step_0_rename_files.py

import os
import numpy as np
import shutil
import nd2
import tifffile
import easygui


path = easygui.diropenbox('Select folder with nd2 images')
output_folder = easygui.diropenbox('Select folder to save preprocessed images')
files = os.listdir(path)
files.sort()

def recombine_file_pair(files, i):
    filename_0 = files[i].split(' ')[0]
    filename_1 = files[i+1].split(' ')[0]
    if os.path.isfile(output_folder + os.path.sep + filename_0 + '.tif'):
        print('file already combined, skipping')
    else: 
        print('loading files ' + str(files[i]) + ' and ' + str(files[i+1]) + ' iteration ' + str(i))
        im_1 = nd2.imread(path + os.path.sep +  files[i])
        im_2 = nd2.imread(path + os.path.sep +  files[i+1])
        
        if len(im_1.shape) == 3:
            assert len(im_2.shape) == 4
            assert im_1.shape[0] == im_2.shape[0]
            assert im_1.shape[1] == im_2.shape[2]
            assert im_1.shape[2] == im_2.shape[3]
            newim = np.stack((im_1, im_2[:,0,:,:], im_2[:,1,:,:], im_2[:,2,:,:]), axis=1)   
            print('saving file ' + str(filename_0 + '.tif'))     
            tifffile.imwrite(output_folder + os.path.sep + filename_0 + '.tif', newim, imagej=True)
        
                                    
        if len(im_1.shape) == 4:
            assert len(im_2.shape) == 3
            assert im_2.shape[0] == im_1.shape[0]
            assert im_2.shape[1] == im_1.shape[2]
            assert im_2.shape[2] == im_1.shape[3]
            newim = np.stack((im_2, im_1[:,0,:,:], im_1[:,1,:,:], im_1[:,2,:,:]), axis=1)        
            print('saving file ' + str(filename_0 + '.tif'))     
            tifffile.imwrite(output_folder + os.path.sep + filename_0 + '.tif', newim, imagej=True)
                                        

for filenum in range(0, len(files), 2):
    recombine_file_pair(files, filenum)