jdaviz: Fix bug when loading level 2 nirspec MSA spectra into mosviz

Reporter: Erik Tollerud

While trying to load a level 2 nirspec MSA file from MAST into mosviz, I got a curious error: mosviz.load_spectra(results['Local Path'][1], results['Local Path'][0]) IORegistryError: Format could not be identified based on the file name or contents, please provide a 'format' argument.

Tracing this a bit further, I tried loading the file as a Spectrum1D and got: specutils.Spectrum1D.read(results['Local Path'][1], format='JWST x1d')

which yielded a more useful error: RuntimeError: Input data has 71 spectra. Use SpectrumList.read() instead. which makes sense, so I then did specutils.SpectrumList.read(results['Local Path'][1], format='JWST x1d') which yielded the exact same error, which does not make sense!

I can provide the file to reproduce if needed, but would have to be via private message because it’s currently proprietary data. (and probably any NIRSpec MSA level 2 files will do? So there might be something public that can be tested on.)

DISCLAIMER: This issue was autocreated by the Jdaviz Issue Creation Bot on behalf of the reporter. If any information is incorrect, please contact Duy Nguyen

About this issue

Original URL
State: open
Created 2 years ago
Comments: 17 (9 by maintainers)

Most upvoted comments

Loading level 2 nirspec data is part of the grand scheme for mosviz, but we are not there yet.

camipacifici on Oct 31, 2022

But to make things more interesting, specutils does grab GWCS depending if your logic goes to the correct loader…

https://github.com/astropy/specutils/blob/695e475ca392eb1c5be8cfff30b144239b777136/specutils/io/default_loaders/jwst_reader.py#L422

pllim on Oct 28, 2022

Ah, asking Mosviz to do this would be a new feature request and should be a separate ticket – cc @camipacifici

from specutils import SpectrumCollection
from jdaviz import Mosviz

sc = SpectrumCollection(blah)

mosviz = Mosviz()
mosviz.load_data(sc)

pllim on Oct 28, 2022

I tracked this down - it’s because for some reason SpectrumCollection.meta defaults to None instead of an empty dict. So I manually set it, and then ran into another problem where the mosviz loader does something.meta = something_else, and SpectrumCollection doesn’t allow setting of meta, which I fixed by just using.update instead. I can make a PR for just that, but it still doesn’t solve the problem because then I get:

TypeError: Could not find a class to translate objects of type SpectrumCollection to Data

Which is pretty clear, but surprising to me: how do we even show 2D spectra that are not rectified without a SpectrumCollection adapter?

eteq on Oct 28, 2022