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Addressing reviewer comment about QC flags and visualization - #12
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frheault
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🟡 Changes recommended
The new figure-generation script can crash when groups exist but none are non-empty due to an unguarded np.concatenate call.
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Pull request overview
This PR incorporates the showcase figure generation workflow into the repository, updates the documentation to reference the scripts and discuss QC flagging concepts, and adds a new bibliography entry used by the updated text.
Changes:
- Added a FURY-based script to programmatically render the showcase whole-brain and bundle figures.
- Updated
showcase.mdto link to the rendering script, expand the scripts section, and add QC/outlier-filtering discussion with citations. - Added a new BibTeX reference and applied minor formatting/cleanup updates across Sphinx config and example scripts.
File summaries
| File | Description |
|---|---|
| source/showcase.md | Adds links to the new rendering script, improves script download listing, and expands QC/outlier filtering discussion with citations. |
| source/references.bib | Adds the Levesque2025TractOracle BibTeX entry referenced from showcase.md. |
| source/conf.py | Fixes/normalizes sidebar dict formatting. |
| source/_static/scripts/showcase_resizing.py | Minor comment/log message wording cleanup. |
| source/_static/scripts/showcase_filtering.py | Removes unused import and applies small formatting changes to logging statements. |
| source/_static/scripts/showcase_concatenation.py | Minor docstring/log formatting improvements. |
| source/_static/scripts/generate_showcase_figure.py | Introduces the script that renders the showcase images using FURY offscreen rendering. |
Review details
- Files reviewed: 6/12 changed files
- Comments generated: 1
- Review effort level: Lite
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| all_grp_indices = np.concatenate( | ||
| [trx.groups[k] for k in trx.groups.keys() if len(trx.groups[k]) > 0] | ||
| ) | ||
| unique_grp_indices = np.unique(all_grp_indices) |
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My script to render the image and streamlines is now part of the repo
Added citations and new images
Ran various formatting tools (markdown, python, etc.)