Re: [Ifeffit] normalization methods
Hi Matthew, George, Zach, Thanks for the discussion! On Wed, May 15, 2013 at 5:41 PM, Matthew Marcus mamar...@lbl.gov wrote: I'm not sure what 'flattening' means. Does that mean dividing by a linear or other polynomial function, fitted to the post-edge? mam Sorry, I should have been clearer. Standard Athena/Ifeffit is to a) regress a pre-edge line to mu(E) (no power laws) b) regress a post-edge quadratic c) set edge_step = post_edge_quadratic(E0) - pre_edge_line(E0) b) set norm(E) = (mu(E) - pre_edge_line(E)) / edge_step. Flattening (Athena only, now backported to larch) fits a quadratic to the post-edge range (typcically E0+100 to end of data) of norm(E), and then sets flattened(E) = norm(E) for E= E0 = norm(E) - quadratic(E) + quadratic(E0) for E E0 I think this was originally meant for display purposes only. Hopefully Bruce can correct me if I'm wrong on any of the details here. I think it's fair to say that the Standard Athena/Ifeffit approach to normalization is simple-minded. It was designed for EXAFS in an era when accessing databases seemed like a challenge, so even for EXAFS it is simple-minded. Flattening might be better at removing instrumental backgrounds, and be better for linear analysis of XANES. The main concern I would have is the potential for a slight discontinuity at E0, or the potential strong dependence from the choice of E0. Using something like bkg_cl() (which matched mu(E) to the data from the Cromer-Liberman tables) or MBACK (which I believe is similar, but also accounts for elastic/Compton leakage into the pre-edge part of fluorescence spectra). From my point of view, the question is: what's the best way to do this?The pre_edge() function in Larch does include an energy exponent term, and now writes out the flattened array, as above. It does not include the scaling MAM described, but that would not be hard. Reimplementing bkg_cl() would not be too hard, but perhaps trying to port MBACK would be better. Perhaps all of the above is best? --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] normalization methods
That 'flattening' function seems over-complicated to me and makes an artificial discontinuity, at least in slope, at E0 which is a somewhat arbitrary quantity. Why not simply divide by the post-edge quadratic (norm(E) = (mu(E)-pre_edge_line(E))/quadratic(E))? In some cases, where there's a big curvature, it may make sense to divide mu(E) by the quadratic, then subtract a pre-edge. What I've never solved satisfactorily is the case in which the extrapolation of the pre-edge line crosses the post-edge, so mu(E)-pre_edge_line(E)0 for some part of the range. I've never understood why this happens. mam On 5/16/2013 4:47 AM, Matt Newville wrote: Hi Matthew, George, Zach, Thanks for the discussion! On Wed, May 15, 2013 at 5:41 PM, Matthew Marcus mamar...@lbl.gov wrote: I'm not sure what 'flattening' means. Does that mean dividing by a linear or other polynomial function, fitted to the post-edge? mam Sorry, I should have been clearer. Standard Athena/Ifeffit is to a) regress a pre-edge line to mu(E) (no power laws) b) regress a post-edge quadratic c) set edge_step = post_edge_quadratic(E0) - pre_edge_line(E0) b) set norm(E) = (mu(E) - pre_edge_line(E)) / edge_step. Flattening (Athena only, now backported to larch) fits a quadratic to the post-edge range (typcically E0+100 to end of data) of norm(E), and then sets flattened(E) = norm(E) for E= E0 = norm(E) - quadratic(E) + quadratic(E0) for E E0 I think this was originally meant for display purposes only. Hopefully Bruce can correct me if I'm wrong on any of the details here. I think it's fair to say that the Standard Athena/Ifeffit approach to normalization is simple-minded. It was designed for EXAFS in an era when accessing databases seemed like a challenge, so even for EXAFS it is simple-minded. Flattening might be better at removing instrumental backgrounds, and be better for linear analysis of XANES. The main concern I would have is the potential for a slight discontinuity at E0, or the potential strong dependence from the choice of E0. Using something like bkg_cl() (which matched mu(E) to the data from the Cromer-Liberman tables) or MBACK (which I believe is similar, but also accounts for elastic/Compton leakage into the pre-edge part of fluorescence spectra). From my point of view, the question is: what's the best way to do this?The pre_edge() function in Larch does include an energy exponent term, and now writes out the flattened array, as above. It does not include the scaling MAM described, but that would not be hard. Reimplementing bkg_cl() would not be too hard, but perhaps trying to port MBACK would be better. Perhaps all of the above is best? --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] normalization methods
What I typically do for XANES is divide mu-mu_pre_edge_line by a linear
function which goes through the post-edge oscillations.
This division goes over the whole data range, including pre-edge. If the data
has obvious curvature in the post-edge, I'll use a higher-order
polynomial. For transmission data, what sometimes linearizes the background is
to change the abscissa to 1/E^2.7 (the rule-of-thumb absorption
shape) and change it back afterward. All this is, of course, highly subjective
and one of the reasons for taking extended XANES data (300eV,
for instance). For short-range XANES, there isn't enough info to do more than
divide by a constant. Once this is done, my LCF programs allow
a slope adjustment as a free parameter, thus muNorm(E) =
(1+a*(E-E0))*Sum_on_ref{x[ref]*muNorm[ref](E)}. A sign that this degree of
freedom
may be being abused is if the sum of the x[ref] is far from 1 or if a*(Emax-E0)
is large. Don't get me started on overabsorption :-)
mam
On 5/15/2013 7:35 AM, Matt Newville wrote:
Hi Folks,
Over on the github pages for larch, Mauro and Bruce raised an issue
about the flattening in Athena. See
https://github.com/xraypy/xraylarch/issues/44
I've added a flattened output from Larch's pre_edge() function, but
the question has been raised of whether this is better than the
simpler normalized spectra, especially for doing PCA and/or LCF for
XANES.
Currently, the normalized spectra is just (mu -
pre_edge_line)/edge_step. Clearly, a line fitted to the pre-edge of
the spectra is not sufficient to remove all instrumental backgrounds.
In some sense, flattening attempts to do a better job, fitting the
post-edge spectra to a quadratic function. As Mauro, Bruce, and
Carmelo have pointed out, it is less clear that it is actually better
for XANES analysis. I think the main concerns are that a) it is so
spectra-specific, and b) it turns on at E0 with a step function.
Bruce suggested doing something more like MBACK or Ifeffit's bkg_cl().
It would certainly be possible to do some sort of flattening so
that mu follows the expected energy dependence from tabularized mu(E).
Does anyone else have suggestions, opinions, etc? Feel free to give
them here or at the github page
--Matt
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Re: [Ifeffit] normalization methods
Hi Matthew,
On Wed, May 15, 2013 at 9:57 AM, Matthew Marcus mamar...@lbl.gov wrote:
What I typically do for XANES is divide mu-mu_pre_edge_line by a linear
function which goes through the post-edge oscillations.
This division goes over the whole data range, including pre-edge. If the
data has obvious curvature in the post-edge, I'll use a higher-order
polynomial. For transmission data, what sometimes linearizes the background
is to change the abscissa to 1/E^2.7 (the rule-of-thumb absorption
shape) and change it back afterward. All this is, of course, highly
subjective and one of the reasons for taking extended XANES data (300eV,
for instance). For short-range XANES, there isn't enough info to do more
than divide by a constant. Once this is done, my LCF programs allow
a slope adjustment as a free parameter, thus muNorm(E) =
(1+a*(E-E0))*Sum_on_ref{x[ref]*muNorm[ref](E)}. A sign that this degree of
freedom
may be being abused is if the sum of the x[ref] is far from 1 or if
a*(Emax-E0) is large. Don't get me started on overabsorption :-)
mam
Thanks -- I should have said that pre_edge() can now do a
victoreen-ish fit, regressing a line to mu*E^nvict (nvict can be any
real value).
Still, it seems that the current flattening is somewhere between
better and worse, which is unsettling... Applying the
flattening polynomial to the pre-edge range definitely seems to give
poor results, but maybe some energy-dependent compromise is possible.
And, of course, over-absorption is next on the list!
--Matt
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Re: [Ifeffit] normalization methods
The way I commonly do pre-edge is to fit with some form plus a power-law
singularity representing the initial rise of the edge, then
subtract out that some form. Now, that form can be either linear,
linear+E^(-2.7) (for transmission), or linear+ another power-law
singularity centered at the center passband energy of the fluorescence
detector. That latter is for fluorescence data which is affected by
the tail of the elastic/Compton peak from the incident energy. Whichever form
is taken gets subtraccted from the whole data range, resulting
in data which is pre-edge-subtracted but not yet post-edge normalized. The
path then splits; for EXAFS, the usual conversion to k-space, spline
fitting in the post-edge, subtraction and division is done, all interactively.
Tensioned spline is also available due to request of a prominent user.
For XANES, the post-edge is fit as previously described. Thus, there's no
distinction made between data above and below E0 in XANES, whereas
there is such a distinction in EXAFS.
mam
On 5/15/2013 8:25 AM, Matt Newville wrote:
Hi Matthew,
On Wed, May 15, 2013 at 9:57 AM, Matthew Marcus mamar...@lbl.gov wrote:
What I typically do for XANES is divide mu-mu_pre_edge_line by a linear
function which goes through the post-edge oscillations.
This division goes over the whole data range, including pre-edge. If the
data has obvious curvature in the post-edge, I'll use a higher-order
polynomial. For transmission data, what sometimes linearizes the background
is to change the abscissa to 1/E^2.7 (the rule-of-thumb absorption
shape) and change it back afterward. All this is, of course, highly
subjective and one of the reasons for taking extended XANES data (300eV,
for instance). For short-range XANES, there isn't enough info to do more
than divide by a constant. Once this is done, my LCF programs allow
a slope adjustment as a free parameter, thus muNorm(E) =
(1+a*(E-E0))*Sum_on_ref{x[ref]*muNorm[ref](E)}. A sign that this degree of
freedom
may be being abused is if the sum of the x[ref] is far from 1 or if
a*(Emax-E0) is large. Don't get me started on overabsorption :-)
mam
Thanks -- I should have said that pre_edge() can now do a
victoreen-ish fit, regressing a line to mu*E^nvict (nvict can be any
real value).
Still, it seems that the current flattening is somewhere between
better and worse, which is unsettling... Applying the
flattening polynomial to the pre-edge range definitely seems to give
poor results, but maybe some energy-dependent compromise is possible.
And, of course, over-absorption is next on the list!
--Matt
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Re: [Ifeffit] normalization methods
The question of whether it is appropriate to use flattened data for
quantitative analysis is something I've been thinking about a lot recently.
In my specific case, I am analyzing XMCD data at the Co L-edge. To obtain
the XMCD, I measure XAS with total electron yield detection using a ~70%
left or right circularly polarized beam and flip the magnetic field on the
sample at every data point. The goal then, is to subtract the XAS measured
in a positive field (p-XAS) from XAS measured in a negative field (n-XAS)
and get something (the XMCD) that is zero in the pre-edge and post-edge
regions. I often find that after removal of a linear pre-edge, the spectra
still have a linearly increasing post edge (with EXAFS oscillations
superimposed on it), and the slope of the n-XAS and p-XAS post-edge lines
are different. In this case simply multiplying the n-XAS and p-XAS by
constants will never give an XMCD spectrum that is zero in the post edge
region. There is then some component of the XAS background that is not
accounted for by linear subtraction and multiplication by a constant. It
seems to me that flattening could be a good way to account for such a
background. So is flattening a reasonable thing to do in a case such as
this, or is there a better way to account for such a background?
Thanks,
George
On Wed, May 15, 2013 at 11:41 AM, Matthew Marcus mamar...@lbl.gov wrote:
The way I commonly do pre-edge is to fit with some form plus a power-law
singularity representing the initial rise of the edge, then
subtract out that some form. Now, that form can be either linear,
linear+E^(-2.7) (for transmission), or linear+ another power-law
singularity centered at the center passband energy of the fluorescence
detector. That latter is for fluorescence data which is affected by
the tail of the elastic/Compton peak from the incident energy. Whichever
form is taken gets subtraccted from the whole data range, resulting
in data which is pre-edge-subtracted but not yet post-edge normalized.
The path then splits; for EXAFS, the usual conversion to k-space, spline
fitting in the post-edge, subtraction and division is done, all
interactively. Tensioned spline is also available due to request of a
prominent user.
For XANES, the post-edge is fit as previously described. Thus, there's no
distinction made between data above and below E0 in XANES, whereas
there is such a distinction in EXAFS.
mam
On 5/15/2013 8:25 AM, Matt Newville wrote:
Hi Matthew,
On Wed, May 15, 2013 at 9:57 AM, Matthew Marcus mamar...@lbl.gov wrote:
What I typically do for XANES is divide mu-mu_pre_edge_line by a linear
function which goes through the post-edge oscillations.
This division goes over the whole data range, including pre-edge. If the
data has obvious curvature in the post-edge, I'll use a higher-order
polynomial. For transmission data, what sometimes linearizes the
background
is to change the abscissa to 1/E^2.7 (the rule-of-thumb absorption
shape) and change it back afterward. All this is, of course, highly
subjective and one of the reasons for taking extended XANES data (300eV,
for instance). For short-range XANES, there isn't enough info to do more
than divide by a constant. Once this is done, my LCF programs allow
a slope adjustment as a free parameter, thus muNorm(E) =
(1+a*(E-E0))*Sum_on_ref{x[ref]***muNorm[ref](E)}. A sign that this
degree of
freedom
may be being abused is if the sum of the x[ref] is far from 1 or if
a*(Emax-E0) is large. Don't get me started on overabsorption :-)
mam
Thanks -- I should have said that pre_edge() can now do a
victoreen-ish fit, regressing a line to mu*E^nvict (nvict can be any
real value).
Still, it seems that the current flattening is somewhere between
better and worse, which is unsettling... Applying the
flattening polynomial to the pre-edge range definitely seems to give
poor results, but maybe some energy-dependent compromise is possible.
And, of course, over-absorption is next on the list!
--Matt
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Re: [Ifeffit] normalization methods
You say that the flipping difference (p - n) is 0 in pre-edge and far post-edge
regions, which is as it should be, but then say that the
slopes of p- and n- post-edges, considered separately, are different. I must
be misunderstanding because those two statements would seem to be
inconsistent. I wonder if the sensitivity of the TEY changes with magnetic
field because of the effect of the field on the trajectories of
the outgoing electrons, which would explain the differing curves. A
possibility - if you divide the p-XAS by n-XAS, do you get something
which is a smooth curve everywhere but where MCD is expected? Does that curve
match in pre- and far post-edge regions? If that miracle occurs,
then perhaps you could fit that to a polynomial, except in the MCD region, then
divide the p-XAS by that polynomial, to remove the effect of
the differing sensitivities.
There are people here at ALS, such as Elke Arenholz earenh...@lbl.gov, who do
this sort of spectroscopy. I suggest asking her.
mam
On 5/15/2013 9:58 AM, George Sterbinsky wrote:
The question of whether it is appropriate to use flattened data for
quantitative analysis is something I've been thinking about a lot recently. In
my specific case, I am analyzing XMCD data at the Co L-edge. To obtain the
XMCD, I measure XAS with total electron yield detection using a ~70% left or
right circularly polarized beam and flip the magnetic field on the sample at
every data point. The goal then, is to subtract the XAS measured in a positive
field (p-XAS) from XAS measured in a negative field (n-XAS) and get something
(the XMCD) that is zero in the pre-edge and post-edge regions. I often find
that after removal of a linear pre-edge, the spectra still have a linearly
increasing post edge (with EXAFS oscillations superimposed on it), and the
slope of the n-XAS and p-XAS post-edge lines are different. In this case simply
multiplying the n-XAS and p-XAS by constants will never give an XMCD spectrum
that is zero in the post edge region. There is then some component of t
he
XAS background that is not accounted for by linear subtraction and
multiplication by a constant. It seems to me that flattening could be a good
way to account for such a background. So is flattening a reasonable thing to do
in a case such as this, or is there a better way to account for such a
background?
Thanks,
George
On Wed, May 15, 2013 at 11:41 AM, Matthew Marcus mamar...@lbl.gov
mailto:mamar...@lbl.gov wrote:
The way I commonly do pre-edge is to fit with some form plus a power-law
singularity representing the initial rise of the edge, then
subtract out that some form. Now, that form can be either linear,
linear+E^(-2.7) (for transmission), or linear+ another power-law
singularity centered at the center passband energy of the fluorescence
detector. That latter is for fluorescence data which is affected by
the tail of the elastic/Compton peak from the incident energy. Whichever
form is taken gets subtraccted from the whole data range, resulting
in data which is pre-edge-subtracted but not yet post-edge normalized. The
path then splits; for EXAFS, the usual conversion to k-space, spline
fitting in the post-edge, subtraction and division is done, all
interactively. Tensioned spline is also available due to request of a
prominent user.
For XANES, the post-edge is fit as previously described. Thus, there's no
distinction made between data above and below E0 in XANES, whereas
there is such a distinction in EXAFS.
mam
On 5/15/2013 8:25 AM, Matt Newville wrote:
Hi Matthew,
On Wed, May 15, 2013 at 9:57 AM, Matthew Marcus mamar...@lbl.gov
mailto:mamar...@lbl.gov wrote:
What I typically do for XANES is divide mu-mu_pre_edge_line by a
linear
function which goes through the post-edge oscillations.
This division goes over the whole data range, including pre-edge.
If the
data has obvious curvature in the post-edge, I'll use a higher-order
polynomial. For transmission data, what sometimes linearizes the
background
is to change the abscissa to 1/E^2.7 (the rule-of-thumb absorption
shape) and change it back afterward. All this is, of course, highly
subjective and one of the reasons for taking extended XANES data
(300eV,
for instance). For short-range XANES, there isn't enough info to
do more
than divide by a constant. Once this is done, my LCF programs allow
a slope adjustment as a free parameter, thus muNorm(E) =
(1+a*(E-E0))*Sum_on_ref{x[ref]__*muNorm[ref](E)}. A sign that this
degree of
freedom
may be being abused is if the sum of the x[ref] is far from 1 or if
a*(Emax-E0) is large. Don't get me started on overabsorption :-)
mam
Thanks -- I should have said that
Re: [Ifeffit] normalization methods
OK, I guess I don't know what 'standard normalization' is. It looks from the quotient that you'll need some sort of curved post-edge. I guess the division didn't work because the electron energy distribution is different pre- and post-edge, so the magnetic effects are different and vary across the edge. Thus, the shapes of the MCD peaks will be at least a little corrupted even if the pre- and post-edge spectra are taken into account. I don't know what to do about this. Did you try asking Elke? mam On 5/15/2013 11:52 AM, George Sterbinsky wrote: Hi Matthew, On Wed, May 15, 2013 at 1:20 PM, Matthew Marcus mamar...@lbl.gov mailto:mamar...@lbl.gov wrote: You say that the flipping difference (p - n) is 0 in pre-edge and far post-edge regions, which is as it should be, but then say that the slopes of p- and n- post-edges, considered separately, are different. I must be misunderstanding because those two statements would seem to be inconsistent. Sorry, I think my wording wasn't particularly clear here. What I should have said is: The goal then is to subtract the /normalized/ XAS measured in a positive field (p-XAS) from /normalized/ XAS measured in a negative field (n-XAS) and get something (the XMCD) that is zero in the pre-edge and post-edge regions. /However, standard normalization does not give this result/ Italics indicate new text. I wonder if the sensitivity of the TEY changes with magnetic field because of the effect of the field on the trajectories of the outgoing electrons, which would explain the differing curves. I would agree, I think the effect of the magnetic field on the electrons is the likely source of the differences in background. A possibility - if you divide the p-XAS by n-XAS, do you get something which is a smooth curve everywhere but where MCD is expected? Does that curve match in pre- and far post-edge regions? No, after division of the p-XAS by the n-XAS (before any normalization), both the pre and post-edge regions are smooth, but one would need a step-like function to connect them. I've attached a plot showing the result of division. If that miracle occurs, then perhaps you could fit that to a polynomial, except in the MCD region, then divide the p-XAS by that polynomial, to remove the effect of the differing sensitivities. There are people here at ALS, such as Elke Arenholz earenh...@lbl.gov mailto:earenh...@lbl.gov, who do this sort of spectroscopy. I suggest asking her. mam Thanks for the suggestion and your reply. George On 5/15/2013 9:58 AM, George Sterbinsky wrote: The question of whether it is appropriate to use flattened data for quantitative analysis is something I've been thinking about a lot recently. In my specific case, I am analyzing XMCD data at the Co L-edge. To obtain the XMCD, I measure XAS with total electron yield detection using a ~70% left or right circularly polarized beam and flip the magnetic field on the sample at every data point. The goal then, is to subtract the XAS measured in a positive field (p-XAS) from XAS measured in a negative field (n-XAS) and get something (the XMCD) that is zero in the pre-edge and post-edge regions. I often find that after removal of a linear pre-edge, the spectra still have a linearly increasing post edge (with EXAFS oscillations superimposed on it), and the slope of the n-XAS and p-XAS post-edge lines are different. In this case simply multiplying the n-XAS and p-XAS by constants will never give an XMCD spectrum that is zero in the post edge region. There is then some component of the XAS background that is not accounted for by linear subtraction and multiplication by a constant. It seems to me that flattening could be a good way to account for such a background. So is flattening a reasonable thing to do in a case such as this, or is there a better way to account for such a background? Thanks, George On Wed, May 15, 2013 at 11:41 AM, Matthew Marcus mamar...@lbl.gov mailto:mamar...@lbl.gov mailto:mamar...@lbl.gov mailto:mamar...@lbl.gov wrote: The way I commonly do pre-edge is to fit with some form plus a power-law singularity representing the initial rise of the edge, then subtract out that some form. Now, that form can be either linear, linear+E^(-2.7) (for transmission), or linear+ another power-law singularity centered at the center passband energy of the fluorescence detector. That latter is for fluorescence data which is affected by the tail of the elastic/Compton peak from the incident energy. Whichever form is taken gets subtraccted from the whole data range, resulting in data which is pre-edge-subtracted but not yet post-edge normalized. The path then splits; for EXAFS, the usual conversion to k-space,
Re: [Ifeffit] normalization methods
By standard normalization, I meant subtraction of a linear pre-edge and multiplication by a constant. If this treatment is applied to the XAS spectra before subtraction, one does not obtain an XMCD spectrum that goes to zero in the post edge region for the data I described. As you noted, that is what would be expected given the p-XAS and n-XAS have different slopes in the post-edge region. On the other hand, standard normalization + flattening does result in pre and post-edge regions that go to zero, again as one might expect. So perhaps, the background modeled by standard normalization + flattening is an accurate representation of the real background in some cases and can be used in quantitative analysis. Is there reason to believe that cannot be the case? Thanks, George On Wed, May 15, 2013 at 3:04 PM, Matthew Marcus mamar...@lbl.gov wrote: OK, I guess I don't know what 'standard normalization' is. It looks from the quotient that you'll need some sort of curved post-edge. I guess the division didn't work because the electron energy distribution is different pre- and post-edge, so the magnetic effects are different and vary across the edge. Thus, the shapes of the MCD peaks will be at least a little corrupted even if the pre- and post-edge spectra are taken into account. I don't know what to do about this. Did you try asking Elke? mam On 5/15/2013 11:52 AM, George Sterbinsky wrote: Hi Matthew, On Wed, May 15, 2013 at 1:20 PM, Matthew Marcus mamar...@lbl.govmailto: mamar...@lbl.gov wrote: You say that the flipping difference (p - n) is 0 in pre-edge and far post-edge regions, which is as it should be, but then say that the slopes of p- and n- post-edges, considered separately, are different. I must be misunderstanding because those two statements would seem to be inconsistent. Sorry, I think my wording wasn't particularly clear here. What I should have said is: The goal then is to subtract the /normalized/ XAS measured in a positive field (p-XAS) from /normalized/ XAS measured in a negative field (n-XAS) and get something (the XMCD) that is zero in the pre-edge and post-edge regions. /However, standard normalization does not give this result/ Italics indicate new text. I wonder if the sensitivity of the TEY changes with magnetic field because of the effect of the field on the trajectories of the outgoing electrons, which would explain the differing curves. I would agree, I think the effect of the magnetic field on the electrons is the likely source of the differences in background. A possibility - if you divide the p-XAS by n-XAS, do you get something which is a smooth curve everywhere but where MCD is expected? Does that curve match in pre- and far post-edge regions? No, after division of the p-XAS by the n-XAS (before any normalization), both the pre and post-edge regions are smooth, but one would need a step-like function to connect them. I've attached a plot showing the result of division. If that miracle occurs, then perhaps you could fit that to a polynomial, except in the MCD region, then divide the p-XAS by that polynomial, to remove the effect of the differing sensitivities. There are people here at ALS, such as Elke Arenholz earenh...@lbl.gov mailto:earenh...@lbl.gov, who do this sort of spectroscopy. I suggest asking her. mam Thanks for the suggestion and your reply. George On 5/15/2013 9:58 AM, George Sterbinsky wrote: The question of whether it is appropriate to use flattened data for quantitative analysis is something I've been thinking about a lot recently. In my specific case, I am analyzing XMCD data at the Co L-edge. To obtain the XMCD, I measure XAS with total electron yield detection using a ~70% left or right circularly polarized beam and flip the magnetic field on the sample at every data point. The goal then, is to subtract the XAS measured in a positive field (p-XAS) from XAS measured in a negative field (n-XAS) and get something (the XMCD) that is zero in the pre-edge and post-edge regions. I often find that after removal of a linear pre-edge, the spectra still have a linearly increasing post edge (with EXAFS oscillations superimposed on it), and the slope of the n-XAS and p-XAS post-edge lines are different. In this case simply multiplying the n-XAS and p-XAS by constants will never give an XMCD spectrum that is zero in the post edge region. There is then some component of the XAS background that is not accounted for by linear subtraction and multiplication by a constant. It seems to me that flattening could be a good way to account for such a background. So is flattening a reasonable thing to do in a case such as this, or is there a better way to account for such a background? Thanks, George On Wed, May 15, 2013
Re: [Ifeffit] normalization methods
I'm not sure what 'flattening' means. Does that mean dividing by a linear or other polynomial function, fitted to the post-edge? mam On 5/15/2013 1:43 PM, George Sterbinsky wrote: By standard normalization, I meant subtraction of a linear pre-edge and multiplication by a constant. If this treatment is applied to the XAS spectra before subtraction, one does not obtain an XMCD spectrum that goes to zero in the post edge region for the data I described. As you noted, that is what would be expected given the p-XAS and n-XAS have different slopes in the post-edge region. On the other hand, standard normalization + flattening does result in pre and post-edge regions that go to zero, again as one might expect. So perhaps, the background modeled by standard normalization + flattening is an accurate representation of the real background in some cases and can be used in quantitative analysis. Is there reason to believe that cannot be the case? Thanks, George On Wed, May 15, 2013 at 3:04 PM, Matthew Marcus mamar...@lbl.gov mailto:mamar...@lbl.gov wrote: OK, I guess I don't know what 'standard normalization' is. It looks from the quotient that you'll need some sort of curved post-edge. I guess the division didn't work because the electron energy distribution is different pre- and post-edge, so the magnetic effects are different and vary across the edge. Thus, the shapes of the MCD peaks will be at least a little corrupted even if the pre- and post-edge spectra are taken into account. I don't know what to do about this. Did you try asking Elke? mam On 5/15/2013 11:52 AM, George Sterbinsky wrote: Hi Matthew, On Wed, May 15, 2013 at 1:20 PM, Matthew Marcus mamar...@lbl.gov mailto:mamar...@lbl.gov mailto:mamar...@lbl.gov mailto:mamar...@lbl.gov wrote: You say that the flipping difference (p - n) is 0 in pre-edge and far post-edge regions, which is as it should be, but then say that the slopes of p- and n- post-edges, considered separately, are different. I must be misunderstanding because those two statements would seem to be inconsistent. Sorry, I think my wording wasn't particularly clear here. What I should have said is: The goal then is to subtract the /normalized/ XAS measured in a positive field (p-XAS) from /normalized/ XAS measured in a negative field (n-XAS) and get something (the XMCD) that is zero in the pre-edge and post-edge regions. /However, standard normalization does not give this result/ Italics indicate new text. I wonder if the sensitivity of the TEY changes with magnetic field because of the effect of the field on the trajectories of the outgoing electrons, which would explain the differing curves. I would agree, I think the effect of the magnetic field on the electrons is the likely source of the differences in background. A possibility - if you divide the p-XAS by n-XAS, do you get something which is a smooth curve everywhere but where MCD is expected? Does that curve match in pre- and far post-edge regions? No, after division of the p-XAS by the n-XAS (before any normalization), both the pre and post-edge regions are smooth, but one would need a step-like function to connect them. I've attached a plot showing the result of division. If that miracle occurs, then perhaps you could fit that to a polynomial, except in the MCD region, then divide the p-XAS by that polynomial, to remove the effect of the differing sensitivities. There are people here at ALS, such as Elke Arenholz earenh...@lbl.gov mailto:earenh...@lbl.gov mailto:earenh...@lbl.gov mailto:earenh...@lbl.gov, who do this sort of spectroscopy. I suggest asking her. mam Thanks for the suggestion and your reply. George On 5/15/2013 9:58 AM, George Sterbinsky wrote: The question of whether it is appropriate to use flattened data for quantitative analysis is something I've been thinking about a lot recently. In my specific case, I am analyzing XMCD data at the Co L-edge. To obtain the XMCD, I measure XAS with total electron yield detection using a ~70% left or right circularly polarized beam and flip the magnetic field on the sample at every data point. The goal then, is to subtract the XAS measured in a positive field (p-XAS) from XAS measured in a negative field (n-XAS) and get something (the XMCD) that is zero in the pre-edge and post-edge regions. I often find that after removal of a linear pre-edge, the spectra still have a linearly increasing post edge (with EXAFS oscillations superimposed on it), and the slope of the n-XAS and p-XAS post-edge lines are different. In this case simply multiplying the n-XAS and p-XAS by constants will
