Created new MIRI imager notebook

[cracraft]

This notebook checklist has been made available to us by the the Notebooks For All team.
Its purpose is to serve as a guide for both the notebook author and the technical reviewer highlighting critical aspects to consider when striving to develop an accessible and effective notebook.

The First Cell

• The title of the notebook in a first-level heading (eg. <h1> or # in markdown).
• A brief description of the notebook.
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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

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• 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.
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Images

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• 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

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  • Title
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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.

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• 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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[drlaw1558]

Thanks @cracraft ! Tagging @rizeladiaz

[rizeladiaz]

Will start checking this notebook now

[drlaw1558]

Checking in on the status of this review? @rizeladiaz

[rizeladiaz]

I finished with the last changes to the notebook and pushed the change to Misty's repo. Now Misty should make a pull request to the main repository to add this notebook.

[drlaw1558]

No new PR should be needed as your changes to Misty's branch should now be reflected in this PR. I'll aim to take a look at this later today if possible.

[drlaw1558]

• Need to change the CRDS cell so that we aren't setting a CRDS version by default (since this should be handled on the CRDS side). Suggest following the updated NIRCam notebook and using the cell entry pasted below.

• Why is this setting det1dict['refpix']['skip'] = True since this is what's already done in the parameter reference files?

• Suggest changing some parameters used for the two plots at the end of the notebook so that they display on the page better instead of being hidden in overflowing-length cells. This should be possible just by setting the figure size to (8,8) instead of (20,20) and modifying the colorbar command to, e.g.,:
  cb = fig.colorbar(cax,fraction=0.046)

------------------------Set CRDS context and paths----------------------

Each version of the calibration pipeline is associated with a specific CRDS

context file. The pipeline will select the appropriate context file behind

the scenes while running. However, if you wish to override the default context

file and run the pipeline with a different context, you can set that using

the CRDS_CONTEXT environment variable. Here we show how this is done,

although we leave the line commented out in order to use the default context.

If you wish to specify a different context, uncomment the line below.

#%env CRDS_CONTEXT jwst_1293.pmap

Check whether the local CRDS cache directory has been set.

If not, set it to the user home directory

if (os.getenv('CRDS_PATH') is None):
os.environ['CRDS_PATH'] = os.path.join(os.path.expanduser('~'), 'crds')

Check whether the CRDS server URL has been set. If not, set it.

if (os.getenv('CRDS_SERVER_URL') is None):
os.environ['CRDS_SERVER_URL'] = 'https://jwst-crds.stsci.edu'

Echo CRDS path in use

print(f"CRDS local filepath: {os.environ['CRDS_PATH']}")
print(f"CRDS file server: {os.environ['CRDS_SERVER_URL']}")
if os.getenv('CRDS_CONTEXT'):
print(f"CRDS CONTEXT: {os.environ['CRDS_CONTEXT']}")

[drlaw1558]

Looks like that cell text failed entirely to format well in my comment, but I'm sure you get the idea.

[rizeladiaz]

HI David, I don't think you are checking the latest version of the notebook. In the new version it is not fixing CRDS and other changes to the text for the context. Not sure why it didn't merge properly to Misty's branch. Please check diaz-miriimager branch in Misty's repo. Though, there are a couple of changes that need to be added.

[drlaw1558]

@rizeladiaz Ah, I see, thanks. Remaining comments on that branch (now merged to Misty's main it looks like):

• For the CRDS context text, I like the text above (comment with the awful formatting) that Bryan put in for the NIRCam notebook, so we should use that here too.
• We should also apply the plot size and colorbar formatting to the third-from-last cell too.

[rizeladiaz]

Ok Done

[drlaw1558]

One final comment- the 20,20 should be changed to (8,8) in two places in that 3rd-to-last cell, not just one (in this case the main and subplot both declare a figure size).

[drlaw1558]

Another case where this is ready to merge, but I can't do so because of glitches in the automated checks (nor can I even click into the stalled check to see what the problem is). @sosey