Add code to convert DICOM to JPG to this repository

[alistairewj]

At the moment the code used to convert the x-rays from DICOMs to JPGs is not publicly available as it's tied up in another repo. It would be good to have a publicly executable set of code that converts DICOMs to JPGs in the same way as we did to create MIMIC-CXR-JPG from MIMIC-CXR. The core function used was:

import numpy as np
import pydicom
import cv2

def dcm2img(input_file_path, output_file_path):
    """Extract the image from a DICOM and write it to an image file."""

    # Read the DICOM and extract the image.
    dcm_file = pydicom.dcmread(input_file_path)
    raw_image = dcm_file.pixel_array

    assert len(raw_image.shape) == 2,\
        "Expecting single channel (grayscale) image."

    # Normalize pixels to be in [0, 255].
    raw_image = raw_image - raw_image.min()
    normalized_image = raw_image / raw_image.max()
    rescaled_image = (normalized_image * 255).astype(np.uint8)

    # Correct image inversion.
    if dcm_file.PhotometricInterpretation == "MONOCHROME1":
        rescaled_image = cv2.bitwise_not(rescaled_image)

    # Perform histogram equalization.
    final_image = cv2.equalizeHist(rescaled_image)

    # Write the image to file.
    cv2.imwrite(output_file_path, final_image)