func.py

# Reference: https://github.com/ucs198604/dicom2jpg
import os
import cv2
import pydicom
import numpy as np
from glob import glob
from pydicom.pixel_data_handlers.util import apply_voi_lut, apply_modality_lut


# Convert dcm to array
def dcm2img(dcm_path):
    ds = pydicom.dcmread(dcm_path)
    pixel_array = ds.pixel_array.astype(float)

    if 'RescaleSlope' in ds and 'RescaleIntercept' in ds:
        rescale_slope = float(ds.RescaleSlope) 
        rescale_intercept = float(ds.RescaleIntercept)
        pixel_array = (pixel_array) * rescale_slope + rescale_intercept
    else:
        pixel_array = apply_modality_lut(pixel_array, ds)

    if 'VOILUTFunction' in ds and ds.VOILUTFunction=='SIGMOID':
        pixel_array = apply_voi_lut(pixel_array, ds)
    elif 'WindowCenter' in ds and 'WindowWidth' in ds:
        window_center = ds.WindowCenter
        window_width = ds.WindowWidth
        if type(window_center)==pydicom.multival.MultiValue:
            window_center = float(window_center[0])
        else:
            window_center = float(window_center)
        if type(window_width)==pydicom.multival.MultiValue:
            window_width = float(window_width[0])
        else:
            window_width = float(window_width)
        pixel_array = np.piecewise(
            pixel_array, [pixel_array<=(window_center-(window_width)/2), pixel_array>(window_center+(window_width)/2)], 
            [pixel_array.min(), pixel_array.max(), lambda data: ((data-window_center+window_width/2)/window_width*(pixel_array.max() - pixel_array.min()))+pixel_array.min()])
    else:
        pixel_array = apply_voi_lut(pixel_array, ds)

    # normalize to 8 bit
    pixel_array = ((pixel_array-pixel_array.min())/(pixel_array.max()-pixel_array.min())) * 255.0

    if 'PhotometricInterpretation' in ds and ds.PhotometricInterpretation == "MONOCHROME1":
        pixel_array = np.max(pixel_array) - pixel_array

    image = pixel_array.astype('uint8')

    return image


# Save dcm to jpg
def dcm2jpg(in_path):
    dcm_path_lst = glob(in_path+'*.dcm')
    jpg_dir_path = in_path + 'jpg/'

    # Make dir
    if not os.path.exists(jpg_dir_path):
        os.makedirs(jpg_dir_path)

    for dcm_path in dcm_path_lst:
        dcm_path = dcm_path.replace('\\', '/')
        jpg_path = jpg_dir_path + dcm_path.split('/')[-1][:-4] + '.jpg'
        # Convert dcm to image
        image = dcm2img(dcm_path)

        # Save iamge
        cv2.imwrite(jpg_path, image)


# Get tag info about converting
def getTag(dcm_path):
    tag = {}
    ds = pydicom.dcmread(dcm_path)

    RescaleSlope = ds.get('RescaleSlope', 'None')
    RescaleIntercept = ds.get('RescaleIntercept', 'None')
    VOILUTFunction = ds.get('VOILUTFunction', 'None')
    WindowCenter = ds.get('WindowCenter', 'None')
    WindowWidth = ds.get('WindowWidth', 'None')
    PhotometricInterpretation = ds.get('PhotometricInterpretation', 'None')

    tag['RescaleSlope'] = RescaleSlope
    tag['RescaleIntercept'] = RescaleIntercept
    tag['VOILUTFunction'] = VOILUTFunction
    tag['WindowCenter'] = WindowCenter
    tag['WindowWidth'] = WindowWidth
    tag['PhotometricInterpretation'] = PhotometricInterpretation
        
    return tag