dicom_viz.py

import shutil
import os
import cv2
import numpy as np
import dicom
import sys
from dicom import dataelem
import pickle

have_PIL = True
try:
    import PIL.Image
    import PIL.ImageOps as ops
except ImportError:
    have_PIL = False

have_numpy = True
try:
    import numpy as np
except ImportError:
    have_numpy = False



def get_LUT_value(data, window, level):
    """Apply the RGB Look-Up Table for the given
       data and window/level value."""
    if not have_numpy:
        raise ImportError("Numpy is not available."
                          "See http://numpy.scipy.org/"
                          "to download and install")

    return np.piecewise(data,
                        [data <= (level - 0.5 - (window - 1) / 2),
                         data > (level - 0.5 + (window - 1) / 2)],
                        [0, 255, lambda data: ((data - (level - 0.5)) /
                         (window - 1) + 0.5) * (255 - 0)])


def get_PIL_image(dataset):
    """Get Image object from Python Imaging Library(PIL)"""
    if not have_PIL:
        raise ImportError("Python Imaging Library is not available. "
                          "See http://www.pythonware.com/products/pil/ "
                          "to download and install")

    if ('PixelData' not in dataset):
        raise TypeError("Cannot show image -- DICOM dataset does not have "
                        "pixel data")
    # can only apply LUT if these window info exists
    if ('WindowWidth' not in dataset) or ('WindowCenter' not in dataset):
        bits = dataset.BitsAllocated
        samples = dataset.SamplesPerPixel
        if bits == 8 and samples == 1:
            mode = "L"
        elif bits == 8 and samples == 3:
            mode = "RGB"
        elif bits == 16:
            # not sure about this -- PIL source says is 'experimental'
            # and no documentation. Also, should bytes swap depending
            # on endian of file and system??
            mode = "I;16"
        else:
            raise TypeError("Don't know PIL mode for %d BitsAllocated "
                            "and %d SamplesPerPixel" % (bits, samples))

        # PIL size = (width, height)
        size = (dataset.Columns, dataset.Rows)

        # Recommended to specify all details
        # by http://www.pythonware.com/library/pil/handbook/image.htm
        im = PIL.Image.frombuffer(mode, size, dataset.PixelData,
                                  "raw", mode, 0, 1)

    else:
        image = get_LUT_value(dataset.pixel_array, dataset.WindowWidth,
                              dataset.WindowCenter)
        # Convert mode to L since LUT has only 256 values:
        #   http://www.pythonware.com/library/pil/handbook/image.htm
        im = PIL.Image.fromarray(image).convert('L')

    return im


def show_PIL(dataset):
    """Display an image using the Python Imaging Library (PIL)"""
    im = get_PIL_image(dataset)
    im.show()
    pil_image = im.convert('RGB')
    open_cv_image = np.array(pil_image)
    cv2.imshow(open_cv_image)


def read_seg(dcm_filename):
    ds = dicom.read_file(dcm_filename)
    img = ds[0x00690069].value
    i = pickle.loads(img)
    cv2.namedWindow('image', cv2.WINDOW_NORMAL)
    cv2.resizeWindow('image', 600, 600)
    cv2.imshow('image', i)
    cv2.waitKey(0)
    cv2.destroyAllWindows()


read_seg(sys.argv[1])