I encountered a quite weird problem when indexing a numpy ndarray. You can produce the result with following code. I don't understand why the result of indexing a is somehow transposed while the result of 2d array b is normal. Thanks.
In [1]: a = np.array(range(6)).reshape((1,2,3))
In [2]: mask = np.array([True, True, True])
In [3]: a
Out[3]:
array([[[0, 1, 2],
[3, 4, 5]]])
In [4]: a[0, :, mask]
Out[4]:
array([[0, 3],
[1, 4],
[2, 5]])
In [5]: a[0, :, mask].shape
Out[5]: (3, 2)
In [6]: b = np.array(range(6)).reshape((2,3))
In [7]: b[:, mask].shape
Out[7]: (2, 3)