neu_morpho.fragments¶

Intermediate per-(body, block) fragments (stage 1 -> stage 2 handoff).

Stage 1 writes one fragment per body per block under <chunked_dir>/h<bucket>/<body_id>/<iz>_<iy>_<ix>.<fmt>, bucket being body_id % FANOUT in three hex digits. Stage 2 finds bodies by listing the buckets. Filesystem-backed.

Buckets keep directories narrow: one directory per body directly under chunked_dir made listing a large run hang. They do not reduce the file count. The h prefix keeps a bucket from parsing as a body id, which is how the old flat layout is recognized and refused.

Meshes (.drc) and skeletons (.skel) share the layout, each in its own store. Skeleton fragments use the precomputed encoding but hold zyx global-nm vertices, the space stage 2 fuses in; the zyx->xyz flip happens once, at output.

Attributes¶

FANOUT

Exceptions¶

OldFragmentLayout

The store holds body directories at its top level, from before bucketing.

Functions¶

`body_dir`(chunked_dir, body_id) → str
`bucket_name`(body_id) → str
`count_bodies`(chunked_dir) → int \| None	How many bodies have fragments. `None` if the store does not exist.
`fragment_path`(chunked_dir, body_id, block_index[, fmt]) → str
`list_bodies`(chunked_dir) → list[int]
`read_body_fragments`(chunked_dir, body_id[, fmt]) → list	Load all of a body's fragment meshes (`vol2mesh.Mesh`).
`read_body_skel_fragments`(chunked_dir, body_id[, fmt]) → list	Load all of a body's skeleton fragments (`osteoid.Skeleton`, zyx nm).
`write_fragment`(chunked_dir, body_id, block_index, mesh) → None
`write_skel_fragment`(chunked_dir, body_id, block_index, ...) → None

Module Contents¶

exception neu_morpho.fragments.OldFragmentLayout¶

Bases: RuntimeError

The store holds body directories at its top level, from before bucketing.

Initialize self. See help(type(self)) for accurate signature.

neu_morpho.fragments.body_dir(chunked_dir: str, body_id: int) → str¶

neu_morpho.fragments.bucket_name(body_id: int) → str¶

neu_morpho.fragments.count_bodies(chunked_dir: str) → int | None¶

How many bodies have fragments. None if the store does not exist.

On CephFS, from the store’s recursive directory counts, which are instant (and may lag the filesystem by seconds); elsewhere one listing per bucket, which on ceph takes tens of seconds for a 4096-bucket store. Never a walk into the body directories.

neu_morpho.fragments.fragment_path(chunked_dir: str, body_id: int, block_index: Sequence[int], fmt: str = 'drc') → str¶

neu_morpho.fragments.list_bodies(chunked_dir: str) → list[int]¶

neu_morpho.fragments.read_body_fragments(chunked_dir: str, body_id: int, fmt: str = 'drc') → list¶: Load all of a body’s fragment meshes (vol2mesh.Mesh).

neu_morpho.fragments.read_body_skel_fragments(chunked_dir: str, body_id: int, fmt: str = 'skel') → list¶: Load all of a body’s skeleton fragments (osteoid.Skeleton, zyx nm).

neu_morpho.fragments.write_fragment(chunked_dir: str, body_id: int, block_index: Sequence[int], mesh, fmt: str = 'drc') → None¶

neu_morpho.fragments.write_skel_fragment(chunked_dir: str, body_id: int, block_index: Sequence[int], skeleton, fmt: str = 'skel') → None¶

neu_morpho.fragments.FANOUT = 4096¶