Hi, Is there anyone who can tell me how to view the residual in Artemis? Every time I checked the residual, only got the data curve. Best, Ye
Dear Ye, On Mon, 28 Feb 2005 yetao@chem.uga.edu wrote:
Is there anyone who can tell me how to view the residual in Artemis? Every time I checked the residual, only got the data curve.
Plotting the residual in Artemis works for me. Just for completeness, first you have toset up a model and then hit the Fit button to run the fit and get a residual. The Data set should then have a Tree that looks like this: (sorry for the bad ASCII art) . [-] data group . |- Fit . |- Residual . [-] Feff 0 . |- feff0001.dat You can then highlight which of these you want to plot (the default is to show highlighted choices in orange). You can use Ctrl-click to select more than one of these (to plot data and Fit and Residual, for example). Then hit one of the Plot buttons below to show what is highlighted. Is that not working for you? If the residual looks just like the data, maybe that's because the Fit = 0 for all k,R??? That might mean that no fit was done, no paths were defined, or that the amplitudes ended up being zero.... Hope that helps. If not, let us know, --Matt
Matt,
sorry to reply so late due to our exp in SSRL.
Residual plotting didn't works for me yet, although I'm sure the path was defined and the fit done. I attached a apj file for your comment.
Best,
Ye
----- Original Message -----
From: "Matt Newville"
Dear Ye,
On Mon, 28 Feb 2005 yetao@chem.uga.edu wrote:
Is there anyone who can tell me how to view the residual in Artemis? Every time I checked the residual, only got the data curve.
Plotting the residual in Artemis works for me. Just for completeness, first you have toset up a model and then hit the Fit button to run the fit and get a residual. The Data set should then have a Tree that looks like this: (sorry for the bad ASCII art)
.. [-] data group .. |- Fit .. |- Residual .. [-] Feff 0 .. |- feff0001.dat
You can then highlight which of these you want to plot (the default is to show highlighted choices in orange). You can use Ctrl-click to select more than one of these (to plot data and Fit and Residual, for example). Then hit one of the Plot buttons below to show what is highlighted.
Is that not working for you? If the residual looks just like the data, maybe that's because the Fit = 0 for all k,R??? That might mean that no fit was done, no paths were defined, or that the amplitudes ended up being zero....
Hope that helps. If not, let us know,
--Matt
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Dear Ye,
sorry to reply so late due to our exp in SSRL.
No problem. I think we all understand the results of beamtime, and we're just glad that SSRL is back!! I also get an effectively NULL residual with your project. It's not exactly identical to the data, but it's very close. For other fits, the plotting of the residual definitely works, so I started looking into what could be the issue with this fit. First, it's a pretty complicated fit, and some of the parameters (notably your delA, delB parameters) are not very well constrained by the data -- that is they give pretty weird values and uncertainties..... For this kind of diagnosis it would really help to simplify the problem. Second, and more important, the arrays for your chi(k) data is not on a uniform k-grid with delta k = 0.05 Ang^-1. In fact, it looks like it there are many repeated k=0 values at the beginning of chi(k) array. I think this is screwing up the taking of the residual for the following reason: The fit in the feffit() command itself does not require the data to start out on a uniform or delta_k=0.05 grid, but it does internally put the data on such a grid, and does calculate the best-fit chi(k) on this grid. Anyway, the point is that Artemis is subtly assuming the chi(k) data is on this grid when it calculates the residual. It simply subtracts the best fit .chi array from the data .chi array, which is done point-by-point. If the data and fit are not on the same k-grids, the subtraction is pretty much useless. A long-term improvement in Artemis could be to make sure the Data and Fit are on the same grid for calculating the residual. A more immediate fix for you would be to save the chi(k) data on the standard chi(k) grid. Here's one way to do that: 1 In Artemis, click the Data and do File->Save Data as... chi(k). note that this file will contain all the data, including the repeated zeros, and the non-uniform grid. 2 Read this file into Athena (where you'll be warned about the repeated values of 0), and save it as chi(k). This will be on the standard delta_k=0.05 grid. 3 Use this data in Artemis. Hope that helps, --Matt
Well it looks like I will be at the APS from the evening of the 14th until the 23. I was hoping I might stop by and say hello to you and perhaps buy you (and Bruce and Julie) a beer (Charlotte is going to have to get by on milk) while I am there. In any case, see you soon. Paul Dr. Paul Fons Senior Researcher National Institute for Advanced Industrial Science & Technology METI Center for Applied Near-Field Optics Research (CANFOR) AIST Central 4, Higashi 1-1-1 Tsukuba, Ibaraki JAPAN 305-8568 tel. +81-298-61-5636 fax. +81-298-61-2939 email: paul-fons@aist.go.jp The lines below are in a Japanese font 〒３０５−８５６８ 茨城県つくば市東１−１−1 つくば中央第４ 近接場光応用工学センター ポール・フォンス主任研究官
Sorry about the noise. I will be more careful when I hit the reply button in the future....
participants (4)
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Matt Newville -
Paul Fons -
TAO,Ye -
yetao＠chem.uga.edu