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