Vaa3D in Python Made Easy

Python library for Vaa3D functions.

Installation

$ pip install v3d-py-helper

By cloning the repo and test the Cyhton usages:

$ python setup.py build_ext --inplace

Usage

Loading Vaa3D format data

from v3dpy.loaders import Raw, PBD

raw = Raw()
img = raw.load('path.v3draw')
raw.save('path.v3draw', img)

pbd = PBD()
img = pbd.load('path.v3dpbd')
pbd.save('path.v3dpbd', img)

Loading TeraFly format data

Currently only support Tiff 3D tiles.

from v3dpy.terafly import TeraflyInterface
import numpy as np

t = TeraflyInterface('teraconvert_path')
x, y, z, c = t.get_dim()
# center block
size = np.array(t.get_dim()[:3])
half_block_size = np.array([128, 128, 64]) // 2
start = size // 2 - half_block_size
end = size // 2 + half_block_size - 1

# 4D image, indexed by c, z, y, x 
img = t.get_sub_volume(start[0], end[0], start[1], end[1], start[2], end[2])

Toubleshooting

On Windows, MS BuildTool >= 16 is required to build the wheel.

Useful Links

Github project: https://github.com/SEU-ALLEN-codebase/v3d-py-helper

Vaa3D source: https://github.com/Vaa3D/v3d_external

Documentation: https://SEU-ALLEN-codebase.github.io/v3d-py-helper