import numpy as np
import os
import dicom


N = 82
W = 512
H = 512
path1 = 'DOI'
path2 = 'images'
if not os.path.exists(path2):
    os.makedirs(path2)

for n in range(N):
    volumeID = '{:0>4}'.format(n + 1)
    print 'Processing File ' + volumeID
    filename1 = 'PANCREAS_' + volumeID
    directory1 = os.path.join(path1, filename1)
    filename2 = volumeID + '.npy'
    for path_, _, file_ in os.walk(directory1):
        L = len(file_)
        if L > 0:
            print '  ' + str(L) + ' slices along the axial view.'
            data = np.zeros((W, H, L), dtype = np.int16)
            for f in sorted(file_):
                file1 = os.path.abspath(os.path.join(path_, f))
                image = dicom.read_file(file1)
                sliceID = image.data_element("InstanceNumber").value - 1
                if image.pixel_array.shape[0] <> 512 or image.pixel_array.shape[1] <> 512:
                    exit('  Error: DICOM image does not fit ' + str(W) + 'x' + str(H) + ' size!')
                data[:, :, sliceID] = image.pixel_array
            file2 = os.path.join(path2, filename2)
            np.save(file2, data)
    print 'File ' + volumeID + ' is saved in ' + file2 + ' .'