On 3/09/2011 10:43 PM, bruceravel1@gmail.com wrote:
Niken Wijaya writes:
Hi Everyone,
I am facing a lot of problems when I am trying to fit my sample's spectra with my standards one. Initially, I used Athena to do the background subtraction, but the fitting results are just too "funny". The fitting does not really fit the actual spectra. Since I am analyzing Sulphur and many papers has reported how it is prone to self-absorption effect, I thought, probably if I am using a better background subtraction such as MBACK, I would get a better results. So I decided to use it for the normalization and unlike in Athena, the normalized intensity of the spectra does not equal to 1. By saying this, the intensity of my standard models is way higher than the actual samples. Hence, when I use Athena to fit my real spectra, I would not get a good results. I have also tried using the 3rd derivative of my absorption spectra, but the fitting results are even worse. The intensity of the "fit" spectra is way higher than the actual spectra of my samples that I am trying to fit it with. In fact, when I stack the spectra from the standards and the sample together, the 3rd derivative peak of the samples is almost completely flat due to the very high intensity of the standards themselves.
What did I do wrong? and what can I do to fix it? I have also attached my samples and standards spectra.
Thank you very much for the assistance.
Hi Niken,
It's a little hard to know what's going on. The reason that we like having Athena project files attached to these postings is because it is then much easier to evaluate the provenance of the problem. That is, the Athena project file retains some of the history of the data. We can evaluate how you have processed the data to arrive at the point of having a problem with the analysis.
Given the text files you have attached, it is very difficult to know how to advise you because it is very difficult to understand the problem you are having. I know that you tried to explain the problem, but a picture is, as they say, worth a thousand (unlear, slightly rambly) words.
That said, I do have a few comments.
1. There are good reasons to use an algorithm like MBACK rather than the simpler pre- and post-edge normalizaton that Athena offers. Fixing the problem of self-absorption is not one of those reasons. Self-absorption makes the fine structure oscillations smaller. No normalization algorithm will magically undo that problem.
Although Athena (or other software) might have a tool for correcting self-absorption, the only really good way of dealing with that problem is to not have it inthe first place. For some samples, self absorption is unavoidable. But if it is possible to modify your sample to minimize that effect, then you should most certainly do so.
2. The third derivative might be a useful tool, as you say. It is, however, esential that you make your Nth derivative spectrum (regardless of the value of N) on normalized data or else the data you examine will not be on the same scale. Another issue with high order derivatives is that they tend to amplify the size of the noise with respect to the signal. One of your spectra has that problem. Analysis of derivative spectra is one of the few situations in which I think that smoothing is helpful and defensible.
If you choose to pursue this issue further here on the mailing list, I encourage you not only to add a project file, but to avoid the sort of fuzzy language you used in this posting. Saying things like "funny fitting results" and "way higher intensities" is just to unclear and subjective. It often helps to attach a screenshot to better demonstrate what you are trying to say.
B
Hi Bruce, Thank you for the comments. Attached is the project files and the figure. Here are the problems and comments I am having right now. 1. As you can see on the figure (i.e. filename: ifeffitlist-sample1 fitting), the intensity of the fitting spectra is higher than the actual sample. This is I believe due to the higher intensity of the individual standard compounds when compared to the spectra of my samples (i.e. filename: ifeffitlist-intensity). This is the case for every fitting I did for my sample so I am just not sure with the fitting results. 2. If we see figure "ifeffitlist-sample39", we can see that the spectra has different slopes on the pre and post-edge region. When I used MBACK for background removal, the normalized spectra is weird, illustrated in "sample39-fig-norm.pdf". What is the best way to fix this issue? I have 5 samples with this feature that I cannot process due to the weird normalized spectra. 3. Regarding the self-absorption correction, I was not aware that Athena has this function. I will have a look at the manual again. Thank you for letting me know. 4. With the 3rd derivative spectrum, I did indeed derive it from the normalized values. As you can see from the file I attached earlier, from the experts points of view, do you think I should go on with the Nth derivative spectra or due to the very low signal-to-noise ratio of the spectra, I should just focus on the absorption spectra? Again, thank you for the invaluable inputs. Regards, Niken