drift_correction.py 文件源码

def compute_pairwise_shifts(imstack):
    # Calculates the pairwise shifts for images in a stack of format [frame, x, y].
    # returns shift vector as [y, x] for each pair, a 2 x N-1 array where N is num_frames

    scan_shape = imstack.shape
    num_pairs = scan_shape[0]-1 
    print('Correcting ' + str(num_pairs) + ' frames...')

    # Prepare window function (Hann)
    win = np.outer(np.hanning(scan_shape[1]),np.hanning(scan_shape[2]))

    # Pairwise shifts
    shift = np.zeros((2, num_pairs))
    for iPair in range(0, num_pairs):
        image = imstack[iPair]
        offset_image = imstack[iPair+1]
        shift[:,iPair], error, diffphase = register_translation_hybrid(image*win, offset_image*win, 
                                                                        exponent = 0.3, upsample_factor = 100)
        # Shifts are defined as [y, x] where y is shift of imaging location 
        # with respect to positive y axis, similarly for x
    return shift