ENH: Minor update to documentation to better explain role of experiments#15
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Pull request overview
This pull request enhances documentation to clarify the role and purpose of the experiments directory, distinguishing it from production-ready code in the scripts directory.
Changes:
- Significantly expanded experiments/README.md with detailed explanations of each experiment, adaptation strategies, and clear warnings against using experiments as production examples
- Added consistent notes across all documentation files (quickstart.rst, index.rst, examples.rst, developer/extending.rst, contributing.rst, cli_scripts/overview.rst, architecture.rst) emphasizing that scripts/ contains production code while experiments/ contains research prototypes
- Established clear guidance for contributors on when to add code to scripts/ vs experiments/ directories
Reviewed changes
Copilot reviewed 8 out of 8 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| experiments/README.md | Major expansion with experiment highlights, adaptation strategies, and comprehensive warnings about production usage |
| docs/quickstart.rst | Added important note distinguishing scripts/ from experiments/ directories |
| docs/index.rst | Added tip about code examples and proper resource usage |
| docs/examples.rst | Added note warning against using experiments as usage examples |
| docs/developer/extending.rst | Added important note on using scripts/ and experiments/ as references when extending |
| docs/contributing.rst | Added section on contributing scripts vs experiments with clear guidelines |
| docs/cli_scripts/overview.rst | Added important note emphasizing scripts/ as definitive resource |
| docs/architecture.rst | Added note pointing to implementation references in scripts/ and experiments/ |
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| **Pipeline stages:** | ||
| 1. 4D CT reconstruction (using methods from `Reconstruct4DCT`) | ||
| 2. AI segmentation (TotalSegmentator, Vista3D/Clara Segment Open Model as NIM or local) |
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Inconsistent naming: "Vista3D" is used here while "VISTA-3D" is used on line 220. Consider using "VISTA-3D" consistently throughout the document.
Suggested change
| 2. AI segmentation (TotalSegmentator, Vista3D/Clara Segment Open Model as NIM or local) | |
| 2. AI segmentation (TotalSegmentator, VISTA-3D/Clara Segment Open Model as NIM or local) |
| - Real-time deformable registration for interventional guidance | ||
| - Integration with simulation engines (PyAnsys, FEniCS, etc.) | ||
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| **Output:** Patient-specific USD models ready for physics simulation or AI training. |
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Trailing whitespace detected at the end of this line. Consider removing the extra spaces.
Suggested change
| **Output:** Patient-specific USD models ready for physics simulation or AI training. | |
| **Output:** Patient-specific USD models ready for physics simulation or AI training. |
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