"""
This is a runfile to apply conduction velocities to a reconstructed mesh.
It's purpose is to provide easy access or terminal-level access to apply conduction velocities to a reconstructed mesh.
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.
The command line arguments can be requested by running ``python apply_cv.py -h``, but are also listed below.
These arguments overwrite any setting defined in settings.ini
Command-line arguments:
name: name of the file containing the conduction velocities. The file must be a .csv file containing the columns
'x', 'y', 'z' and 'speed'
--write_adjust (optional): Whether or not to write an adjustment file for closing off Na2+ channels.
--region_dir (optional): Name of the directory containing .csv files with indices of mesh points that need to be
set to a conduction velocity of 0, if this is wanted.
By default, it does not look for this directory
--speed_file (optional): Name of the .csv file containing coordinates and conduction velocity values to
interpolate. Default = 'speed.csv'
--ncv (optional): Amount of conduction velocity distributions to calculate based on the given file.
If ncv > 1, then random distributions will be calculated based on the input file.
--speed_col (optional): Name of the column in speed.csv that contains the conduction velocity values.
Default='speed'
--writeVTK (optional): write out the reconstructed mesh with its speed values interpolated in .vtk format.
These meshes will have a suffix '_CV=n' where n denotes the conduction velocity variation.
"""
from carto_mesh import *
import argparse
[docs]def run(meshname: str = '', speed_file: str = "speed.csv", region_dir: str = '', write_adjust: bool = False,
writeVTK: bool = False, ncv=None, speed_col: str = 'speed'):
"""
Reads in a reconstructed .vtk mesh and interpolates conduction velocities from <speed_file>. If region_dir
is given, also reads in the point indices from the .csv files in this directory and sets the conduction velocity
of these points to 0.
Args:
meshname: Name of the reconstructed .vtk mesh to interpolate conduction velocities on, or the directory containing this mesh
speed_file: Name of the file containing the coordinates and conduction velocity values to interpolate.
region_dir: Name of the directory containing indices of regions whose conduction velocity should be 0, if this directory exists.
write_adjust: Write an adjustment file to close off Na2+ channels.
writeVTK: Write the interpolated mesh to .vtk for inspection.
ncv: Amount of conduction velocity distributions to calculate. If ncv > 1, then random conduction velocity
distributions will be calculated based on the input file
speed_col: Name of the column in speed.csv that contains the conduction velocity values. Default='speed'
Returns:
Nothing
"""
if '.vtk' not in meshname:
meshname += '*.vtk' # assure initialisation from .vtk file
mesh = CartoMesh(meshname)
mesh.applyCV(speed_file, region_dir=region_dir, write_VTK_file=writeVTK, ncv=ncv, speed_col=speed_col)
if write_adjust:
mesh.writeAdjustNa2()
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument('name', type=str, nargs='?',
help='Name of the reconstructed .vtk mesh (including .vtk extension), '
'or the directory that contains the carto mesh.',
default='')
parser.add_argument('--write_adjust', nargs='?',
help="Write an adjustment file to close off the Na2+ channel where CV=0",
default=False, const=True)
parser.add_argument('--region_dir', nargs='?', type=str,
help='Name of the directory containing .csv files with indices of mesh points that need to be '
'set to a conduction velocity of 0, if this is wanted. '
'By default, it does not look for this directory',
default='')
parser.add_argument('--speed_file', type=str,
help="Name of the .csv file containing coordinates and conduction velocity values to "
"interpolate.\n"
"Default = \'speed.csv\'",
default='speed.csv')
parser.add_argument('--ncv', nargs='?', type=int,
help='Amount of conduction velocity distributions to calculate based on the given file.'
'If ncv > 1, then random distributions will be calculated based on the input file.')
parser.add_argument('--speed_col', nargs='?', type=str,
help='Name of the column in speed.csv that contains the conduction velocity values.'
'Default=\'speed\'', default='speed')
parser.add_argument('--writeVTK', nargs='?', type=bool, default=False, const=True)
args = parser.parse_args()
run(args.name, args.speed_file, args.region_dir, args.write_adjust, args.writeVTK, args.ncv)
