Athena reporting incorrect element on import
Hi, I am having a number of issues with importing my data into Athema, the data that I collected was on the carbon K edge. As there is an issue with recording carbon (as it builds up on the mirrors), the synchrotron that I performed my measurments at (Australian Synchrotron) has developed software to perform a double normalization to remove these effects. The problem comes when importing the now normalized data into Athena. As it doesn't require normalization again, I select the norm(E) data type and the correct column for energy and response which produces the correct plot of the data. When I click OK it attempts to produce the other plots, sometimes it manages to make a k-space and R-space but q-space is never displayed and other times it only manages the energy plot. Additionally, the word element is lit up red and it has selected beryllium as the element on the L2 edge. Changing this to carbon does not seem to fix the problem as it reverts back to beryllium as soon as I leave the main page. Finally, when I go to peak fitting, any value added for peaks informs me that it is out of range. I have attached some normalized data. Any help with this would be greatly appreciated. Regards, Ken Latham
Hi, Ken, try to load your data as raw data and let the Athena normalized your "already normalized" data again. As far as I understand, the normalized data for Athena means special format of the data (equidistance E step?) which you do not get from your treated data. Hope it helps a bit, Anna. Von: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] Im Auftrag von Kenneth Latham Gesendet: Montag, 20. April 2015 07:40 An: ifeffit@millenia.cars.aps.anl.gov Betreff: [Ifeffit] Athena reporting incorrect element on import Hi, I am having a number of issues with importing my data into Athema, the data that I collected was on the carbon K edge. As there is an issue with recording carbon (as it builds up on the mirrors), the synchrotron that I performed my measurments at (Australian Synchrotron) has developed software to perform a double normalization to remove these effects. The problem comes when importing the now normalized data into Athena. As it doesn't require normalization again, I select the norm(E) data type and the correct column for energy and response which produces the correct plot of the data. When I click OK it attempts to produce the other plots, sometimes it manages to make a k-space and R-space but q-space is never displayed and other times it only manages the energy plot. Additionally, the word element is lit up red and it has selected beryllium as the element on the L2 edge. Changing this to carbon does not seem to fix the problem as it reverts back to beryllium as soon as I leave the main page. Finally, when I go to peak fitting, any value added for peaks informs me that it is out of range. I have attached some normalized data. Any help with this would be greatly appreciated. Regards, Ken Latham
Following up on Anna's suggestion, note that when you let Athena normalize, you can instruct it to fix the edge step at 1. In effect, that tells it to not actually renormalize (soft x-ray edges can be tricky to normalize, and you may like what the Australian synchrotron has already done), but it does let it do its interpolations to get the data in the format it needs.
--Scott Calvin
Sarah Lawrence College
On Apr 20, 2015, at 2:48 AM, Zimina, Anna (IKFT)
Hi Ken, I agree that Athena is not working as advertised for selecting the norm(E) option in the column selection dialog. I'll look into it. Happily, Anna and Scott have suggested some work-arounds to keep you going for now. Thanks for the bug report. B On 04/20/2015 01:40 AM, Kenneth Latham wrote:
Hi,
I am having a number of issues with importing my data into Athema, the data that I collected was on the carbon K edge. As there is an issue with recording carbon (as it builds up on the mirrors), the synchrotron that I performed my measurments at (Australian Synchrotron) has developed software to perform a double normalization to remove these effects.
The problem comes when importing the now normalized data into Athena. As it doesn't require normalization again, I select the norm(E) data type and the correct column for energy and response which produces the correct plot of the data. When I click OK it attempts to produce the other plots, sometimes it manages to make a k-space and R-space but q-space is never displayed and other times it only manages the energy plot. Additionally, the word element is lit up red and it has selected beryllium as the element on the L2 edge. Changing this to carbon does not seem to fix the problem as it reverts back to beryllium as soon as I leave the main page.
Finally, when I go to peak fitting, any value added for peaks informs me that it is out of range.
I have attached some normalized data.
Any help with this would be greatly appreciated.
Regards,
Ken Latham
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-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
On 04/20/2015 08:34 AM, Bruce Ravel wrote:
I agree that Athena is not working as advertised for selecting the norm(E) option in the column selection dialog. I'll look into it. Happily, Anna and Scott have suggested some work-arounds to keep you going for now.
I just pushed a fix for this problem to github. This fix will import your data as XANES data flagged as having already been normalized. With this fix, Athena will display the data correctly upon import, find the absorber element and edge sensibly, and other wise work as advertised. This fix will be included the next time I make a windows installer. Thanks again, B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/
participants (4)
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Bruce Ravel
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Kenneth Latham
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Scott Calvin
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Zimina, Anna (IKFT)