Source code for miv_simulator.simulator.generate_synapse_forest

import os
import shutil
import subprocess

import h5py
from miv_simulator import config


def _bin_check(bin: str) -> None:
    if not shutil.which(bin):
        raise FileNotFoundError(f"{bin} not found. Did you add it to the PATH?")


def _run(cmd):
    try:
        subprocess.check_output(
            cmd,
            stderr=subprocess.STDOUT,
        )
    except subprocess.CalledProcessError as e:
        error_message = e.output.decode()
        print(f"{os.getcwd()}$:")
        print(" ".join(cmd))
        print("Error:", error_message)
        raise subprocess.CalledProcessError(
            e.returncode, e.cmd, output=error_message
        )


def generate_synapse_forest(
    filepath: str,
    tree_output_filepath: str,
    output_filepath: str,
    population: config.PopulationName,
    morphology: config.SWCFilePath,
) -> None:
    # create tree
    if not os.path.isfile(tree_output_filepath):
        _bin_check("neurotrees_import")
        _run(
            [
                "neurotrees_import",
                population,
                tree_output_filepath,
                morphology,
            ]
        )

        _run(
            [
                "h5copy",
                "-p",
                "-s",
                "/H5Types",
                "-d",
                "/H5Types",
                "-i",
                filepath,
                "-o",
                tree_output_filepath,
            ]
        )

    if not os.path.isfile(output_filepath):
        # determine population ranges
        with h5py.File(filepath, "r") as f:
            idx = list(
                reversed(
                    f["H5Types"]["Population labels"].dtype.metadata["enum"]
                )
            ).index(population)
            offset = f["H5Types"]["Populations"][idx][0]

        _bin_check("neurotrees_copy")
        _run(
            [
                "neurotrees_copy",
                "--fill",
                "--output",
                output_filepath,
                tree_output_filepath,
                population,
                str(offset),
            ]
        )