How to generate png data?

[ee-hash]

Hi! I am interested in the repo. But the released code have not mention how to generate png data. Could you share the preprocessing dataset code? Thanks!

[White1Scorpion]

import os import SimpleITK import pydicom import numpy as np import cv2 from tqdm import tqdm

def is_dicom_file(filename):

#判断某文件是否是dicom格式的文件
file_stream = open(filename, 'rb')
file_stream.seek(128)
data = file_stream.read(4)
file_stream.close()
if data == b'DICM':
    return True
return False

def load_patient(src_dir): ''' 读取某文件夹内的所有dicom文件 :param src_dir: dicom文件夹路径 :return: dicom list ''' files = os.listdir(src_dir) slices = [] for s in files: if is_dicom_file(src_dir + '/' + s): instance = pydicom.read_file(src_dir + '/' + s) slices.append(instance)

try:
    slice_thickness = np.abs(slices[0].ImagePositionPatient[2] - slices[1].ImagePositionPatient[2])
except:
    slice_thickness = np.abs(slices[0].SliceLocation - slices[1].SliceLocation)

for s in slices:
    s.SliceThickness = slice_thickness
return slices

def get_pixels_hu_by_simpleitk(dicom_dir): ''' 读取某文件夹内的所有dicom文件 :param src_dir: dicom文件夹路径 :return: image array ''' reader = SimpleITK.ImageSeriesReader() dicom_names = reader.GetGDCMSeriesFileNames(dicom_dir) reader.SetFileNames(dicom_names) image = reader.Execute() img_array = SimpleITK.GetArrayFromImage(image) img_array[img_array == -2000] = 0 return img_array

if name == 'main': #dicom文件目录 dicom_dir = 'dcm/' # 读取dicom文件的元数据(dicom tags) slices = load_patient(dicom_dir) print('The number of dicom files : ', len(slices)) # 提取dicom文件中的像素值 image = get_pixels_hu_by_simpleitk(dicom_dir) for i in tqdm(range(image.shape[0])): #输出png文件目录 img_path = "dcm_2_png/img_" + str(i).rjust(4, '0') + "_i.png" org_img =image[i]*20 # 保存图像数组 cv2.imwrite(img_path, org_img )