Builds lung dataset from mat file

build_dataset.py

import scipy.io as sio
import numpy as np
import scipy.misc

mat_contents = sio.loadmat('LungTrainingData.mat')
#matrix is of the form [x,y,n]

#['CT2', 'Right2', 'Left2', '__header__', '__globals__', '__version__', 'Trachea2']
images = mat_contents['CT2']
left_lung = mat_contents['Left2']
right_lung = mat_contents['Right2']
trachea = mat_contents['Trachea2']

m = np.max(images)
n = np.min(images)

print m
print n
shuffled = range(513)
np.random.shuffle(shuffled)

for i in range(513):
  valid = i>500
  t_v = 'validation' if valid else 'test'
  
  ind = shuffled[i]
  scipy.misc.toimage(images[:,:,ind], cmin=n, cmax=m).save('data/' + t_v + '/img' + str(i) + '.png')
  
  left = left_lung[:,:,ind]
  right = right_lung[:,:,ind]
  trach = trachea[:,:,ind]
  ann = left + right * 2 + trach * 3
  scipy.misc.toimage(ann, cmin=0, cmax=255).save('data/' + t_v + '/annotation' + str(i) + '.png')