I have a $100$x$100$ covariance matrix that looks like this. enter image description here

Some rows/cols are all-zero because those corresponding elements are not present in the sample from which covariance is calculated. I'm doing it this way:

    adjmats = [get_adjmat(graph) for graph in samples]                   # array of adjacency matrices
    reduced = functools.reduce(lambda x, y: np.add(x, y), adjmats)       # add all elem-wise
    adjacency = np.divide(reduced, len(adjmats))                         # divide by number: "mean"

    fig, ax = plt.subplots()

    covariance= np.cov(adjacency)                                        # getting covariance 

    def correlation_from_covariance(covariance):
        v = np.sqrt(np.diag(covariance))
        outer_v = np.outer(v, v)
        correlation = covariance / outer_v                   <<<<<<      # complains here!
        correlation[covariance == 0] = 0
        return correlation

    correlation = correlation_from_covariance(covariance)                # attempting to convert

    im = ax.imshow(correlation)

When i try to get the correlation matrix, which i vaguely know to be the std-"normalized" version of covariance matrix, numpy complains : subunit_graph.py:218: RuntimeWarning: invalid value encountered in true_divide correlation = covariance / outer_v, but i still get a sensible correlation matrix. Can somebody explain to me what exactly is going on with true_divide in there?
Thank you very much!

enter image description here


1 Answer 1


What about the following?

Dinv = np.diag(1.0 / np.sqrt(np.diag(cov_matrix)))
corr = Dinv @ cov_matrix @ Dinv

The above avoids any division except by the diagonal values, which should be nonzero anyway.


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