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from pathlib import Path
import typer
from vcelldata.mesh import CartesianMesh
from vcelldata.simdata_models import PdeDataSet, DataFunctions
from vcelldata.zarr_writer import write_zarr
app = typer.Typer()
@app.command(name="vc_to_zarr", help="Convert a VCell FiniteVolume simulation dataset to Zarr")
def n5_to_zarr(
sim_data_dir: Path = typer.Argument(..., help="path to vcell dataset directory"),
sim_id: int = typer.Argument(..., help="simulation id (e.g. 946368938)"),
job_id: int = typer.Argument(..., help="job id (e.g. 0"),
zarr_path: Path = typer.Argument(..., help="path to zarr dataset to write to")):
pde_dataset = PdeDataSet(base_dir=sim_data_dir, log_filename=f"SimID_{sim_id}_{job_id}_.log")
pde_dataset.read()
data_functions = DataFunctions(function_file=sim_data_dir / f"SimID_{sim_id}_{job_id}_.functions")
data_functions.read()
mesh = CartesianMesh(mesh_file=sim_data_dir / f"SimID_{sim_id}_{job_id}_.mesh")
mesh.read()
write_zarr(pde_dataset=pde_dataset, data_functions=data_functions, mesh=mesh, zarr_dir=zarr_path)
def main():
app()
if __name__ == "__main__":
main() |