Convert a list of numpy arrays to a 5D numpy array

Question

I am having a database of 7000 objects (list_of_objects), each one of these files contains a numpy array with size of 10x5x50x50x3. I would like to create a 5d numpy array that will contain 7000*10x5x50x50x3. I tried to do so using two for-loops. My sample code:

fnl_lst = []
for object in list_of_objects:
     my_array = read_array(object) # size 10x5x50x50x3
     for ind in my_array:
        fnl_lst.append(ind)
fnl_lst= np.asarray( fnl_lst) # print(fnl_lst) -> (70000,)

That code result in the end in a nested numpy array which contains 70000 arrays each of them has a size of 5x50x50x3. However, I would like instead to build a 5d array with size 70000x5x50x50x3. How can I do that instead?

Possible duplicate of How to convert list of numpy arrays into single numpy array? — w-m
– w-m, Commented Apr 9, 2019 at 16:17
Are you sure all the ind are the same shape? What does np.vstack([read_array(o) for o in list_of_objects]) produce? — hpaulj
– hpaulj, Commented Apr 9, 2019 at 16:33
@hpaulj I will cross-check. Maybe that is my issue that the ind for some reason do not have the same size. — Jose Ramon
– Jose Ramon, Commented Apr 9, 2019 at 17:17
What is fnl_lst.dtype? If object, then yes, there's some variation in the shapes. — hpaulj
– hpaulj, Commented Apr 9, 2019 at 17:45
True one files have different size and could not monitor it. Now it works properly. — Jose Ramon
– Jose Ramon, Commented Apr 9, 2019 at 18:47

Marat · Accepted Answer · 2019-04-09 16:34:18Z

2

fnl_lst = np.stack([ind for ind in read_array(obj) for obj in list_of_objects])

or, just append to the existing code:

fnl_lst = np.stack(fnl_lst)

UPD: by hpaulj's comment, if my_array is indeed 10x5x50x50x3, this might be enough:

fnl_lst = np.stack([read_array(obj) for obj in list_of_objects])

answered Apr 9, 2019 at 16:34

Marat

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