Hack to split images along black gaps

convert.py

from numpy import array
from thunder import Images, ThunderContext

tsc = ThunderContext.start()

rawpath = ''
savepath = ''

data = tsc.loadImages(rawpath, inputFormat='tif', nplanes=1)

width = 512
gap = 102
n = 4

def split(oim):
    im = array([oim[width*i + gap*i: width*(i + 1) + gap*i, 0:width] for i in range(n)])
    return im.transpose(1, 2, 0)

corrected = Images(data.rdd.mapValues(split))

corrected.saveAsBinaryImages(savepath)