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 + ' .'