An ndio script to download a full dataset

download-as-png.py

# Jordan Matelsky (https://github.com/j6k4m8)
# uses ndio>=0.1.3
#
# Usage: python download-as-png.py token channel res startslice stopslice
# Example:
#   python download-as-png.py kasthuri11 image 3 1100 1110
# (Will download slices 1100-1110 of the kasthuri11 dataset at resolution 3)

import ndio.remote.neurodata as ND
import ndio.convert.png as ndpng
import sys
nd = ND()

# get the information about the token:channel that we're downloading
# so that if it changes for some weird reason, we'll still download
# everything correctly.
if len(sys.argv) != 5:
    raise ValueError("Usage: python download-as-png.py token channel res startslice stopslice")

token = sys.argv[1]
channel = sys.argv[2]
resolution = int(sys.argv[3])

img_size = nd.get_image_size(token, resolution=resolution)
img_offset = nd.get_image_offset(token, resolution=resolution)

start = int(sys.argv[4])
stop  = int(sys.argv[5])

query = {
    "token":      token,
    "channel":    channel,
    "x_start":    img_offset[0],
    "y_start":    img_offset[1],
    "z_start":    start,
    "x_stop":     img_size[0],
    "y_stop":     img_size[1],
    "z_stop":     stop,
    "resolution": resolution
}

vol = nd.get_cutout(**query)
ndpng.export_png_collection('png/*', vol, start)