 4 >> > *************************************** >> > >> >> >> >> -- >> Dr. Abhijeet Gaur >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20140702/2db87206/attachment.htm >> > >> >> ------------------------------ >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit@millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >> End of Ifeffit Digest, Vol 137, Issue 5 >> *************************************** >> > >
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