feat: Allen atlas improvements and RAS alignment

[FIrgolitsch]

Stacked PR 4/22 — review order: #115 → #97 → #98 → #99 → #100 → #101 → #108 → #106 → #107 → #87 → #116 → #110 → #111 → #40 → #112 → #113 → #117 → #118 → #120 → #121 → #122 → #123 → #124 → #125

Base: pr-g-diagnostics-analysis. Retargets to main as upstream PRs merge.

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PR #101 — Allen Atlas & RAS Alignment

Two commits: initial Allen/RAS work, then a fix for the RAS orientation logic plus a full test suite.

Changes

• scripts/linum_align_to_ras.py (new, then refined) — align a reconstructed OME-Zarr volume to RAS orientation. Second commit fixes the orientation-code mapping (some axis flips were inverted) and tightens the auto-crop bounding box so background padding is removed consistently.
• linumpy/io/allen.py — improved Allen atlas download / caching; adds numpy_to_sitk_image() and sitk_image_to_numpy() helpers used by the align-to-RAS pipeline and by feat: diagnostic and analysis scripts #100's diagnostics.
• scripts/linum_download_allen.py — cache location made consistent with linumpy/io/allen.py; retries on transient HTTP errors.

Tests

• linumpy/tests/test_io_allen.py — full unit coverage for linumpy/io/allen.py including the new SimpleITK helpers
• scripts/tests/test_align_to_ras.py — regression tests covering the orientation-code mapping and the auto-crop bbox fixes

Notes

• Uses linumpy/utils/orientation.py from feat: utility modules, preprocessing improvements, galvo correction #97