Add example recreating SMART paper Figures 3, 5 and 11 (partially)

[samaloney]

No description provided.

[Copilot]

🟡 Changes recommended

Several issues need correction (example misuse of preprocessing, inconsistent kwargs propagation, and a couple of correctness/documentation/error-message problems) before the changes are safe and clear to users.

Once you've addressed the issues Copilot identified, you can request another Copilot review.

Pull request overview

This PR adds a new end-to-end example that reproduces selected figures from Higgins et al. (2011) and updates the SMART processing pipeline to better match the paper (smoothing → threshold → LOS correction), including improved off-disk handling and transient removal.

Changes:

• Replace in-place map_threshold with remove_off_disk that returns a copied map and sets off-limb pixels to NaN.
• Rework smooth_los_threshold and transient removal (index_and_grow_mask) to follow the paper’s intended processing order and enable “un-grown” masks for callers that do their own growing.
• Add a comprehensive Sphinx-gallery example reproducing SMART paper Figures 3, 5, and (partially) 11, and update docs/changelog accordingly.

File summaries

File	Description
smart/tests/test_map_processing.py	Updates tests to cover remove_off_disk behavior and non-mutating semantics.
smart/tests/test_calculate_properties.py	Updates the integration-style test data URL/time for the previous magnetogram.
smart/processing.py	Introduces remove_off_disk, reorders smoothing/threshold/LOS correction, adds configurable caps, and updates smart_prep pass-through.
smart/indexed_grown_mask.py	Reworks transient removal to rotate the earlier frame after smoothing/thresholding and compares masks as in the paper.
smart/calculate_properties.py	Updates pipeline to use the new indexing/transient-removal flow and forwards kwargs to IGM.
pyproject.toml	Adds sunpy[net] to docs extras to support the new example’s JSOC/HEK fetching.
examples/smart_process.py	Updates processing example to use remove_off_disk and the updated IGM call shape.
examples/reproducing_higgins_2011.py	New example script reproducing key Higgins et al. (2011) figures using JSOC/HEK data.
examples/full_walkthrough.py	Updates walkthrough to match the new mask-indexing workflow.
docs/explanation.rst	Updates pipeline documentation references from map_threshold to remove_off_disk.
changelog/22.doc.rst	Adds documentation changelog entry for the new reproduction example.
changelog/22.bugfix.rst	Adds bugfix changelog entry describing pipeline/algorithm fixes made during reproduction.

Review details

Suppressed comments (1)

smart/processing.py:192

• cosine_correct_data also needs to validate limit before using it in arcsin(limit) and to compute the clipping cap; otherwise callers can trigger invalid math by passing out-of-range values.

    if cosmap is None:
        cosmap = calculate_cosine_correction(im_map, limit=limit)

    cosmap = np.clip(cosmap, None, 1 / np.cos(np.arcsin(limit)))

• Files reviewed: 12/12 changed files
• Comments generated: 9
• Review effort level: Lite

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