Error on command line option with Gemini GMOS 2D spectrum

[Karuntg]

Hi Chengyuan
I am testing Cosmic-Conn for CR masking on Gemini-S GMOS 2D spectrum

When I tried the command line option:

cosmic-conn -i cr_tst -e SCI

INFO:root:Initializing Cosmic-CoNN CR detection ground_imaging model...

INFO:root:...GPU or CUDA not detected, using CPU (slower).
INFO:root:...training on CPU is not recommended.
INFO:root:ground_imaging model initialized.

1 FITS found in cr_tst
ERROR:root:No valid data found in extention 0, 1 or SCI, to specify extension name: -e SCI.

GMOS fits has the SCI extension in extension 2. I tried -e 2, but still no success

I have posted the 2D spectrum at:
https://www.astro.uvic.ca/~karun/tgsqgsS20221115S0065.fits
if you wish to try

pls advise. I also embedded cosmic-conn in a py script, but am getting a different error, will post it as a separate issue
thx
karun

[cy-xu]

Hi Karun,

Thanks for providing the sample file, which helps identify the problem.

It turns out that this file's SCI extension name is a string with extra spaces in it. I found out by checking its header info in DS9. So I managed to process the file successfully with the following command (note the quotation marks to include the two spaces) --

cosmic-conn -i tgsqgsS20221115S0065.fits -e "SCI  "

Then you should be able to check the processed file in the "cosmic_conn_output" directory --> Open as "Multiple Extension Frames" --> the CR mask is appended in a new frame with the extension "CR_PROBABILITY".

If this is a common issue in other GMOS fits as well, I will make a simple update in the package to handle this.

Thanks for reporting the issue!

Best,
CY

[Karuntg]

Great, thanks a lot, CY! Given this header issue in the GMOS fits, and perhaps with fits files from other instruments too, perhaps, after reading the header of each fits extension, Cosmic-cnn could use, sci_header.strip() before comparing? I am sure you have a neater way of addressing this

On a related note, why didn't the option, -e 2 for extension 2 not work? just curious?
thx
karun

[Karuntg]

Great, thanks a lot, CY! Given this header issue in the GMOS fits, and perhaps with fits files from other instruments too, perhaps, after reading the header of each fits extension, Cosmic-cnn could sci_header.strip() before comparing? I am sure you have a neater way of addressing this On a related note, why didn't the option, -e 2 for extension 2 not work? just curious? thx karun

…

________________________________ From: CY Xu ***@***.***> Sent: Wednesday, April 5, 2023 3:30:44 PM To: cy-xu/cosmic-conn Cc: Karun Thanjavur; Author Subject: Re: [cy-xu/cosmic-conn] Error on command line option with Gemini GMOS 2D spectrum (Issue #11) Hi Karun, Thanks for providing the sample file, which helps identify the problem. It turns out that this file's SCI extension name is a string with extra spaces in it. I found out by checking its header info in DS9. So I managed to process the file successfully with the following command (note the quotation marks to include the two spaces) -- cosmic-conn -i tgsqgsS20221115S0065.fits -e "SCI " Then you should be able to check the processed file with DS9 or another software you like --> Open as "Multiple Extension Frames" --> the CR mask is appended in a new frame with the extension "CR_PROBABILITY". [Screenshot 2023-04-05 at 3 21 02 PM]<https://user-images.githubusercontent.com/24612082/230225840-b15b4b94-2f80-4f47-83e1-ebcd15160a33.png> If this is a common issue in other GMOS fits as well, I will make a simple update in the package to handle this. Thanks for reporting the issue! Best, CY — Reply to this email directly, view it on GitHub<#11 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AB4RODK7BQYTSWQ7RQSHUYDW7XXBJANCNFSM6AAAAAAWTTKOQQ>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[cy-xu]

Hi karun, sorry for the late reply. We had a baby girl four weeks ago, and I am behind on many things. What you suggested seems like a straightforward fix. Please feel free to make a pull request! Also please suggest other features or improvements to make the tool easier for you and other astronomers! Thanks!

Best,
CY