scripts/apply_window.py

"""
Apply CT windowing parameter from DL_info.csv to Images_png
"""

import os
import cv2

import numpy as np
import pandas as pd

from glob import glob
from tqdm import tqdm


dir_in = '../Images_png'
dir_out = '../Images_png_wn'
info_fn = '../DL_info.csv'

if not os.path.exists(dir_out):
    os.mkdir(dir_out)

dl_info = pd.read_csv(info_fn)

def clip_and_normalize(np_image: np.ndarray,
                       clip_min: int = -150,
                       clip_max: int = 250
                       ) -> np.ndarray:
    np_image = np.clip(np_image, clip_min, clip_max)
    np_image = (np_image - clip_min) / (clip_max - clip_min)
    return np_image


for idx, row in tqdm(dl_info.iterrows(), total=len(dl_info)):

    folder = row['File_name'].rsplit('_', 1)[0]
    images = sorted(glob(f'{dir_in}/{folder}/*.png'))

    if not os.path.exists(f'{dir_out}/{folder}'):
        os.mkdir(f'{dir_out}/{folder}')
    DICOM_windows = [float(value.strip()) for value in row['DICOM_windows'].split(',')]

    for im in images:
        try:
            image = cv2.imread(im, cv2.IMREAD_UNCHANGED)
            image = image.astype('int32') - 32768
            image = clip_and_normalize(image, *DICOM_windows)
            image = (image*255).astype('uint8')
            cv2.imwrite(f'{dir_out}/{folder}/{os.path.basename(im)}', image)
        except AttributeError:
            # Broken Images
            # 001821_07_01/372.png
            # 002161_04_02/116.png
            print(f'Conversion failed: {im}')
            continue