example_signed_int.py

import argparse

import neuroglancer
import neuroglancer.cli
import numpy as np


def add_example_layer(state):
    ix, iy, iz = np.meshgrid(
        *[np.linspace(0, 1, n) for n in [100, 100, 100]], indexing="ij"
    )
    b = (
        np.asarray(
            np.floor(np.sqrt((ix - 0.5) ** 2 + (iy - 0.5) ** 2 + (iz - 0.5) ** 2) * 10),
            dtype=np.int32,
        )
        - 2
    )
    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="b",
        layer=neuroglancer.SegmentationLayer(
            source=neuroglancer.LocalVolume(
                data=b,
                dimensions=dimensions,
            )
        ),
    )
    return b


if __name__ == "__main__":
    ap = argparse.ArgumentParser()
    neuroglancer.cli.add_server_arguments(ap)
    args = ap.parse_args()
    neuroglancer.cli.handle_server_arguments(args)
    viewer = neuroglancer.Viewer()
    with viewer.txn() as s:
        add_example_layer(s)
    print(viewer)