Issue with Peak Parameters and Fityk Plot vs Exported Data or Points

[Chris Ryder]

Hi Fityk Users,

I am a new user of the software and have found it to be a great tool. While fitting Raman peaks with Lorentzians, hwoever, I encountered an issue:

1. I do a baseline spline subtraction of the data and fit to Lorentzians
2. Once the plot looks like the sum of the component functions match the data well (see attached fityk1.png) I export the fitted data
3. Once I plot the fit components and sum against the data there is a clear mismatch in the peak heights
4. I investigate the exported points and find a large discrepancy in the peak height of the component function and the sum at the global maximum of the data. (fityk2.png)
5. The peak parameters look correct. (fityk3.png)

Any help would be appreciated. I hope there is something simple that I am missing, as I have really enjoyed using the software so far.

Thanks,

Chris

[Dan Parshall]

Can you make a script (.fit) file that reproduces the problem?  My first guess is that you aren't handling the background subtraction correctly when you replot the data, but I can't be sure.

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Dan Parshall
Shorty George Productions
Boulder, CO

[Chris Ryder]

Hi Dan,

Thanks for your quick response. I have attached a file that has the data, background, and fits that I (unsuccessfully) export from. I have recently subtracted backgrounds from other data and the output files clearly represent this on all of the data and fits, although in this case it was a linear subtraction.

Best,

Chris

[Dan Parshall]

I can't see the problem.  Please describe it in more detail.  Better yet, provide a .fit file that has 2 separate datasets

1) the raw data + BG function + peaks

2) the BG-subtracted data + peaks

I'm glad to help, but the onus is on you to provide a clear and minimal example of the problem.  Odds are very high that in the process of providing that clear and minimal example, you will solve the problem yourself.  But if not, at least we will then be in a position to help you.

[Francisco Gonçalves]

Hi Dan,
I am running 0.9.4 on windows7 and I am trying to write a script that
saves all peak info's from all the datasets(100 datasets, each with 2
gaussians).
I tried following some of the examples available but I'm struggling
with he syntax.

Thanks in advance.
francis

Regards,
Francisco

[Chris Ryder]

Hi Dan,

Thanks for your help so far. From the Fityk file that I posted, it is pretty simple to replicate the issue by outputting the fit, however, yes I agree that it is my responsibility to make it clear. Here is another .fit file that should have everything and should make it clear. In particular, if you zoom in on the peak at ~467 cm-1 (the highest intensity peak), you can see how the fit on the bg subtracted data looks more or less correct, if you then view the output of the fit as it is re-plotted back in fityk, you can see that the peak does not match the bg subtracted data. I have included the raw data and the bg subtracted data for reference as well.

Thanks,

Chris

[Marcin Wojdyr]

I'm a bit late to reply to this:

> I am running 0.9.4 on windows7 and I am trying to write a script that
> saves all peak info's from all the datasets(100 datasets, each with 2
> gaussians).

I don't remember how it was in 0.9.4, now it's:
@*: info peaks >> my.peaks
If you'd like to export it in different format, give an example of the
output you'd like to get.

Marcin