Add code showing how to remove NIRCam wisps

[bsunnquist]

This notebook demonstrates how to scale, subtract, and/or flag the scattered light "wisps" from NIRCam data using new templates provided by the NIRCam team. The subtract_wisp.py contains the code, and the notebook shows how to use it and its optional arguments.

The First Cell

• The title of the notebook in a first-level heading (eg. <h1> or # in markdown).
• A brief description of the notebook.
• A table of contents in an ordered list (1., 2., etc. in Markdown).
• The author(s) and affiliation(s) (if relevant).
• The date first published.
• The date last edited (if relevant).
• A link to the notebook's source(s) (if relevant).

The Rest of the Cells

• There is only one H1 (# in Markdown) used in the notebook.
• The notebook uses other heading tags in order (meaning it does not skip numbers).

Text

• All link text is descriptive. It tells users where they will be taken if they open the link.
• All acronyms are defined at least the first time they are used.
• Field-specific/specialized terms are used when needed, but not excessively.

Code

• Code sections are introduced and explained before they appear in the notebook. This can be fulfilled with a heading in a prior Markdown cell, a sentence preceding it, or a code comment in the code section.
• Code has explanatory comments (if relevant). This is most important for long sections of code.
• If the author has control over the syntax highlighting theme in the notebook, that theme has enough color contrast to be legible.
• Code and code explanations focus on one task at a time. Unless comparison is the point of the notebook, only one method for completing the task is described at a time.

Images

• All images (jpg, png, svgs) have an image description. This could be

  • Alt text (an alt property)
  • Empty alt text for decorative images/images meant to be skipped (an alt attribute with no value)
  • Captions
  • If no other options will work, the image is decribed in surrounding paragraphs.

• Any text present in images exists in a text form outside of the image (this can be alt text, captions, or surrounding text.)

Visualizations

• All visualizations have an image description. Review the previous section, Images, for more information on how to add it.

• Visualization descriptions include

  • The type of visualization (like bar chart, scatter plot, etc.)
  • Title
  • Axis labels and range
  • Key or legend
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• All visualizations and their parts have enough color contrast (color contrast checker) to be legible. Remember that transparent colors have lower contrast than their opaque versions.

• All visualizations convey information with more visual cues than color coding. Use text labels, patterns, or icons alongside color to achieve this.

• All visualizations have an additional way for notebook readers to access the information. Linking to the original data, including a table of the data in the same notebook, or sonifying the plot are all options.

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[camipacifici]

Hi @bsunnquist, thank you for the notebook! Is this ready for technical review?

[bsunnquist]

Hi @camipacifici - yes, I think it's ready - thanks!

The only thing I wasn't sure on is the downloading of the wisp templates. We store them on Box, so I just provide a link for users to download them manually before running the notebook. I tried downloading them programmatically from Box but wasn't able to get it working, but let me know if that's preferred.

[camipacifici]

The technical reviewer will help you solve that, no problem!
I forgot to ask, has this been scientifically reviewed? Maybe by somebody on the NIRCam team?

[bsunnquist]

Sounds good thanks! And I've just tested it by myself, i.e. running on NIRCam data to make sure it works as expected.

[camipacifici]

Ok, thanks. I leave it to @bhilbert4 and Roeland to decide if a science review is needed.

[bhilbert4]

I just reviewed the notebook, and it looks good to me. The only question I have @bsunnquist: is it possible for a user to turn on the scaling when they supply their own wisp template?
e.g. results = subtract_wisp('jw01063006004_02101_00005_nrcb4_cal.fits', wisp_data, scale_wisp=True, show_plot=True)
If so, it may be worth mentioning that explicitly.

[bsunnquist]

@bhilbert4 Yes that's possible; I've added some clarification on that to the custom templates section.

[camipacifici]

@bhilbert4 is this ready for technical review?

[bhilbert4]

@camipacifici yes, ready for technical review.

[rizeladiaz]

@bsunnquist I forgot to mention that I had also changed the requirements.txt file to point to jwst 1.15.1 but I didn't send you that one. I tested it with that version.

1. Could you please change the requirements.txt file to use 1.15.1
2. Could you remove the last cell of the notebook? It adds a new empty cell after running the last cell. Probably we have to add a footer to prevent that from happening whenever there is a revision.

[bsunnquist]

@rizeladiaz updated with those changes

[rizeladiaz]

Ready to merge

[camipacifici]

Good to go.

[camipacifici]

Thank you @bsunnquist and @rizeladiaz!