aligning_code_1

import numpy as np
from skimage.registration import phase_cross_correlation
#numpy for numerical operations
#phase_cross_relation to align the images

#modify the size of the array to fit the size of your image
Dim_size1 = np.array((1000, 1000, 1000), dtype=int)

#read image from a raw file
with open('C:/Users/XXX/sequence_8bit-scaled.raw', 'rb') as f:
    img_pre = np.fromfile(f, dtype=np.uint8)                            #open raw image file and read it into img_pre
    img_pre = img_pre.reshape(Dim_size1[0], Dim_size1[1], Dim_size1[2]) #reshape the image data into the dimensions given for the array before

#empty list to store aligned images
aligned_images = []

#reference image for alignment
reference_image = img_pre[0, :, :]    #set as the first slice of the image stack

#loop through each slice to align the images
for i in range(0, Dim_size1[0]):                                        #start from the first slice
    imgtest = img_pre[i, :, :]                                          #extract the current slice

    #calculate the shift needed to align the current slice with the reference image
    shift = phase_cross_correlation(reference_image, imgtest)[0]

    #apply the calculated shift to align the current slice
    aligned_image = np.roll(imgtest, shift.astype(int), axis=(0, 1))
    aligned_images.append(aligned_image)
#save the aligned images
save_path = 'C:/Users/XXXX/sequence_8bit_aligned.raw'                   #define save path
with open(save_path, 'wb') as f:
    for aligned_image in aligned_images:
        f.write(aligned_image.tobytes())                                #write each aligned image to file