import os from os import path from tqdm import tqdm import numpy as np import SimpleITK as sitk def calc_adc(b50,b400): mean_dwi = (50 + 400) / 2 mean_si = np.divide(np.add(np.log(b50), np.log(b400)), 2) denominator = np.multiply((50 - mean_dwi), np.subtract(np.log(b50), mean_si)) + np.multiply((400 - mean_dwi), np.subtract(np.log(b400), mean_si)) numerator = np.power((50 - mean_dwi), 2) + np.power((400 - mean_dwi), 2) adc_with_zeros = np.divide(denominator, numerator) * -1000000 adc = np.clip(adc_with_zeros,0,np.amax(adc_with_zeros)) return adc def calc_high_b(b_value_high,b_value,b_image,ADC_map): high_b = np.multiply(b_image, np.exp(np.multiply(np.subtract(b_value,b_value_high), (np.divide(ADC_map,1000000))))) return high_b def append_new_line(file_name, text_to_append): """Append given text as a new line at the end of file""" # Open the file in append & read mode ('a+') with open(file_name, "a+") as file_object: # Move read cursor to the start of file. file_object.seek(0) # If file is not empty then append '\n' data = file_object.read(100) if len(data) > 0: file_object.write("\n") # Append text at the end of file file_object.write(text_to_append) series = ['b50','b400'] # series = ['t2'] DATA_DIR = "./../data/Nijmegen paths/" # Read the image paths from the data directory. # Texts files are expected to have the name "[series_name].txt" images, image_paths = {s: [] for s in series}, {} segmentations = [] for s in series: with open(path.join(DATA_DIR, f"{s}.txt"), 'r') as f: image_paths[s] = [l.strip() for l in f.readlines()] with open(path.join(DATA_DIR, f"seg.txt"), 'r') as f: seg_paths = [l.strip() for l in f.readlines()] num_images = len(seg_paths) for img_idx in tqdm(range(num_images)): img_b50 = sitk.ReadImage(image_paths['b50'][img_idx], sitk.sitkFloat32) arr_b50 = sitk.GetArrayFromImage(img_b50) img_b400 = sitk.ReadImage(image_paths['b400'][img_idx], sitk.sitkFloat32) arr_b400 = sitk.GetArrayFromImage(img_b400) # img_b800 = sitk.ReadImage(image_paths['b800'][img_idx], sitk.sitkFloat32) # arr_b800 = sitk.GetArrayFromImage(img_b800) # img_t2 = sitk.ReadImage(image_paths['t2'][img_idx], sitk.sitkFloat32) # img_t2 = sitk.GetArrayFromImage(img_t2) # img_seg = sitk.ReadImage(seg_paths[img_idx], sitk.sitkFloat32) # img_seg = sitk.GetArrayFromImage(img_seg) adc = calc_adc(arr_b50,arr_b400) high_b = calc_high_b(1400,50,arr_b50,adc) adc = sitk.GetImageFromArray(adc) high_b = sitk.GetImageFromArray(high_b) # t2 = sitk.GetImageFromArray(img_t2) # seg = sitk.GetImageFromArray(img_seg) patient_ID = os.path.split(os.path.dirname(os.path.dirname(os.path.dirname(os.path.dirname(image_paths['b50'][img_idx])))))[1] path_adc = f'./../data/adc_calc_2/{patient_ID}.nii.gz' path_high_b = f'./../data/b1400_calc_2/{patient_ID}.nii.gz' # patient_ID = os.path.split(os.path.dirname(os.path.dirname(os.path.dirname(image_paths['t2'][img_idx]))))[1] # path_t2 = f'./../data/t2_calc/{patient_ID}.nii.gz' # path_seg = f'./../data/seg_calc/{patient_ID}.nii.gz' adc.CopyInformation(img_b50) high_b.CopyInformation(img_b50) sitk.WriteImage(adc, path_adc) sitk.WriteImage(high_b, path_high_b) # sitk.WriteImage(t2, path_t2) # sitk.WriteImage(seg, path_seg) append_new_line('adccalc2.txt',path_adc) append_new_line('b1400calc2.txt',path_high_b) # append_new_line('t2calc.txt',path_t2) # append_new_line('segcalc.txt',path_seg)