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dcm2nii_v2.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Wed Oct 28 19:06:29 2020
@author: wangmeiqi
"""
import os
import SimpleITK as sitk
#route = your dicom folder
route = '/Volumes/dataBackup/HCC/ntuh/non_labeled/CT_orginal_six_examples'
#save_route = the folder where you want to save your output files
save_route = '/Volumes/dataBackup/HCC/ntuh/non_labeled' #/CT_3D_10282020
slice_list = []
dir_ = []
dir_ = os.listdir(route)
num1 = len(dir_)
for i4 in range(len(dir_)):
file = dir_[i4]
print(str(i4+1) + '/' + str(num1))
print(file)
dicomPath = os.path.join(route, file)
reader = sitk.ImageSeriesReader()
series_ids = reader.GetGDCMSeriesIDs(dicomPath)
for i in range(len(series_ids)): #series
series_id = series_ids[i]
dicom_filenames = reader.GetGDCMSeriesFileNames(dicomPath, series_id)
if len(dicom_filenames)>10:
print(series_id)
sitkReader = sitk.ImageFileReader()
#找有幾種acquisition number
max_acquisition = 1
for i1 in range(len(dicom_filenames)):
fileReader = sitk.ImageFileReader()
fileReader.SetFileName(dicom_filenames[i1])
fileImage = fileReader.Execute()
#print(dicom_filenames[i1])
if fileImage.GetMetaData("0020|0012") == '':
# 設定 DICOM 影像序列檔案名稱
reader.SetFileNames(dicom_filenames)
# 載入後設資料
reader.MetaDataDictionaryArrayUpdateOn()
# 載入私有後設資料
reader.LoadPrivateTagsOn()
image = reader.Execute()
size = image.GetSize()
print("Image size: {} x {} x {}".format(size[0], size[1], size[2]))
save_path = os.path.join(save_route, file)
if not os.path.isdir(save_path):
os.mkdir(save_path)
outFile = os.path.join(save_path, series_ids[i] + ".nii.gz") # xxx.nii.gz
sitk.WriteImage(image, outFile)
continue
else:
acquisition = int(fileImage.GetMetaData("0020|0012"))
if acquisition > max_acquisition:
max_acquisition = acquisition
#print(str(max_acquisition))
for i3 in range(1, max_acquisition + 1): #1~3
for i2 in range(len(dicom_filenames)):
fileReader = sitk.ImageFileReader()
fileReader.SetFileName(dicom_filenames[i2])
fileImage = fileReader.Execute()
acquisition = int(fileImage.GetMetaData("0020|0012"))
if acquisition == i3:
slice_list.append(dicom_filenames[i2])
try:
print(len(slice_list))
# 設定 DICOM 影像序列檔案名稱
reader.SetFileNames(slice_list)
# 載入後設資料
reader.MetaDataDictionaryArrayUpdateOn()
# 載入私有後設資料
reader.LoadPrivateTagsOn()
image = reader.Execute()
size = image.GetSize()
print("Image size: {} x {} x {}".format(size[0], size[1], size[2]))
save_path = os.path.join(save_route, file)
if not os.path.isdir(save_path):
os.mkdir(save_path)
outFile = os.path.join(save_path, series_ids[i] + "_acq_" + str(i3) + ".nii.gz") # xxx.nii.gz
sitk.WriteImage(image, outFile)
except Exception as e:
print(f'An Error occurred: {e}')
slice_list = []