get_anno_array_from_state_file - jaybgager/tracertools GitHub Wiki

This function extracts a numpy array of point coordinates from a point annotation layer in a locally-stored neuroglancer JSON state file.

Arguments:

• layer_name (string, mandatory)
  • the name of the point annotation layer in the JSON state file
• json_path (type, mandatory)
  • the absolute file path to the JSON state file on your local machine
  • e.g. "/home/username/ng_jsons/state.json"

Returns:

• points ((n,3)-shape numpy array of integers)
  • array of 3-integer arrays representing point coordinates

Example

INPUT:

import tracertools as tt

anno_array = tt.get_anno_array_from_state_file(
    json_filepath = "/home/user/ng_states/state01.json",
    layer_name = "annotation1"
)

print(anno_array)

OUTPUT:

array([
    [x1, y1, z1],
    [x2, y2, z2],
    [x3, y3, z3],
    ...
    [xn, yn, zn]
])