Stack 2D array to 4D

Question

Given a list with 6 2D arrays with the same dimension (200, 200). Every three consecutive arrays can be stacked up to a 3D array.

Desired output:

array = (200, 200, 3, 2)

I am familiar with np.dstack:

n = 6
array = []
for i in range(n):
    x = np.random.randn(n1, n2)
    array.append(x)
array = np.dstack(array)

Speed should be considered as I am working with large data sets.

Edit: I created images for testing: https://wetransfer.com/downloads/afb0a2fbfbd8b6047a68dad41b56a0d520200509184625/761355

Adapted Paddy's answer:

import numpy as np
from skimage import io
import glob
from natsort import natsorted

DIR = (Set folder path with the test images)

list_path = glob.glob(DIR + "/*.png")
list_path_sorted = natsorted(list_path)
array = []
for i in range(len(list_path_sorted)):
    image = np.array( io.imread(list_path_sorted[i]) )
    array.append(image)
a = np.dstack(array).reshape(200, 200, 3, 2)

a.shape
>>> (200, 200, 3, 2)

Issue: The order in the third dimension doesn't match. To test this:

plt.imshow(a[:,:,0,0]) -> should show picture with A1
plt.imshow(a[:,:,2,0]) -> should show picture with A3
plt.imshow(a[:,:,0,1]) -> should show picture with B1
plt.imshow(a[:,:,2,1]) -> should show picture with B3

I stuck with the condition that three consecutive arrays in a list forms a 3D stack. — ChristineP
– ChristineP, Commented May 9, 2020 at 17:37

Paddy Harrison · Accepted Answer · 2020-05-09 19:04:55Z

2

dstack as you suggested then reshape the resulting array:

import numpy as np

# six arrays of (200, 200)
n = 6
array = []
for i in range(n):
    x = np.random.randn(n1, n2)
    array.append(x)

# EDIT to use 'F' ordering
a = np.dstack(array).reshape(200, 200, 3, 2, order='F')

a.shape
>>> (200, 200, 3, 2)

edited May 9, 2020 at 19:04

answered May 9, 2020 at 17:37

Paddy Harrison

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2 Comments

ChristineP Over a year ago

Thanks for the quick answer. It seems the order of the arrays are not correct. I replaced the line: x = np.random.randn(n1, n2) with random test images to test this.

Paddy Harrison Over a year ago

Made an edit to fix the problem. Normally uses 'C' (row) ordering, but it can also use 'F' (column, F for Fortran) ordering. In this case the images should be in the correct place, ie. a[:,:,0,0] = 'A1', a[:,:,0,1] = 'B1' (whereas before a[:,:,0,1] = 'A2').

hpaulj · Accepted Answer · 2020-05-09 20:13:48Z

1

I can't play with your images, so I'll generate a list of distinctive (2,2) arrays:

In [412]: alist = [np.arange(i,i+4).reshape(2,2) for i in range(6)]                                    
In [413]: alist                                                                                        
Out[413]: 
[array([[0, 1],
        [2, 3]]), array([[1, 2],
        [3, 4]]), array([[2, 3],
        [4, 5]]), array([[3, 4],
        [5, 6]]), array([[4, 5],
        [6, 7]]), array([[5, 6],
        [7, 8]])]

With dstack we get a (2,2,6) array

In [414]: arr = np.dstack(alist)                                                                       
In [415]: arr                                                                                          
Out[415]: 
array([[[0, 1, 2, 3, 4, 5],
        [1, 2, 3, 4, 5, 6]],

       [[2, 3, 4, 5, 6, 7],
        [3, 4, 5, 6, 7, 8]]])

The (3,2) reshape produces:

In [417]: arr.reshape(2,2,3,2)                                                                         
Out[417]: 
array([[[[0, 1],
         [2, 3],
         [4, 5]],

        [[1, 2],
         [3, 4],
         [5, 6]]],


       [[[2, 3],
         [4, 5],
         [6, 7]],

        [[3, 4],
         [5, 6],
         [7, 8]]]])

Sounds like you aren't happy with that layout (your edits are bit unclear). We can transpose values

In [419]: arr.reshape(2,2,2,3).transpose(0,1,3,2)                                                      
Out[419]: 
array([[[[0, 3],
         [1, 4],
         [2, 5]],

        [[1, 4],
         [2, 5],
         [3, 6]]],


       [[[2, 5],
         [3, 6],
         [4, 7]],

        [[3, 6],
         [4, 7],
         [5, 8]]]])

With this last arrangement,

In [431]: _419[:,:,2,0]                                                                                
Out[431]: 
array([[2, 3],
       [4, 5]])
In [432]: _413[2]       # alist                                                                               
Out[432]: 
array([[2, 3],
       [4, 5]])

In [435]: _419[:,:,0,1]                                                                                
Out[435]: 
array([[3, 4],
       [5, 6]])
In [436]: _413[3]                                                                                      
Out[436]: 
array([[3, 4],
       [5, 6]])

edited May 9, 2020 at 20:13

answered May 9, 2020 at 18:42

hpaulj

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2 Comments

ChristineP Over a year ago

I apologise for the poor edits. Please see the updated edits with a working code and download link to the images. Just set the DIR to the download folder with the images. I hope it makes it clearer.

hpaulj Over a year ago

Assuming your images are in the list in the order [A1,A2,A3,B1,B2,B3], then my last ordering is one you want - see my edit

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