Enhance Allen atlas integration and add RAS orientation alignment#92
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FIrgolitsch wants to merge 1 commit intomainfrom
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Enhance Allen atlas integration and add RAS orientation alignment#92FIrgolitsch wants to merge 1 commit intomainfrom
FIrgolitsch wants to merge 1 commit intomainfrom
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Extends linumpy/io/allen.py with atlas downloading, parsing, and registration helper functions. Adds linum_align_to_ras.py for full RAS-orientation alignment pipeline with optional Allen atlas registration support. Updates linum_download_allen.py with improved download logic.
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Closing in favour of #101 (recreated with squashed commits as part of the PR split plan refresh). |
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Summary
Extends the Allen atlas I/O module and adds a full pipeline for aligning reconstructed volumes to RAS orientation with optional atlas registration.
Changes
linumpy/io/allen.py— major additions: atlas downloading, parsing, and registration helper functions for mapping to the Allen Common Coordinate Frameworkscripts/linum_align_to_ras.py(~980 lines) — full pipeline:scripts/linum_download_allen.py— updated with improved download logicDependencies
Depends on PR #85 (thread config module) and PR #89 (
utils/orientation.py).