example.py

from __future__ import print_function

import argparse
import sys
import numpy as np

import neuroglancer
import neuroglancer.cli
from syconn.analysis.backend import SyConnBackend


def add_example_layers(state):
    a = np.zeros((3, 100, 100, 100), dtype=np.uint8)
    ix, iy, iz = np.meshgrid(*[np.linspace(0, 1, n) for n in a.shape[1:]], indexing='ij')
    a[0, :, :, :] = np.abs(np.sin(4 * (ix + iy))) * 255
    a[1, :, :, :] = np.abs(np.sin(4 * (iy + iz))) * 255
    a[2, :, :, :] = np.abs(np.sin(4 * (ix + iz))) * 255

    b = np.cast[np.uint32](np.floor(np.sqrt((ix - 0.5)**2 + (iy - 0.5)**2 + (iz - 0.5)**2) * 10))
    b = np.pad(b, 1, 'constant')
    dimensions = neuroglancer.CoordinateSpace(names=['x', 'y', 'z'],
                                              units='nm',
                                              scales=[10, 10, 10])

    state.dimensions = dimensions
    state.layers.append(
        name='a',
        layer=neuroglancer.LocalVolume(
            data=a,
            dimensions=neuroglancer.CoordinateSpace(
                names=['c^', 'x', 'y', 'z'],
                units=['', 'nm', 'nm', 'nm'],
                scales=[1, 10, 10, 10],
                coordinate_arrays=[
                    neuroglancer.CoordinateArray(labels=['red', 'green', 'blue']), None, None, None
                ]),
            voxel_offset=(0, 20, 30, 15),
        ),
        shader="""
void main() {
  emitRGB(vec3(toNormalized(getDataValue(0)),
               toNormalized(getDataValue(1)),
               toNormalized(getDataValue(2))));
}
""",
    )
    state.layers.append(
        name='b',
        layer=neuroglancer.LocalVolume(
            data=b,
            dimensions=dimensions,
        ),
    )
    return a, b


if __name__ == '__main__':
    ap = argparse.ArgumentParser()
    neuroglancer.cli.add_server_arguments(ap)
    args = ap.parse_args(sys.argv[1:])
    # TODO delete this print
    print(args.host)
    print(args.port)
    neuroglancer.cli.handle_server_arguments(args)
    viewer = neuroglancer.Viewer()
    with viewer.txn() as s:
        a, b = add_example_layers(s)
    print(viewer)