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NIHPancreasCT.py
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NIHPancreasCT.py
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# -*- coding: utf-8 -*-
"""
Created on Tue May 7 14:18:05 2019
Convert following pancreas CT dcm dataset to nii
https://wiki.cancerimagingarchive.net/display/Public/Pancreas-CT
@author: Jun
"""
import os
import SimpleITK as sitk
import nibabel as nb
import numpy as np
import re
import glob
path = r'Pancreas-CT' # dcm path
save_path = r'Pancreas\NIH'
filenames = os.listdir(path)
filenames.sort()
for name in filenames:
namepath = os.path.join(path, name)
dicom_names = glob.glob(namepath + r'\*\*\*.dcm')
dicom_names.sort()
DicomReader = sitk.ImageSeriesReader()
# seriesIDs = DicomReader.GetGDCMSeriesIDs(filepath)
# dicom_names = DicomReader.GetGDCMSeriesFileNames(filepath, seriesIDs[0])
DicomReader.SetFileNames(dicom_names)
LiverImg = DicomReader.Execute()
# LiverData = sitk.GetArrayFromImage(LiverImg)
save_name = name + '.nii.gz'
sitk.WriteImage(LiverImg, os.path.join(save_path, save_name))
print(save_name)