Pairwise bootstrap ISC doesn't work

Hi,

I’m using bootstrap_isc with pairwise=True. The first time I ran it, I got the error from assert np.allclose(voxel_iscs, voxel_iscs.T) because my isc_data has nan. When we do a comparison, nan is never equal to nan. So I applied np.nan_to_num(isc_data) and I ran a whole night for a (378, 161032) ISC data, neither any results nor errors. It’s weird.

My questions are:

1. is assert np.allclose(voxel_iscs, voxel_iscs.T) that necessary to be here? Since nan != nan, whenever we compare two matrices with nans, even if they are identical, we’ll always get False.
2. what happened to my second try with np.nan_to_num(isc_data)? There is no error so I don’t what was going on. I guess, it just needs more time to do the computation.

Thank you!

[snastase]

@Yibeichan squareform is kind of like a toggle: if you input a distance vector, it outputs the distance matrix; if you input a distance matrix, it outputs the distance vector. Those assert statements probably snuck in there when I was initially writing the code (and hadn’t thought about force='tomatrix'). I don’t think the force='tomatrix' is strictly necessary given the tests in _check_isc_input, but I don’t mind a little redundancy if it makes the squareform easier to interpret.

[yibeichan]

oh yeah, assert voxel_iscs.shape[0] == voxel_iscs.shape[1] only checks the shape, but force='tomatrix' actually returns you a matrix. But I thought a matrix is default if the input is in the correct shape?

I’m just curious when we will get a vector, not a matrix from squareform() if we don’t specify force='tovector'. I mean, do we have to add force='tomatrix' in _check_isc_input?