make_point_cloud_from_state_file - jaybgager/tracertools GitHub Wiki

This function generates a point cloud as an OBJ file from a specified point annotation layer in a locally-stored neuroglancer JSON state file.

Arguments:

• datastack (string, mandatory)
  • the name of the CAVE datastack the JSON state is from
  • for a list of datastacks currently supported with tracertools configs, use get_supported_configs
• json_path (string, mandatory)
  • the absolute path to the neuroglancer JSON state file to pull annotations from
  • e.g. "/home/username/ng_jsons/state.json"
• layer_name (string, mandatory)
  • the name of the point annotation layer to pull from, e.g. "annotation1"
• output_path (string, mandatory)
  • the absolute path to the folder where you want to save the OBJ output file, e.g. '/home/username/ng_meshes'
  • file will be named whatever the layer name was in the JSON state

Returns: OBJ file will be created in chosen directory

Example

The code below will create a point cloud OBJ file in the /home/user/point_clouds directory called annotation1.obj using the annotation layer annotation1 of the state.json file in the directory /home/user/ng_states.

INPUT:

import tracertools as tt

tt.make_point_cloud_from_state_file(
    datastack = "brain_and_nerve_cord",
    json_path = "/home/user/ng_states/state.json",
    layer_name = "annotation1",
    output_path = "/home/user/point_clouds",
)