Allen atlas alignment follow-ups#121
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…lace rint/clip, contig once, sample bg estimate)
…test
The Allen ABC Atlas docs describe `average_template_<res>.nrrd` as ASL
("first axis is anterior-to-posterior, second is superior-to-inferior,
third is left-to-right"), while the rest of linumpy uses the
NIfTI/radiology convention where each letter names the direction the
axis points toward -- under which the same layout is PIR. Both names
describe the identical voxel layout, but the existing docstring only
mentioned PIR, which made it easy to suspect the conversion code when a
downstream RAS preview looked flipped.
* Rewrite the `download_template_ras_aligned` docstring to spell out
both names, cite the empirical landmarks (olfactory tip vs. cerebellum
along SITK X), and note that the legacy informatics-archive nrrd and
the newer ABC-Atlas template share this orientation. The
`PermuteAxes((2, 0, 1)) + Flip(F, T, T)` recipe is unchanged --
verified correct on the cached 100 µm template.
* Add `TestRealAllenTemplateOrientation` (skipped when the nrrd is not
cached) so future changes to either the upstream file or the RAS
recipe trip a regression test:
- raw nrrd: anterior tip < posterior mass on SITK X (PIR/ASL)
- RAS-aligned: +dim1 mass concentrated at anterior end
- RAS-aligned: dim2 (R) mass roughly L/R symmetric within 10 %
This was referenced May 20, 2026
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Allen atlas alignment follow-ups
Stacked on the new pr-q-perf-pipeline. Five small follow-ups to the Allen / RAS alignment work originally landed in #101.
Commits
apply_transformnow accepts a reference grid + py3.12 compat fixes.These could not be folded back into #101 because pr-i (#108) deletes
scripts/linum_align_to_ras.py; the follow-ups touch the script as it lives indev, so they belong after the script gets restored downstream.