feat(atlas): multi-region get_mesh and batched atlas mesh prefetch - #448
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📖 Doc preview: https://confusius.tools/pr-preview/pr-448/ |
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@sdiebolt this should be good to be reviewed! |
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get_atlas_mesh's clip step materialized the full lazily derived z/y/x coordinate grids of an oblique atlas only to reduce them to per-axis min/max. Add get_bounding_box, which maps the 8 corners of the voxel-coordinate box through the voxel-to-world affine (identical bounds, O(1) in grid size), and clip meshes with it. Closes #444
…dict
`get_mesh`/`get_atlas_mesh` now mirror `get_masks`: `regions` and `sides`
broadcast through a shared `_normalize_regions_and_sides` helper, all vertices
are warped through `world_to_base` in one batched pass, and the result is a
`{acronym: (vertices, faces)}` dict with `_L`/`_R` keys for single-hemisphere
requests.
The atlas fixtures move to `tests/unit/conftest.py` so other test modules can
build on the same mock atlas, and the child region gains its own mesh so a
multi-region call that mis-splits the batched vertex transform cannot pass.
BrainGlobe 3 downloads each region mesh lazily on first access, one S3 `exists` + `get` round trip per region (about a second each). On the first fetch of an atlas, `fetch_brainglobe_atlas` now lists the remote mesh directory once and pulls every missing mesh in a single concurrent `s3fs.get` call (839 Allen mouse meshes in ~20 s instead of ~14 min), so `get_mesh` works offline afterwards. Regions with no remote mesh (e.g. RSPd4 in the Allen mouse atlas) and an unreachable bucket both warn and fall back to BrainGlobe's lazy download, and a failed batch removes any partially written file, as BrainGlobe does, since it treats any existing file as a valid cached mesh.
Both now return a dict of meshes, so the plural name matches the API.
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Stacked on #446; #263 stacks on top of this one.
What
get_mesh/get_atlas_meshnow takeregionsandsideslikeget_masks(one region or a sequence, one side for all or one per region) and return a{acronym: (vertices, faces)}dict, with_L/_R-suffixed keys for single-hemisphere requests. All vertices go throughworld_to_basein one batched pass.fetch_brainglobe_atlasprefetches every region mesh on the first fetch of an atlas. BrainGlobe 3 downloads meshes lazily, one S3exists+getround trip per region (about 1 s each). We list the remote mesh directory once and pull every missing mesh in a single concurrents3fs.getcall: the 839 Allen mouse meshes take about 20 s instead of about 14 min, andget_meshworks offline afterwards.Notes
remote_url_s3andV3_MESHES_DIRECTORYinbrainglobe_atlasapi.descriptors. Upstream has no bulk download API yet ([Feature] Allow users to force download individual atlas components on install brainglobe/brainglobe-atlasapi#784).tests/unit/conftest.pyso other test modules can reuse the mock atlas.