synapses_index.py

"""
    Blue Brain Project - Spatial-Index

    A small example script on how to load circuits,
    index them and perform some queries
"""

import brain_indexer
from brain_indexer import SynapseIndexBuilder
from libsonata import Selection

import os.path
import sys

CIRCUIT_2K = "/gpfs/bbp.cscs.ch/project/proj12/spatial_index/v4/circuit-2k"
EDGE_FILE = os.path.join(CIRCUIT_2K, "edges.h5")


def example_syn_index():
    # Creating a synapse index from SONATA input files:
    index = SynapseIndexBuilder.from_sonata_file(EDGE_FILE, "All")
    print("Index size:", len(index))

    # Specify the corners for the box query
    min_corner = [200, 200, 480]
    max_corner = [300, 300, 520]

    # Method #1 - Get the ids, then query the edge file for ANY data
    ids_in_region = index.box_query(min_corner, max_corner, fields="id")
    print("Found N points:", len(ids_in_region))

    # additional SONATA attributes can be retrieved during a query:
    z_coords = index.box_query(min_corner, max_corner, fields="afferent_center_z")

    # or by using the `ids`:
    sonata_dataset = brain_indexer.io.open_sonata_edges(EDGE_FILE, "All")
    z_coords = sonata_dataset.get_attribute(
        "afferent_center_z", Selection(ids_in_region)
    )
    print("First 10 Z coordinates: ", z_coords[:10])

    # Method #2, get the objects: position and id directly from index
    objs_in_region = index.box_query(min_corner, max_corner, fields="raw_elements")
    for i, obj in enumerate(objs_in_region):
        if i % 20 == 0:
            print("Sample synapse id:", obj.id, "Position", obj.centroid)
            print("Post-syn Neuron gid:", obj.post_gid,
                  "pre-syn Neuron gid:", obj.pre_gid)

    # Method #3, get the information as a dictionary of numpy arrays
    # Information for synapses includes: id, pre_gid, post_gid,
    # centroid and kind.
    dict_query = index.box_query(min_corner, max_corner)
    print(dict_query)


if __name__ == "__main__":
    if len(sys.argv) > 1:
        EDGE_FILE = sys.argv[1]
    if not os.path.exists(EDGE_FILE):
        print("EDGE file is not available:", EDGE_FILE)
        sys.exit(1)
    example_syn_index()