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Not able to read in wavelength unit with MUSE data cubes? #2502
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Thank you for reaching out to us.
Are you able to get anything useful only using specutils? https://specutils.readthedocs.io/en/stable/ from specutils import Spectrum1D
sp = Spectrum1D.read(filename)
sp.spectral_axis # check the printed unit
Can you please clarify what you were doing when you saw the lag? Is the lag temporary or persistent? |
Also to be sure I am not misunderstanding, is there an extra period in your CUNIT3 value? You said |
Thank you so much for your response! Trying to read my fits file using specutils throws me the following error:
And, apologies, autocorrect threw the period in there. It's CUNIT3='Angstrom' |
It lags on the order for 3-10s whenever I try to use any of the plugin tools. I have had to refresh my page a few times, as well. |
I think to effectively debug this, we would need a copy of the data or something equivalent if the original data is not public. Is this from VLT MUSE archive or something? How are we able to get a copy? Thanks. |
Thanks! Looks like the cube is a whooping 3 GB.
|
First of all, the slider tool is broken because of the wonky wavelength axis in spectrum viewer. Still investigating why spectral axis won't load. Looks like Cubeviz isn't using Secondly, any tool that results in re-collapsing the cube (e.g., drawing a circle on the image viewer) would be laggy. Otherwise, if I just pan/zoom on the image, I do not see any lag, so please be more specific on what tool you were using and how. Maybe would also be helpful to pull up your OS memory monitoring app to make sure it is not memory swapping. This is because to collapse a 3 GB cube for the spectrum viewer would require pulling in the whole cube into memory; I saw my RAM usage jump a whole 20% during that process on load (and also waiting a long time for it). |
Okay, great, thank you for checking. Ahh, gotcha. Yes, I was trying to draw circles and to select a spectral region so that makes sense. Thanks for clearing that up. |
So, I fixed the unit in #2504 (feel free to try it out if you know how to install Jdaviz from an unmerged PR branch). Unfortunately the performance issues are real and not trivial to fix, so I will bring them back to the team and add info to your original post above. Thank you for reporting this! |
This issue is tracked on JIRA as JDAT-3884. |
Two problems
Jdaviz component
Cubeviz
Description
Hi,
I'm trying to analyze VLT MUSE data cubes and I'm running into a problem where cubeviz is unable to recognize the wavelength units from the fits header. Opening the cube in DS9 allows me to toggle through the different wavelength bins, and looking at the header, the unit is given in CUNIT3='Angstrom.'
I was going to see if this was a display issue by trying to use the unit conversion functionality detailed in the documents, but that option is unavailable to me in the GUI (see screenshot in how to reproduce).
Also, is Cubeviz supposed to lag a bit?
Thanks for your help,
Kelly
How to Reproduce
See screenshot.
Expected behavior
I expected to be able to have the tab for unit conversion
Browser
No response
Jupyter
jupyter notebook version 7.0.2
Software versions
No response
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