[Bug]: If a user marks a column as saturated in every group in S1, the column is still used in S3

[erinmmay]

FAQ check

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Instrument

NIRSpec (Stages 1-3)

What happened?

From a chat with @gianninapr - Currently Stage 1 has the option for a user to define which columns are saturated in which group so they can be ignored for GLBS and ramp fitting. However in some cases a user may want to manually flag a column as saturated in every group. In this case, the column isn't ignored in Stage 3 because there we only ignore pixels with an odd DQ (or bad pixels) and saturated pixels are not necessarily flagged as bad pixels. This means the Stage 3 code tries to use them for the median frame etc. We should add a check in the Stage 1 saturation flagging code so that columns flagged as saturated in every group get an updated DQ value so that they are also flagged as bad pixels.

Along the same lines: allow a user to supply a custom DQ mask in Stage 1. I'll include that option in a PR to address this bug.

Error traceback output

No response

What operating system are you using?

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What version of Python are you running?

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What Python packages do you have installed?

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[gianninapr]

Some notes on this issue:

After my conversation with Erin, I tried running a quick fix, but the results were still not ideal. After going over the definitions of the masks and a conversation with Caleb Cañas we both noticed the issue as it stands.

In update_saturation.py around line 46 the user-provided custom saturation columns are set to the sat_flag value, which is defined as the 'SATURATED' jwst dq flag. When the flags are passed in s3_reduce.py, the code marks all odd entries as do not use, yet the dq flag for 'SATURATED' is an even number (2), so it isn't marking the user-defined saturated columns as do not use, which is why we still see them on the median frame in the end.

I'm happy to take care of this if there's a straightforward fix (like adding a condition to also catch the saturation flag in the if statement in s3_reduce.py) that would be sufficient, but just wanted to check in and see if there was more thoughts people had and what they thought an elegant solution is.

[erinmmay]

My plan is to add a check in stage 1's update_saturation.py to flag a pixel as bad (odd number) if the user marks it as saturated in all groups. Some pixels may be marked as saturated in only later groups and still have a good ramp fit, so we don't want all saturated pixels ignored in stage 3.

[gianninapr]

Given that the update_saturation.py script removes any saturation flags if they're present in the first group for use in ramp fitting, how would we want to update given that portion of the code? Do we just make sure the fully saturated pixels are marked as do not use before that step?

[taylorbell57]

@gianninapr and @erinmmay, do one of you have a PR to resolve this issue coming soon?

[gianninapr]

Yes, I was hoping to have a PR for this before our next meeting. I've had some conversations with Caleb on how to go about it!!