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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