import SimpleITK as sitk
import numpy as np
import os
import shutil
def format_conversion(work_path):
'''
:params work_path: work dir path
---root
--sud_dir(fixed dir)
--other_files
:To Do: get dicom dir
'''
case_list = os.listdir(path = work_path)
case_list.sort()
for case in case_list:
# print('case = {}'.format(case))
subdir = os.listdir(os.path.join(work_path, case))
for ssubdir in subdir:
if os.path.isdir(os.path.join(work_path, case, ssubdir)):
# print('case = {}'.format(os.path.join(work_path, case, ssubdir)))
image_path = os.path.join(work_path, case, ssubdir)
read_write_dicom(image_path)
def read_write_dicom(dicom_dir_path):
'''
:params dicom_dir_path: dicom dir
:To Do: read dicom and write to nii.gz
'''
reader = sitk.ImageSeriesReader()
img_name = reader.GetGDCMSeriesFileNames(dicom_dir_path)
reader.SetFileNames(img_name)
image = reader.Execute()
image_array = sitk.GetArrayFromImage(image) # z y x
# print(image_array.shape)
image_out = sitk.GetImageFromArray(image_array)
image_out.SetOrigin(image.GetOrigin()) # recovery ori size
image_out.SetSpacing(image.GetSpacing())
image_out.SetDirection(image.GetDirection())
sitk.WriteImage(image_out, 'mr_image.nii.gz')
if os.path.isfile(os.path.join(os.path.abspath(os.path.dirname(dicom_dir_path)), 'mr_image.nii.gz')):
os.remove(os.path.join(os.path.abspath(os.path.dirname(dicom_dir_path)), 'mr_image.nii.gz'))
shutil.move(os.path.join(os.getcwd(), 'mr_image.nii.gz'), os.path.abspath(os.path.dirname(dicom_dir_path)))
if __name__ == '__main__':
root_path = r'F:\project\xxx\Task\ROI_Testis_02'
format_conversion(root_path)
Python SimpleITK 将dicom数据转为nii.gz
最新推荐文章于 2023-12-28 11:32:26 发布