Note
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Synthesize a cell with external diametrizerΒΆ
This example shows how to synthesize a cell with an external diametrizer.
An external diametrizer should have the signature described in
neurots.generate.diametrizer.build.
The code diameter_synthesis provides an example of such external diametrizer.
Warning
Note that the diameter-synthesis package must be installed.
33 from pathlib import Path
34
35 from diameter_synthesis import build_diameters # pylint: disable=import-error
36
37 import neurots
38
39
40 def run(output_dir, data_dir):
41 """Run the example for generating a cell with external diametrizer."""
42 # Initialize a neuron with an external diametrizer
43 N = neurots.NeuronGrower(
44 input_distributions=data_dir / "IN_distr.json",
45 input_parameters=data_dir / "IN_params.json",
46 external_diametrizer=build_diameters.build,
47 )
48
49 # Grow the neuron
50 neuron = N.grow()
51
52 # Export the synthesized cell
53 neuron.write(output_dir / "generated_cell.asc")
54 neuron.write(output_dir / "generated_cell.swc")
55 neuron.write(output_dir / "generated_cell.h5")
56
57
58 if __name__ == "__main__":
59 result_dir = Path("results_neuron_external_diameter")
60 result_dir.mkdir(parents=True, exist_ok=True)
61
62 run(result_dir, Path("data"))