Atmospheric telluric lines on ISIS

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David Cejudo
Posts: 45
Joined: Mon Apr 23, 2018 9:01 pm

Atmospheric telluric lines on ISIS

Post by David Cejudo »

Hello.

I am still fighting to fully understand how to use ISIS. I found another problem.
After processing the spectrum, i get the telluric lines at the red part of the spectrum as emision lines, obviously wrong.
In the next image, the blue filter, processed with ISIS shows some of those lines. On the other hand, the same one processed with Demetra -green spectrum- does not. It seems Demetra is doing a better job.
ISIS vs Demetra.jpg
ISIS vs Demetra.jpg (41.82 KiB) Viewed 3546 times
I found out that the aparition of those lines depends on how the instrumental response is built.
In Demetra, in the "Instrumental response builder", there is the option to tick or not the button "Atmospheric lines". I always leave it ticked ON, as then, when the reponse line is fitted, the area of the instrumental response where the atmospheric lines is will stay flat. While if i untick it OFF, that line shows waves and the resulting spectrum will result with atmospheric lines on emission. See the next attached image. The inset shows how the instrumental response, at the red end of the spectrum, will look if "Atmospheric lines" is not ticked.
Demetra response.jpg
Demetra response.jpg (43.62 KiB) Viewed 3546 times
I did not find how to do this same and simple procedure with ISIS, while Demetra makes it very simple.
Building the instrumental response with ISIS, if the curve is properly fitted, the atmospheric lines area is not correct. With the following curve the final spectrum will show those atmospheric emissions.
ISIS response atmo wrong.jpg
ISIS response atmo wrong.jpg (36.9 KiB) Viewed 3546 times
While to fit the curve in the atmospheric area correctly, the rest of the curve will be poorly fitted.
ISIS response fit wrong.jpg
ISIS response fit wrong.jpg (32.21 KiB) Viewed 3546 times
I already tried many fittings to arrive at a good final result but i did not manage to achieve it.

I found a workaround, though. I just build the response with Demetra and afterwards i use this response in ISIS, instead of building it with ISIS directly.

Anyway i would like to do all with ISIS directly, but i did not find out how. I am probably missing a step here.
Any advice would be most welcome.
ISIS learning curve is very very steep indeed!
David Cejudo.
Observatorio El gallinero.
El berrueco, Madrid.
Robin Leadbeater
Posts: 1926
Joined: Mon Sep 26, 2011 4:41 pm
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Re: Atmospheric telluric lines on ISIS

Post by Robin Leadbeater »

In ISIS you crop out the parts of the spectrum you do not want to appear in the response before fitting a smooth curve. (Double click at the start and end of each region) This is typically used to remove the Telluric band but also for example any residual Balmer lines which have not exactly divided out. This makes it very flexible. (Demetra must do something similar but perhaps automatically)

The flexibility of ISIS means you can remove exactly the regions you do not want to include and you can smooth the profile by exactly the amount you need without losing the important detail in the response. The test that the resulting response is correct is to run the reference star spectrum again using the calculated response. If the response is correct the result should closely match the spectrum from the library (except that the resolution may be different and the measured spectrum will have Telluric bands in it) For example this is what my typical ALPY600 response looks like
alpy600_response.png
alpy600_response.png (15.96 KiB) Viewed 3524 times
Cheers
Robin
Last edited by Robin Leadbeater on Wed Sep 21, 2022 10:19 pm, edited 1 time in total.
LHIRES III #29 ATIK314 ALPY 600/200 ATIK428 Star Analyser 100/200 C11 EQ6
http://www.threehillsobservatory.co.uk
David Cejudo
Posts: 45
Joined: Mon Apr 23, 2018 9:01 pm

Re: Atmospheric telluric lines on ISIS

Post by David Cejudo »

If i crop out the telluric lines area, the final spectrum will not show that area neither.

Demetra does not crop it out. It just smoothes that area with a filter, i guess. I can also use a filter in ISIS but it will smooth the whole response spectrum, not just an area.
With Demetra, the final spectrum shows the atmospheric absortion lines. It does not crop it.
David Cejudo.
Observatorio El gallinero.
El berrueco, Madrid.
Robin Leadbeater
Posts: 1926
Joined: Mon Sep 26, 2011 4:41 pm
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Re: Atmospheric telluric lines on ISIS

Post by Robin Leadbeater »

David Cejudo wrote:If i crop out the telluric lines area, the final spectrum will not show that area neither.
ISIS puts a smooth line through the missing parts when it produces the response curve. It is important that you have some way of removing the bad parts otherwise you have to do too much smoothing.

Here is another example
alpy600_flux_calib.png
alpy600_flux_calib.png (20.72 KiB) Viewed 3519 times
green is the calculated response.
blue is the spectrum with the response applied
red is the library spectrum.
You can hardly tell the difference between the measured and library spectrum except at the telluric bands. This is an example of how good a result you can get using ISIS
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Robin Leadbeater
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Re: Atmospheric telluric lines on ISIS

Post by Robin Leadbeater »

If you want to remove the Telluric bands, you should not try to include them in the response. You should remove them in a separate step using a separate telluric band template. This is not easy to do with low resolution spectra so the bands are usually left in. It is easier to do at high resolution though where the individual telluric lines can be seen and ISIS has a tool separate tool to do this. Some databases (eg BeSS) prefer the tellurics to be left in even in high resolution spectra. The end user can then remove them if they want.

Cheers
Robin
LHIRES III #29 ATIK314 ALPY 600/200 ATIK428 Star Analyser 100/200 C11 EQ6
http://www.threehillsobservatory.co.uk
David Cejudo
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Joined: Mon Apr 23, 2018 9:01 pm

Re: Atmospheric telluric lines on ISIS

Post by David Cejudo »

I understand the procedure. I reckon it can not be done in the "profile" tab.
In "calibration" tab there is a "response assistant" button. Using this seems to work pretty well.

I tried and obtained this comparison between the result and the Mile's spectrum.
Comparison.jpg
Comparison.jpg (64.69 KiB) Viewed 3504 times
I am not sure if this is correct as the spectra are similar but with different intensities. The telluric lines now look fine, though.
David Cejudo.
Observatorio El gallinero.
El berrueco, Madrid.
Robin Leadbeater
Posts: 1926
Joined: Mon Sep 26, 2011 4:41 pm
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Re: Atmospheric telluric lines on ISIS

Post by Robin Leadbeater »

David Cejudo wrote:I understand the procedure. I reckon it can not be done in the "profile" tab.
Yes it can all be done from the "Profile" tab using the "Response" and "Continuum" functions on the right. (I prefer to do it manually rather than use the assistant as it gives better control of the result)

I have made a document with screen shots showing the steps (zipped pdf file attached)

Note this was done using ISIS 5.9.3 which corrects for the black body curve of the flat lamp. Later versions do not do this. I prefer this version as it has the advantage of showing the response shape without the effect of the flat lamp spectrum, removing the large hump at the blue end which can be difficult to fit a curve to

Cheers
Robin
ISIS_response_instructions.zip
(1.08 MiB) Downloaded 111 times
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David Cejudo
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Re: Atmospheric telluric lines on ISIS

Post by David Cejudo »

Thanks, Robin.

I was missing the step "First crop the bad regions by double clicking either side of them."
David Boyd pointed me to this and then again your instructions are crystal clear!

My processing seems to be fully working at last.
David Cejudo.
Observatorio El gallinero.
El berrueco, Madrid.
Robin Leadbeater
Posts: 1926
Joined: Mon Sep 26, 2011 4:41 pm
Contact:

Re: Atmospheric telluric lines on ISIS

Post by Robin Leadbeater »

David Cejudo wrote:
I was missing the step "First crop the bad regions by double clicking either side of them."
Yes I mentioned this at the start
http://www.spectro-aras.com/forum/viewt ... 026#p17246

Cheers
Robin
LHIRES III #29 ATIK314 ALPY 600/200 ATIK428 Star Analyser 100/200 C11 EQ6
http://www.threehillsobservatory.co.uk
Terry Bohlsen
Posts: 191
Joined: Thu Sep 29, 2011 7:40 am

Re: Atmospheric telluric lines on ISIS

Post by Terry Bohlsen »

Hi David
I made some instructions for using Isis some years ago but the place I put it on the web no longer exists. It was made for a LISA but the process is very similar for any low resolution spectrograph.
I have saved a pdf version to dropbox that should be available here
https://www.dropbox.com/s/1qbgxkkq8rieq ... s.pdf?dl=0
This might explain the process better.
Terry
Terry Bohlsen
Armidale NSW
Australia
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