So I found this:
When converting MATLAB code it might be necessary to first reshape a matrix to a linear sequence, perform some indexing operations
Example:
>> mafs = [(1:16)' (17:32)']
mafs =
1 17
2 18
3 19
4 20
5 21
6 22
7 23
8 24
9 25
10 26
11 27
12 28
13 29
14 30
15 31
16 32
>> reshape(mafs,[4 4 2])
ans(:,:,1) =
1 5 9 13
2 6 10 14
3 7 11 15
4 8 12 16
ans(:,:,2) =
17 21 25 29
18 22 26 30
19 23 27 31
20 24 28 32
>>> import numpy as np
>>> mafs = np.c_[np.arange(1,17), np.arange(17,33)]
>>> mafs.shape
(16, 2)
>>> mafs[:,0]
array([ 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16])
>>> mafs[:,1]
array([17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32])
>>> r = np.reshape(mafs, (4,4,2), order="F")
>>> r.shape
(4, 4, 2)
>>> r[:,:,0]
array([[ 1, 5, 9, 13],
[ 2, 6, 10, 14],
[ 3, 7, 11, 15],
[ 4, 8, 12, 16]])
>>> r[:,:,1]
array([[17, 21, 25, 29],
[18, 22, 26, 30],
[19, 23, 27, 31],
[20, 24, 28, 32]])
I was having a similar issue myself, as I am also trying to make the transition from MATLAB to Python. I was finally able to convert a numpy matrix, given in depth, row, col, format to a single sheet of column vectors (per image).
In MATLAB I would have done something like:
output = reshape(imStack,[row*col,depth])
In Python this seems to translate to:
import numpy as np
output=np.transpose(imStack)
output=output.reshape((row*col, depth), order='F')