vlsi 0.0.1

variable length spatial index - encode arbitary length bytes in nifti + data sidecar file

vlsi

Variable-Length-Spatial-Index (or velvet-silk) is an implementation of variable length datatype for 3-dimensional array. It is designed with write-once-read-many paradigm, and is thus optimized for fast and memory efficient read operations.

Background

see background.md

Specification

see specifications.md

Usages

A trivial example is included below. For more realistic usages, please refer to e2e tests.

import numpy as np
from vlsi import WritableSpatialIndex, ReadableSpatialIndex, SpatialIndexWriteExc

def main():

    windex = WritableSpatialIndex("testfile")
    windex.write(
        [
            [0, 0, 0],
            [42, 42, 42],
        ],
        [b"origin of life", b"meaning of life"],
    )
    windex.write([[0, 0, 0]], [b"another write"])
    windex.save(np.eye(4), shape=(100, 200, 100))

    try:
        windex.write([[0, 0, 0]], [b"should fail"])
    except SpatialIndexWriteExc:
        ...

    try:
        windex.save(np.eye(4), shape=(100, 200, 100))
    except SpatialIndexWriteExc:
        ...

        
    rindex = ReadableSpatialIndex("testfile")
    assert rindex.read([[0, 0, 0]]) == [b"origin of lifeanother write"]
    assert rindex.read([[42, 42, 42]]) == [b"meaning of life"]
    assert rindex.read([[1, 1, 1]]) == []

if __name__ == "__main__":
    main()

Similar projects

sparseindex in siibra-python (original inspiration of this project)

v2 sparsedex in siibra-python (first implementation of vlsi)

vlen codec in numcodecs

numpy.save

LICENSE

apache 2.0