Stage 3 optical spectrum extraction and obtaining 2-D Spectrum plot with a linear wavelength x-axis for NIRSpec G395H

[kohhei315]

Instrument

NIRSpec (Stages 1-3)

What happened?

I am currently Running Stage 3 of Eureka! Pipeline, specifically in generating 2-D spectrum plot with linear wavelength x-axis. It seems that the normalized flux from integration number 0 to 155 only has a value in the wavelength around 2.8 μm (x-axis is from 2.8 ~ 3.8 μm) shown in the given png file. However, it must have some flux in all the region across x-axis (wavelength). I thought that the results from optimal spectrum extraction contributes to this error and so I would like to also provide my results for optimal spectrum extraction below.

I will also provide some details of the code below during optimal spectrum extraction.

Performing optimal spectral extraction...
  0%|                                                   | 0/155 [00:00<?, ?it/s]
Figure(800x400)
...
  1%|▎                                        | 1/155 [00:32<1:22:12, 32.03s/it]Figure(800x400)
...
100%|█████████████████████████████████████████| 155/155 [20:02<00:00,  7.76s/it]
  Creating figures for optimal spectral extraction
  0%|                                                     | 0/5 [00:00<?, ?it/s]Figure(640x480)
 20%|█████████                                    | 1/5 [00:00<00:03,  1.16it/s]Figure(640x480)
 40%|██████████████████                           | 2/5 [00:01<00:02,  1.21it/s]Figure(640x480)
 60%|███████████████████████████                  | 3/5 [00:02<00:01,  1.22it/s]Figure(640x480)
 80%|████████████████████████████████████         | 4/5 [00:03<00:00,  1.16it/s]Figure(640x480)
100%|█████████████████████████████████████████████| 5/5 [00:04<00:00,  1.19it/s]
Figure(800x400)

Error traceback output

No response

What operating system are you using?

macOS Sonoma 14.5

What version of Python are you running?

Python 3.11.9

What Python packages do you have installed?

# Name                    Version                   Build  Channel
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Code of Conduct

• I agree to follow this project's Code of Conduct

[kevin218]

It looks like most of your pixels are getting flagged as bad. You can start by adjusting the settings in your Stage 3 file to get cleaner results.

[taylorbell57]

I agree with Kevin that this is likely not a bug with Eureka but more likely an issue with how you have setup you ECF. I recommend you look carefully at all of your plots and ECF settings to try to troubleshoot the issue yourself. I recommend you set isplots_S3 to 5 and nplots to 5 so that you get several useful troubleshooting plots. And to help you understand the ECF settings, please take a look at our documentation at https://eurekadocs.readthedocs.io/en/latest/ecf.html

If you're still unable to resolve the issue yourself after carefully looking at all the plots and ECF settings, can copy-paste the contents of your Stage 3 ECF; that'll make it easier for us to help you troubleshoot

[kohhei315]

Thank you for your suggestions. I will change some settings in stage3 ecf files and redo the process. I will let send the details about my defined parameters in ecf if I have more troubles in the output results.

[taylorbell57]

@kohhei315, were you able to resolve this issue? Since we haven't heard back from you in more than a month, I'm going to close this issue as stale for now, but feel free to reopen the issue if it isn't resolved for you