lib5c.util.mathematics module¶

Module for mathematical utility functions.

lib5c.util.mathematics.gmean(array, pseudocount=1, axis=None)[source]¶

Compute the geometric mean of an input array.

Parameters

array (np.ndarray) – The array to take the geometric mean over.
pseudocount (float) – The pseudocount to add to the elements of array before logging.
axis (int, optional) – The axis to compute the mean over.

Returns

The geometric mean.

Return type

float

lib5c.util.mathematics.symmetrize(array, source='lower')[source]¶

Symmetrizes a square array using its lower triangular entries.

Parameters

array (np.ndarray) – Array to symmetrize. Must be square.
source ({'lower', 'upper'}) – What triangle of the matrix to symmetrize with.

Returns

A symmetrized copy of array.

Return type

np.ndarray

lib5c.util.mathematics.zero_nans(array)[source]¶

Zeros all the nan’s in an array. Useful for cases where functions like np.nansum() are not available (e.g., scipy.ndimage.convolve()).