tomodrgn.convergence.calc_ccs_pairwise_epochs#
- calc_ccs_pairwise_epochs(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 successive pair of epochs in epochs, calculates the (auto-masked) correlation coefficient between the same particle’s tomoDRGN-evaluated volume at those epochs. Assumes that volume paths look like outdir/vols.epoch/vol_123.mrc. Assumes that vol_000 in epoch X is generated from the same particle as vol_000 in epoch Y. Saves a plot of the successive pairwise correlation coefficient across training epochs.
- 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