cellmap_flow.io.geometry

Where an array’s voxels are in the world, and boxes of voxels.

World coordinates are nanometers. A Grid is an array’s voxel size and the lower corner of its voxel 0 (ArrayMeta.voxel_size/translation on the spatial axes): voxel i covers [corner + i*vs, corner + (i+1)*vs). Voxel sizes can be fractional (5.24 nm) and a corner need not lie on the grid (Janelia raw is at -4 nm with 8 nm voxels), so nothing here goes through funlib’s Coordinate, which truncates both. A Box is a range of voxel indices, which may start before the array or run past it.

Grid.world_to_box(roi): the voxels a read of a world Roi returns.
Grid.box_to_world(box): the whole-nm Roi around a box, which world_to_box maps back to the same box.
coordinate_or_floats: a voxel size or offset as a Coordinate when it is whole, else as floats.
list_populated_chunks: the chunks of a local zarr v2 array that have a file, by index.

Attributes

`logger`
`CHUNK_KEY_RE`

Classes

`Box`	Voxel indices `begin` up to `begin + shape`, per axis.
`Grid`	`voxel_size` and the lower corner of voxel 0 (`translation`),

Functions

`coordinate_or_floats`(values[, what, where])	A Coordinate when every value is a whole number, else a tuple of floats.
`list_populated_chunks`(→ List[Tuple[int, ...]])	The indices of the chunks of a local zarr v2 array that have a file.

Module Contents

cellmap_flow.io.geometry.logger

cellmap_flow.io.geometry.CHUNK_KEY_RE

class cellmap_flow.io.geometry.Box

Voxel indices begin up to begin + shape, per axis.

begin: Tuple[int, ...]

shape: Tuple[int, ...]

property end: Tuple[int, ...]

class cellmap_flow.io.geometry.Grid

voxel_size and the lower corner of voxel 0 (translation), nanometer floats, one per axis.

voxel_size: Tuple[float, ...]

translation: Tuple[float, ...]

world_to_box(roi: funlib.geometry.Roi) → Box

The voxels a read of roi returns: as many whole voxels as fit in roi.shape, from the one roi.begin is in.

That is the voxel below an off-grid start on either side of voxel 0: half a voxel before the array starts at voxel -1. Float noise from the division (9.9999999 voxels) counts as the whole number it is.

A start less than 1 nm below a voxel boundary (and nearer it than half a voxel) is read from that boundary. A Roi holds whole nanometers, so it cannot start on a boundary that is not one: OpenOrganelle’s voxel 0 starts at -2.62 nm (10.48 nm voxels), and both box_to_world (which floors) and the served and blockwise output grids (which round) start it at -3 nm. Read from the voxel -3 nm is in, the array’s own roi came back as a voxel of padding and then voxels 0 to n-2, and a model reading such a grid (resampled to 8 nm, say) got its input a voxel early. On a whole-nm grid (8 and 16 nm, a -4 nm corner) every whole-nm start is on a boundary or at least 1 nm past one, so nothing changes there.

box_to_world(box: Box) → funlib.geometry.Roi

The integer-nm Roi covering box: exactly its extent when that is whole nanometers, else rounded out to them (a Roi holds integers).

world_to_box maps it back to box when the voxels are 2 nm or more. On a finer grid whose boundaries are not whole nanometers (1 nm voxels centred on whole nm), each nanometer the rounding adds can be half a voxel, and the box reads back with a voxel of padding.

cellmap_flow.io.geometry.coordinate_or_floats(values, what='voxel size', where='')

A Coordinate when every value is a whole number, else a tuple of floats.

Coordinate truncates: Coordinate(5.24) is 5, and a dataset at 5.24 nm then read 5% of the wrong voxels. Non-integer values are kept as floats (with a one-time warning) instead.

cellmap_flow.io.geometry.list_populated_chunks(array_dir) → List[Tuple[int, ...]]

The indices of the chunks of a local zarr v2 array that have a file.

array_dir is the array’s directory; its chunk files are the names CHUNK_KEY_RE matches, and .zarray and the rest are not chunks. In index order, not os.listdir’s: that order differs between filesystems (ext4 orders names by a per-filesystem hash), so the same seed would draw different patches on another machine.