preprocess_JSRT.py

import os
import numpy as np
from skimage import io, exposure

def make_lungs():
    path = '/path/to/JSRT/All247images/'
    for i, filename in enumerate(os.listdir(path)):
        img = 1.0 - np.fromfile(path + filename, dtype='>u2').reshape((2048, 2048)) * 1. / 4096
        img = exposure.equalize_hist(img)
        io.imsave('/path/to/JSRT/new/' + filename[:-4] + '.png', img)
        print 'Lung', i, filename

def make_masks():
    path = '/path/to/JSRT/All247images/'
    for i, filename in enumerate(os.listdir(path)):
        left = io.imread('/path/to/JSRT/Masks/left lung/' + filename[:-4] + '.gif')
        right = io.imread('/path/to/JSRT/Masks/right lung/' + filename[:-4] + '.gif')
        io.imsave('/path/to/JSRT/new/' + filename[:-4] + 'msk.png', np.clip(left + right, 0, 255))
        print 'Mask', i, filename

make_lungs()
make_masks()