simple_mat_to_npy.py

import os
import numpy as np
from scipy.io import loadmat

def simple_mat_to_npy(file_name):
    '''Convert a .mat file  generated by Sources2D_to_simple_mat containing CNMFe
    data into a folder of .npy files.  The A matrix is reshaped such that neuron 
    footprints can be visualised with imshow(A[0]) etc.
    (c) Thomas Akam 2019. GPL-3 open source licence.
    '''
    data = loadmat(file_name)
    folder_name = data['file_name'][0].split('.')[0] + '_npy'
    os.mkdir(folder_name)
    # Reshape A to be size [n_neurons, image_y_dim, image_x_dim]
    A = data['A'].toarray().reshape([*np.flip(data['image_size'][0]),-1]).transpose()
    # Convert A from sparse matrix to numpy array.
    S = data['S'].toarray()
    np.save(os.path.join(folder_name, 'A')    , A            , allow_pickle=False)
    np.save(os.path.join(folder_name, 'S')    , S            , allow_pickle=False) 
    np.save(os.path.join(folder_name, 'C')    , data['C']    , allow_pickle=False)
    np.save(os.path.join(folder_name, 'C_raw'), data['C_raw'], allow_pickle=False)