tomodrgn.convergence.calc_ccs_alltoall_intraepoch#

calc_ccs_alltoall_intraepoch(outdir: str, plot_format: Literal['png', 'svg'], epochs: ndarray, labels: str, mask: str | None = None, thresh: int = 99, dilate: int | None = None, dist: int | None = None) → None[source]#

For each epoch in epochs, calculates the (auto-masked) correlation coefficient between each pair of volumes generated at that epoch. Assumes that volume paths look like outdir/vols.epoch/vol_123.mrc. Saves a clustermap of the all-to-all correlation coefficients at each epoch.

Parameters:

  • outdir – path to base directory to save outputs

  • plot_format – file format with which to save plots

  • epochs – array of epochs to analyze

  • labels – a unique letter assigned to each local maxima particle

  • mask – mask to calculate from volumes, one of [None, ‘sphere’, ‘tight’, ‘soft’]

  • thresh – data percentile threshold at which to binarize mask when calculating ‘tight’ or initializing ‘soft’ masks

  • dilate – for soft mask, number of pixels to expand auto-determined tight mask

  • dist – for soft mask, number of pixels over which to apply soft edge

Returns:

None