Output of data fit in k-space from current version of Artemis
Hi Guys, I am embarrassed to ask this question, but I am fairly new to Artemis (moving over from the dark side of EXAFSPak) Could anyone advise me how to export a fit in k-space? If I go to the Artemis data window and go Data “save data and fit as” it doesn’t seem to match up with the simulations on the window. Exports in R-space seem sensible, but no amount of repetition and changes alternation, of fits etc seems to result in similarly sensible output in k-space. If anyone could help I would appreciate it- I can email you my fit file if it would help. kind regards, Rosalie
On 05/25/2015 08:37 PM, Rosalie Hocking wrote:
If I go to the Artemis data window and go Data “save data and fit as” it doesn’t seem to match up with the simulations on the window.
Hi Rosalie, I don't see a problem. In the submenu you mention, there are options for saving data and fit in k-space with various different k-weightings. When I select the same k-weighting that I am currently using in the plot, save the file, then replot, the data -- it looks the same to me. I hate to be the jerk who says "have you considered this thing which is plainly obvious?" ... but ... are you sure that you are saving the data with the same k-weighting as the plot? Also, I just want to point out that the k-weighted data are in column 2 of that file and the k-weighted fit is in column 3. 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/
Hi Rosalie, After spending some time with this, I agree that there is something very wrong that manifests itself when you attempt to save the data+fit file in k-space. The executive summary is that there is a problem deep under the hood with the k-grid that Artemis uses for the fitted function. The fitted function is not wrong -- but there is a confusion regarding the k-grid. For reasons of how Artemis does it's various chores, this is manifested when saving the data+fit file in k, but it is not manifested when making certain kinds of plots. That is, as you noticed, the plot looks sensible but the data+fit save file is incorrect. I have a work-around for you while to try I continue to puzzle over this one. Download a copy of this small text file: https://raw.githubusercontent.com/bruceravel/demeter/master/lib/Demeter/temp... On your computer, overwrite this file: C:\strawberry\perl\site\lib\Demeter\templates\fit\ifeffit\residual.tmpl preserving the file name. Rerun your fit, then try saving the data+fit output file. Let me know if that works for you. Hopefully I will figure out the underlying problem. If not, it will be good to know if this crude fix works for you. Cheers, B On 05/26/2015 09:18 AM, Bruce Ravel wrote:
On 05/25/2015 08:37 PM, Rosalie Hocking wrote:
If I go to the Artemis data window and go Data “save data and fit as” it doesn’t seem to match up with the simulations on the window.
Hi Rosalie,
I don't see a problem. In the submenu you mention, there are options for saving data and fit in k-space with various different k-weightings. When I select the same k-weighting that I am currently using in the plot, save the file, then replot, the data -- it looks the same to me.
I hate to be the jerk who says "have you considered this thing which is plainly obvious?" ... but ... are you sure that you are saving the data with the same k-weighting as the plot?
Also, I just want to point out that the k-weighted data are in column 2 of that file and the k-weighted fit is in column 3.
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/
I should also say that I have never seen this problem except in the project file Rosalie sent to me. I cannot reproduce it with any of the project files I have lying around here in my office. It seems possible -- maybe even likely -- that few other Artemis users are seeing this problem. B On 05/27/2015 03:41 PM, Bruce Ravel wrote:
Hi Rosalie,
After spending some time with this, I agree that there is something very wrong that manifests itself when you attempt to save the data+fit file in k-space.
The executive summary is that there is a problem deep under the hood with the k-grid that Artemis uses for the fitted function. The fitted function is not wrong -- but there is a confusion regarding the k-grid. For reasons of how Artemis does it's various chores, this is manifested when saving the data+fit file in k, but it is not manifested when making certain kinds of plots. That is, as you noticed, the plot looks sensible but the data+fit save file is incorrect.
I have a work-around for you while to try I continue to puzzle over this one. Download a copy of this small text file:
https://raw.githubusercontent.com/bruceravel/demeter/master/lib/Demeter/temp...
On your computer, overwrite this file:
C:\strawberry\perl\site\lib\Demeter\templates\fit\ifeffit\residual.tmpl
preserving the file name.
Rerun your fit, then try saving the data+fit output file.
Let me know if that works for you. Hopefully I will figure out the underlying problem. If not, it will be good to know if this crude fix works for you.
Cheers, B
On 05/26/2015 09:18 AM, Bruce Ravel wrote:
On 05/25/2015 08:37 PM, Rosalie Hocking wrote:
If I go to the Artemis data window and go Data “save data and fit as” it doesn’t seem to match up with the simulations on the window.
Hi Rosalie,
I don't see a problem. In the submenu you mention, there are options for saving data and fit in k-space with various different k-weightings. When I select the same k-weighting that I am currently using in the plot, save the file, then replot, the data -- it looks the same to me.
I hate to be the jerk who says "have you considered this thing which is plainly obvious?" ... but ... are you sure that you are saving the data with the same k-weighting as the plot?
Also, I just want to point out that the k-weighted data are in column 2 of that file and the k-weighted fit is in column 3.
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/
On 05/27/2015 03:41 PM, Bruce Ravel wrote:
I have a work-around for you while to try I continue to puzzle over this one. Download a copy of this small text file:
https://raw.githubusercontent.com/bruceravel/demeter/master/lib/Demeter/temp...
On your computer, overwrite this file:
C:\strawberry\perl\site\lib\Demeter\templates\fit\ifeffit\residual.tmpl
preserving the file name.
Oh! And be sure that your browser doesn't "help" you out by appending ".txt" to the file name, or some such.... 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 (2)
-
Bruce Ravel -
Rosalie Hocking