betweenness failure
Closed this issue · 4 comments
Hi Roan,
Good to meet you via Bug Reporting. I'm working on a new pipeline called PyNets (see my repo) that integrates bctpy with nilearn, and I'm testing the variety of functions that you ported over from the BCT into bctpy, so you may hear a lot from me in the coming months/years.
First order of business, and I'm probably just being amateur here, but any idea why I'm having trouble extracting betweenness measures?
In [28]: in_mat_wei
Out[28]:
array([[ 0. , 0.68737646, 0.48285148, ..., 0.09148687,
0.4492529 , 0.48168688],
[ 0.68737646, 0. , 0.3552837 , ..., 0. ,
0.25858502, 0.25389435],
[ 0.48285148, 0.3552837 , 0. , ..., 0. ,
0.40509753, 0.33309095],
...,
[ 0.09148687, 0. , 0. , ..., 0. ,
0.09396403, 0.45157042],
[ 0.4492529 , 0.25858502, 0.40509753, ..., 0.09396403,
0. , 0.54513586],
[ 0.48168688, 0.25389435, 0.33309095, ..., 0.45157042,
0.54513586, 0. ]])
In [37]: bct.betweenness_wei(in_mat_wei)
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
<ipython-input-37-8ce1fdf60561> in <module>()
----> 1 bct.betweenness_wei(in_mat_wei)
/work/04171/dpisner/stampede/lib/python2.7/site-packages/bct/algorithms/centrality.pyc in betweenness_wei(G)
131 DP = np.zeros((n,))
132 for w in Q[:n - 1]:
--> 133 BC[w] += DP[w]
134 for v in np.where(P[w, :])[0]:
135 DP[v] += (1 + DP[w]) * NP[v] / NP[w]
IndexError: only integers, slices (`:`), ellipsis (`...`), numpy.newaxis (`None`) and integer or boolean arrays are valid indicesI ran the betweenness_wei code up to that point with a sample matrix, and it looks like w is a float being used as an index. That's apparently not permitted, so it looks like we'll want to cast Q to a dtype like np.int64 or just cast w to an int.
Does that binarization fix the original issue? I couldn't reproduce it with my sample matrices but I didn't any time to investigate it.
I had been able to reproduce the error, and I didn't get it after the change. I also changed two other functions that seemed susceptible to the same issue: edge_betweenness_bin and edge_betweenness_wei. I didn't produce an error for either of those, but I verified that they ran without errors for me after the change. I'm still curious if this fixed problems for @dpisner453.