Copy upper triangle to lower triangle in a python matrix

Question

       iluropoda_melanoleuca  bos_taurus  callithrix_jacchus  canis_familiaris
ailuropoda_melanoleuca     0        84.6                97.4                44
bos_taurus                 0           0                97.4              84.6
callithrix_jacchus         0           0                   0              97.4
canis_familiaris           0           0                   0                 0

This is a short version of the python matrix I have. I have the information in the upper triangle. Is there an easy function to copy the upper triangle to the down triangle of the matrix?

question from:https://stackoverflow.com/questions/16444930/copy-upper-triangle-to-lower-triangle-in-a-python-matrix

Answer 1

To do this in NumPy, without using a double loop, you can use tril_indices. Note that depending on your matrix size, this may be slower that adding the transpose and subtracting the diagonal though perhaps this method is more readable.

>>> i_lower = np.tril_indices(n, -1)
>>> matrix[i_lower] = matrix.T[i_lower]  # make the matrix symmetric

Be careful that you do not try to mix tril_indices and triu_indices as they both use row major indexing, i.e., this does not work:

>>> i_upper = np.triu_indices(n, 1)
>>> i_lower = np.tril_indices(n, -1)
>>> matrix[i_lower] = matrix[i_upper]  # make the matrix symmetric
>>> np.allclose(matrix.T, matrix)
False