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Allow specification of backgrounds in MIRI imaging notebook #33

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Updates MIRI imaging notebook to pipeline version 1.16.1, and adds the ability to specify a dedicated background directory, in which case those backgrounds will be used in calwebb_image2.

This PR can be reviewed after the January AAS meeting.

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
    • An explanation of the visualization's significance to the notebook (like the trend, an outlier in the data, what the author learned from it, etc.)
  • 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.

@drlaw1558 drlaw1558 requested a review from sosey as a code owner December 18, 2024 02:11
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@drlaw1558 drlaw1558 requested review from rizeladiaz and removed request for sosey December 18, 2024 02:12
@drlaw1558
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Tagging @cracraft to look over these changes as well

@rizeladiaz
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David, when running this notebook I get this error in Stage3 "ValueError: cannot convert float NaN to integer." I don't think these have to do with the latest changes but probably with the change in pipeline version. Do you see that?

@drlaw1558
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Yes, that's a new issue I ran into earlier today in some last-minute testing ahead of the AAS workshop. See https://jira.stsci.edu/browse/JP-3840

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