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org: Remove pydanclick as cli generator
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,167 @@ | ||
| """Simple run script.""" | ||
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| import click | ||
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| from ttsim3d.models import Simulator, SimulatorConfig | ||
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| @click.command() | ||
| @click.option( | ||
| "--pdb-filepath", | ||
| type=click.Path(), | ||
| required=True, | ||
| help="The path to the PDB file containing the atomic structure to simulate.", | ||
| ) | ||
| @click.option( | ||
| "--mrc-filepath", | ||
| type=click.Path(), | ||
| required=True, | ||
| help="File path to save simulated volume.", | ||
| ) | ||
| @click.option( | ||
| "--pixel-spacing", | ||
| type=float, | ||
| help=( | ||
| "The pixel spacing of the simulated volume in units of Angstroms. " | ||
| "Must be greater than 0." | ||
| ), | ||
| ) | ||
| @click.option( | ||
| "--volume-shape", | ||
| type=(int, int, int), | ||
| help="The shape of the simulated volume in pixels.", | ||
| ) | ||
| @click.option( | ||
| "--voltage", | ||
| type=float, | ||
| default=300.0, | ||
| help="The voltage of the microscope in kV. Default is 300 kV.", | ||
| ) | ||
| @click.option( | ||
| "--upsampling", | ||
| type=int, | ||
| default=-1, | ||
| help=( | ||
| "The upsampling factor to apply to the simulation. The default is -1 " | ||
| "and corresponds to automatic calculation of the upsampling factor." | ||
| ), | ||
| ) | ||
| @click.option( | ||
| "--b-factor-scaling", | ||
| type=float, | ||
| default=1.0, | ||
| help=( | ||
| "The scaling factor to apply to the B-factors of the atoms in the " | ||
| "pdb file. The default is 1.0." | ||
| ), | ||
| ) | ||
| @click.option( | ||
| "--additional-b-factor", | ||
| type=float, | ||
| default=0.0, | ||
| help=( | ||
| "Additional B-factor to apply to the atoms in the pdb file. The " | ||
| "default is 0.0." | ||
| ), | ||
| ) | ||
| @click.option( | ||
| "--apply-dose-weighting", | ||
| type=bool, | ||
| default=True, | ||
| help="If True, apply dose weighting to the simulation. Default is True.", | ||
| ) | ||
| @click.option( | ||
| "--crit-exposure-bfactor", | ||
| type=float, | ||
| default=-1.0, | ||
| help=( | ||
| "B-factor to use in critical exposure calculations. The default is -1 " | ||
| "and corresponds to the fitted critical exposure function in Grant " | ||
| "and Grigorieff, 2015." | ||
| ), | ||
| ) | ||
| @click.option( | ||
| "--dose-filter-modify-signal", | ||
| type=click.Choice(["None", "sqrt", "rel_diff"]), | ||
| default="None", | ||
| help=( | ||
| "Signal modification to apply to the dose filter. Currently supports " | ||
| "'None', 'sqrt', and 'rel_diff'." | ||
| ), | ||
| ) | ||
| @click.option( | ||
| "--dose-start", | ||
| type=float, | ||
| default=0.0, | ||
| help="The starting dose in e/A^2. Default is 0.0.", | ||
| ) | ||
| @click.option( | ||
| "--dose-end", | ||
| type=float, | ||
| default=30.0, | ||
| help="The ending dose in e/A^2. Default is 30.0.", | ||
| ) | ||
| @click.option( | ||
| "--apply-dqe", | ||
| is_flag=True, | ||
| help="If True, apply a DQE filter to the simulation.", | ||
| ) | ||
| @click.option( | ||
| "--mtf-reference", | ||
| type=str, | ||
| default="k2_300kV", | ||
| help=( | ||
| "Path to the modulation transfer function (MTF) reference star " | ||
| "file, or one of the known MTF reference files. " | ||
| "Default is 'k2_300kV'." | ||
| ), | ||
| ) | ||
| @click.option( | ||
| "--gpu-ids", | ||
| type=list[int], | ||
| multiple=True, | ||
| help="A list of GPU IDs to use for the simulation. Currently unused.", | ||
| ) | ||
| def main( | ||
| pdb_filepath: str, | ||
| mrc_filepath: str, | ||
| pixel_spacing: float, | ||
| volume_shape: tuple[int, int, int], | ||
| voltage: float, | ||
| upsampling: int, | ||
| b_factor_scaling: float, | ||
| additional_b_factor: float, | ||
| apply_dose_weighting: bool, | ||
| crit_exposure_bfactor: float, | ||
| dose_filter_modify_signal: str, | ||
| dose_start: float, | ||
| dose_end: float, | ||
| apply_dqe: bool, | ||
| mtf_reference: str, | ||
| gpu_ids: list[int], | ||
| ) -> None: | ||
| """Run a structure simulation through the CLI.""" | ||
| simulator_config = SimulatorConfig( | ||
| voltage=voltage, | ||
| apply_dose_weighting=apply_dose_weighting, | ||
| crit_exposure_bfactor=crit_exposure_bfactor, | ||
| dose_filter_modify_signal=dose_filter_modify_signal, # type: ignore | ||
| dose_start=dose_start, | ||
| dose_end=dose_end, | ||
| apply_dqe=apply_dqe, | ||
| mtf_reference=mtf_reference, | ||
| upsampling=upsampling, | ||
| ) | ||
| simulator = Simulator( | ||
| pixel_spacing=pixel_spacing, | ||
| volume_shape=volume_shape, | ||
| pdb_filepath=pdb_filepath, | ||
| b_factor_scaling=b_factor_scaling, | ||
| additional_b_factor=additional_b_factor, | ||
| simulator_config=simulator_config, | ||
| ) | ||
| simulator.export_to_mrc(mrc_filepath=mrc_filepath) | ||
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| if __name__ == "__main__": | ||
| main() |
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