JPEG200_MRI_Compression

jpeg2000_compression.py

import numpy as np
import h5py
import glymur

def image_space_save_as_jpg2000(in_dir, out_dir):
    """

       :param file_name: image_space file name for compression i.e. 58 x 640 x 129 x 240; 58 coils, oversampled x-axis by factor 2,
        zero value removed y axis, z are number of slices
       :param out_dir: output dir for storing imaginary and real parts of image space

       """
    compression_ratio = [5]
    file_name = in_dir
    file_name += "original_img_space_oversampled_without_grappa.h5"

    img_space_file = h5py.File(file_name, "r")
    img_space_matrix = img_space_file["imgspace"]
    data = np.array(img_space_matrix)

    ## Normalizing the intensity scale
    for c in range(0, img_space_matrix.shape[0]):
        print("creating files for coil: ", c)
        for slice in range(0, img_space_matrix.shape[3]):
            one_slice = data[c, :, :, slice]
            real_min_val = np.amin(one_slice.real)
            real_max_val = np.amax(one_slice.real)
            imag_min_val = np.amin(one_slice.imag)
            imag_max_val = np.amax(one_slice.imag)
            one_slice.real -= real_min_val
            one_slice.real /= (real_max_val - real_min_val)
            one_slice.imag -= imag_min_val
            one_slice.imag /= (imag_max_val - imag_min_val)

            real_part = img_as_uint(one_slice.real)
            imag_part = img_as_uint(one_slice.imag)
            print("real_part data type: ", real_part.dtype)
            print("imaginary part data typ: ", imag_part.dtype)
            jp2 = glymur.Jp2k(out_dir + str(c) + "_" + str(slice) + "_real.jp2", data=real_part, cratios=compression_ratio)
            jp2 = glymur.Jp2k(out_dir + str(c) + "_" + str(slice) + "_imag.jp2", data=imag_part, cratios=compression_ratio)