Source code for reconstruct

"""
This is a runfile to reconstruct an input carto mesh to a simulatable mesh.

It's purpose is to provide easy access or terminal-level access to reconstruct a .mesh file.
It uses the :class:`~carto_mesh.CartoMesh` class from the :mod:`carto_mesh` module along with its dependencies.
If you like more control over this reconstruction process than the ``settings.ini`` file and the runfiles
:mod:`reconstruct` and :mod:`apply_cv`, then you can also ``from carto_mesh import *`` in python and use the class as you please.

If a speed.csv file is present in the same folder as the carto mesh and N_CV > 1 in ``settings.ini``, then these speeds
will be interpolated on the mesh.

If you want to apply conduction velocities after the mesh reconstruction (e.g. in case you want to select
non-conductive regions on the mesh *after* reconstruction), you must set N_CV = 0 in ``settings.ini``, reconstruct,
reset N_CV to a value of choice and run :mod:`apply_cv` with arguments of your choice.

This file can reconstruct an input Carto .mesh file when run in the terminal.
The command line arguments can be requested by running ``python reconstruct.py -h``, but are also listed below.
These arguments overwrite any setting defined in ``settings.ini``

Args:
    name: name of the input carto .mesh file or its parent directory.
    Default: the first .mesh file found in the given directory.

    --speed_file (optional): name of the .csv file containing columns 'x', 'y', 'z' and 'speed'.
    The conduction velocities as defined in this file will be interpolated on the finalised reconstructed mesh.
"""

import carto_mesh
import argparse


def run(meshname, speed_file):
    """
    Reconstructs an input carto .mesh file.
    Args:
        meshname: Name of the .mesh file to reconstruct, or name of the directory containing this file.
        speed_file: Name of the file containing the coordinates and conduction velocity values to interpolate, if this is wanted.

    Returns:

    """
    mesh = carto_mesh.CartoMesh(meshname)
    mesh.reconstruct()
    if speed_file:
        mesh.applyCV(speed_file, write_VTK_file=True)


if __name__ == '__main__':
    parser = argparse.ArgumentParser()
    parser.add_argument('name', type=str, nargs='?',
                        help='Name of the carto mesh, or the directory that contains the carto mesh.',
                        default='')
    parser.add_argument('--speed_file', type=str,
                        help='Name of the file containing coordinates and speed values to interpolate on the mesh, '
                             'if this file exists and you want to interpolate these immediately.',
                        defaul='')
    args = parser.parse_args()

    run(args.name, args.speed_file)