cellmap_flow.io.metadata

Opening a path as cellmap-flow reads it, and nanometers per unit.

Array metadata is worldarray’s: wa.open(path).meta or wa.metadata(path) give an ArrayMeta (every axis in the array’s order, the store’s units, translation the centre of voxel 0 and .corner its lower corner), wa.open_pyramid(path) a group’s levels, and .in_nm() the spatial axes in nanometers. This module keeps the two things cellmap-flow adds on top:

• open_level: the one way every reader opens a path, so that a group is read at its first level when no voxel size asks for another;

• nm_per_unit and _NM_PER_UNIT: worldarray’s unit table as nanometers per unit, forgiving of a missing or unknown unit, which the browser shares (web/build/export_data.py).

snap_integral takes the float noise out of unit conversions.

Attributes

logger
NANOMETER

Functions

nm_per_unit(unit) → float	How many nanometers one unit is; 1 for a missing, "pixel" or unknown
snap_integral(values)	values as floats, with near-whole numbers made exactly whole.
open_level(path[, voxel_size]) → worldarray.WorldArray	The worldarray array path names, as cellmap-flow reads a path: an

Module Contents

cellmap_flow.io.metadata.logger

cellmap_flow.io.metadata.NANOMETER = 'nanometer'

cellmap_flow.io.metadata.nm_per_unit(unit) → float

How many nanometers one unit is; 1 for a missing, “pixel” or unknown unit, with a warning for an unknown one.

cellmap_flow.io.metadata.snap_integral(values)

values as floats, with near-whole numbers made exactly whole.

cellmap_flow.io.metadata.open_level(path: str, voxel_size=None, **kwargs) → worldarray.WorldArray

The worldarray array path names, as cellmap-flow reads a path: an array, or one scale of a precomputed volume, as it is whatever is asked for; a group or precomputed volume at its level for voxel_size (worldarray chooses it from the group’s document), its first without one. kwargs are wa.open’s (on_mismatch, padding, units, context, …); units it cannot convert are left as they are rather than refused.