configuring .read() functions for IGRINS retell files

[ericasaw]

Hi Gully, I've been working on refining the IGRINS plp reductions using a legacy script. In that script, the SNR 's are written to an additional HDU extension named "SNR". I was wondering if there was a way to change the statement on line 199 of igrins.py to be another try/except statement that checks the .spec_a0v.fits file for a "SNR" extension before raising an error. Like

try: 
 sn_hdus = fits.open(sn_file, memmap=False)
 cached_hdus = [hdus, sn_hdus]
except FileNotFoundError:
  try:
    #just to test if the SNR extension exists
    sn_hdus = hdus['SNR'] 
    cached_hdus = [hdus[:-1], sn_hdus] #SNR is always the last extension in the new files
  except KeyError:
    #raise error about no .sn file or SNR extension

or something of the sort. Let me know what you think!

[gully]

Thank you @ericasaw for opening an Issue! 🙏

@kfkaplan and I started an overhaul to the IGRINS uncertainty in Issue #89. Do you know to-what-extent that proposed fix could address your Issue?

It sounds like you are working with a custom script, so my suspicion is that the Pull Request does not achieve your goals. Would you be open to making a pull request to address your use case?

We should consider finishing and merging #89 at some point because it makes the SNR more accurate and supports wider use cases.

[kfkaplan]

The IGRINS PLP should output .spec.fits and .variance.fits files for the flux and variance. I highly recommend you use those files to read into muler. If you are using an older version of the IGRINS PLP, I recommend you update to the latest version and re-reduce your data.

[ericasaw]

@kfkaplan The reduction is in addition to using the IGRINS PLP, a step afterward, the output is different than the IGRINS PLP output. The script I am using checks the pixel alignment between the standard star and the target using a strong telluric feature and shifts so the pixels are aligned. Usually, the offset is small and negligible, but sometimes it can provide some good SNR improvements for reduced data.

[kfkaplan]

Ah I see. In that case, I would go with @gully's suggestion that you make the changes you need to Muler and submit them as a pull request. Alternatively, your custom script could output modified files in the same format as the IGRINS PLP that Muler could then read in.

[kfkaplan]

Also I almost forgot, this sounds very similar to my IGRINS A0V corrector code which shifts pixels to correct for flexure (https://github.com/kfkaplan/IGRINS_A0V_corrector).

Feel free to use it as an example or copy code from for outputting modified files in the IGRINS PLP format.