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Hi
Thanks, sounds good. I need to find the time to give this site an up-to-date treatment, and this may prompt me into doing that.

cheers
katrina

by katrinamaxkatrinamax, 24 Mar 2017 12:12
John Beckman (guest) 24 Feb 2017 21:28
in discussion Hidden / Per page discussions » Reducing Data from Fabry-Pérot Spectrographs

I have just found this wiki site. My group runs the GHaFaS Fabry-Perot IFS on the William Herschel Telescope, La Palma. We should prepare some notes on reduction and analysis of our data, as we have considerable experience and good results. I commit to doing this within the next couple of months. The GHaFaS website is also underpopulated, but we are just about to put our data archive on, and will offer help in handling the data to prospective users. Efficient use of FP data is not as formidable as it was, say a decade ago. There is now good purpose designed software. I'll get back to this page when I can.

by John Beckman (guest), 24 Feb 2017 21:28

Hi
I vaguely remember how this is done. If you want to fix the FWHM for any Gaussian you can do it in the panel where you define the Gaussian parameters. If you want to fit many Gaussians at the same time and fix their FWHM each also, I think you need to define a new model, which is a combination of Gaussians, and in which you can either fix parameters or tie them to each other (fwhm of gauss1 = fwhm of gauss2). I don't have PAN on my laptop, but if you cannot work out yourself how to do this, I could see if I can install it and try to remember how it was done.
Katrina

I am using PAN - Peak Analysis. Does anybody know how to fit multiple gaussians but fixing FWHM ?

Multiple Gaussian Fitting by Reinaldo (guest), 06 Oct 2015 18:20
Re: extracting wavelength calibration from .FITS by Becky (guest), 19 Aug 2010 09:48

Ha,

so, in iraf I simply added in/made sure were there (with "ehead") the following fits-headers
CDELT1/2/3 (dispersion)
CRVAL1/2/3 (1st value)
CD1_1/2/3 (dispersion also)
CTYPE1/2/3 (being 'RA', 'DEC', 'Lambda')
and qfitsview is happy with that
I don't know which one(s) did the job, but all together certainly did
my data have axes of RA, Dec, wavelength, in that order. so if doing this on other cubes does not work, then I guess maybe the cubes have to be organised in that order

Re: extracting wavelength calibration from .FITS by katrina (guest), 03 Aug 2010 16:52

I didn't try very hard to get it to work. I am wondering whether it is because qfitsview expect the wavelength array to be a particular one of axis 1 2 or 3, but I have not looked into the code to see. I'll have another poke about later this week

Re: extracting wavelength calibration from .FITS by katrina (guest), 03 Aug 2010 16:06

Hi Katrina,

I was wondering if you managed to fix the wavelength scale problem in Qfitsview with VIMOS data? I'm having the same problem, I usually just use idl to look at the cubes but Qfitsview seems like a handy tool for a quick look at the data.

Cheers,

Becky

Re: extracting wavelength calibration from .FITS by Becky (guest), 30 Jul 2010 16:10

I don't have vipgi cubes in front of me, but the wavelength information, along with the spatial information, is usually stored in the fits header entries CDELT1/2/3, CRVAL1/2/3. The first is the dispersion, the second the starting wavelength. There may also be something including "PIX1/2/3", which indicates to which pixel the CRVAL refers (usually 0/1 but sometimes not).
I'm curious - our vimos cubes don't display the wavelength scale in QFITSVIEW, can you tell me what CDELT1/2/3 and CRVAL1/2/3 values you have in your fits header? I am wondering if our cubes are just the "wrong way around", so-to-speak.
I have always just created the wavelength array in IDL from these information, I am not sure if any of the fits readers of IDL do this. It would make sense if there were one!

Re: extracting wavelength calibration from .FITS by Katrina (guest), 18 May 2010 08:41

I've been reducing data with VIPGI, which I have now exported to a FITS datacube. When I open the cube with a program like QFitsView, the spectrum for each spaxel is displayed along the bottom of the window when I mouse over the corresponding region of the image, along with the axis scale calibrated to wavelength. Obviously then, the wavelength calibration must be stored somewhere in the FITS header or something.

However, I am performing most of my data analysis and manipulation in IDL and Matlab. Importing the datacubes with the standard fitsread functions does not automatically recognise this calibration, and when I plot spectra, they are calibrated to pixel number. I pretty much expected that this would be the case, but my question is, how does one extract the wavelength calibration from the FITS file? Are there any tools to do this in IDL for datacubes? Failing that, where abouts in the FITS header is this information stored?

Any help or info would be most appreciated…

extracting wavelength calibration from .FITS by Craig (guest), 18 May 2010 06:02

OK, thanks for that Katrina. I'll have a bit more of a think about my options. If I have any more questions, I'll be back!

Re: Subtraction of sky from object frames by NewToIFU (guest), 23 Apr 2010 03:28

I've not actually used Slink Datacube before, but since I work on data where the sky is either taken from the astro FoV (eg VIMOS) or is taken from a few isolated spaxels that where placed around the target's FoV (eg GMOS), I always simply make the best sky spectrum (singular) I can (using eg iraf or qfitsview or IDL), then I scale that spectrum to each and every astro spaxel (usually on the 5577 sky line flux, and I do this if I suspect that there are variations in the sky flux across the FoV, tho actually that should have already been corrected for), and subtract it (again using IDL or iraf).

Whether you do this by subtracting a single spectrum (scaled) from a cube, or make a cube of the same size as the astro cube but containing all the sky spectra (scaled), does not really matter - whichever is easier.

So basically, you've got the right idea but everyone I know always does it "manually". I'm using python now to do that. Once I have a script, it works for all subsequent datasets. But I alway check afterwards, as even small changes to the spectral PSF with spaxel will result in sharp residuals in the sky-subtracted spectra, tho this is usually only a problem when I am working in the Ha or red [OI] region.

Re: Subtraction of sky from object frames by katrina (guest), 22 Apr 2010 11:48

Hmmm - first post in the forum ever. Not an encouraging sign but here goes anyway.

I am wanting to subtract sky frames from my object frames for my IFU data. I was going to do this by taking my sky frames and averaging the sky spectra over each frame, for all of the frames that I have. Then I was going to subtract this from my object frames to get the sky subtracted datacubes.

My question is - is the Starlink Datacube package capable of doing this? I've been reading the documentation, and it does seem to have the functionality for averaging groupings of spectra and plotting the results, but it doesn't seem to say anything about whether one can average the spectra and then go on to use the results to add/combine/subtract from other datacubes. Is it possible? Is there any other program out there that would be better for this function?

Subtraction of sky from object frames by NewToIFU (guest), 21 Apr 2010 12:18

CR rejection, expected dead fibres, mis-match problems between the quadrants (flux, wavelength)

info needed by westmoquettewestmoquette, 07 Jul 2009 17:49

Welcome to this Forum for discussion on all things IFS :-) We hope that people will post here comments on anything to do with Instruments and their pipelines, be it queries, comments on what is in this wiki, small contributions you want to make but where you don't want to actually join this wiki, and the like. At the end of most pages on this wiki is also a "comment" section, in which you can also post comments. Every now and then Mark and Katrina will check this forum and answer any unanswered questions (if they can!) and take note of any comments.

Please feel free to not only post yourself, but also to reply to those of others.

muchas gracias!

Welcome by katrinamaxkatrinamax, 12 May 2009 13:24

Welcome to this Forum for discussion on all things IFS :-) We hope that people will post here comments on anything to do with data reduction and analysis issues, be it queries, comments on what is in this wiki, small contributions you want to make but where you don't want to actually join this wiki, and the like. At the end of most pages on this wiki is also a "comment" section, in which you can also post comments. Every now and then Mark and Katrina will check this forum and answer any unanswered questions (if they can!) and take note of any comments.

Please feel free to not only post yourself, but also to reply to those of others.

muchas gracias!

Welcome by katrinamaxkatrinamax, 12 May 2009 13:22
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