tomodrgn.commands.analyze.analyze_z_onedimensional

analyze_z_onedimensional(z: ndarray, outdir: str, plot_format: Literal['png', 'svgz'], vg: VolumeGenerator, skip_vol: bool = False, ondata: bool = False, downsample: int | None = None, lowpass: float | None = None, flip: bool = False, invert: bool = False) → None

Plotting and volume generation for 1D z

Parameters:

• z – array of 1-D latent embeddings, shape (nptcls, 1)

• outdir – directory in which to save all outputs (plots and generated volumes)

• plot_format – file format with which to save plots

• vg – VolumeGenerator instance to aid volume generation at specficied z values

• skip_vol – whether to skip generation of volumes

• ondata – whether to use the closest on-data latent point to each z percentile for plotting and volume generation

• downsample – downsample reconstructed volumes to this box size (units: px) by Fourier cropping, None means to skip downsampling

• lowpass – lowpass filter reconstructed volumes to this resolution (units: Å), None means to skip lowpass filtering

• flip – flip the chirality of the reconstructed volumes by inverting along the z axis

• invert – invert the data sign of the reconstructed volumes (light-on-dark vs dark-on-light)

Returns:

None