LIDC_IRDI数据DICOM加载顺序错误问题解决方案

在处理LIDC_IPDI时，处理到后期发现一个问题，在每一个病例中，切片的命名的编号，跟dicom中给出的命名的编号不一致，这在处理数据时，无形的增加则一些难度，尤其是在运行别人的代码时，这个问题尤为突出，经过不断的搜索，最终在官网的一个页面上发现了这个问题的一种解决方式，先付上官网的连接：

https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=24283641
如何下载LIDR_IRDI数据就不多说了，很多博客中都讲的很细致，下面具体的描述一下我遇到的问题。
从NBIA上下载下来数据后，是这样的

打开第一个病例，如图所示：

其中问题出在，此时的第一个文件对应的切片的标号为：80

但是其实我想要的效果是，这样的，标号为000.dcm的文件里存放的时切片号为1的切片：

二、解决

# noinspection PyPep8Naming
import SimpleITK as sitk
import glob as gb
import os
import shutil


def safe_sitk_read(img_list, *args, **kwargs):
    """
 Since the default function just looks at images 0 and 1 to determine slice thickness
 and the images are often not correctly alphabetically sorted, much slower
 :param img_list:
 :return:
 """
    pimg_list = []
    reader = sitk.ImageSeriesReader()
    seriesIDs = reader.GetGDCMSeriesIDs(x_path)
    dicom_names = reader.GetGDCMSeriesFileNames(x_path, seriesIDs[0])
    reader.SetFileNames(dicom_names)
    image_list = reader.GetFileNames()
    pimg_list = [(sitk.ReadImage(x).GetOrigin(), x) for x in image_list]
    s_img_list = [path for _, path in sorted(pimg_list, key = lambda x: x[0][2])]
    print('s_img_list',s_img_list)
    return s_img_list
x_path= 'E:/qiepianmingming/LIDC-IDRI-0002/01-01-2000-98329/3000522-04919/'  #从NBIA上下载的一个病例
jieguo_path = 'E:/qiepianmingming/LIDC-IDRI-0002/1/0'  #随便设的一个路径
z_sort = safe_sitk_read(x_path)

i = len(z_sort)+1
for img in z_sort:
    i -=1
    if i !=0:
        if i <=9:
            dst = os.path.join(jieguo_path+str(0)+str(0)+str(i)+'.dcm')
        elif  i>=10 and i <= 99:
            dst = os.path.join(jieguo_path+str(0)+ str(i) + '.dcm')
        else:
            dst = os.path.join(jieguo_path+ str(i) + '.dcm')
        shutil.copy(img, dst)

有待解决的问题是，将所有的数据都进行转化

补充

通过一个程序实现所有的文件内的dcm图片按编号排列

# noinspection PyPep8Naming
import SimpleITK as sitk
import glob as gb
import os
import shutil

#这个函数是为了提取每个bcm图片中的InstanceNumber，由与图片的编号用过z的大小提现，我们用z轴进行排序，找到编号
def safe_sitk_read(img_list, *args, **kwargs):
    """
 Since the default function just looks at images 0 and 1 to determine slice thickness
 and the images are often not correctly alphabetically sorted, much slower
 :param img_list:
 :return:
 """
    pimg_list = []
    reader = sitk.ImageSeriesReader()
    seriesIDs = reader.GetGDCMSeriesIDs(img_list)
    dicom_names = reader.GetGDCMSeriesFileNames(img_list, seriesIDs[0])
    reader.SetFileNames(dicom_names)
    image_list = reader.GetFileNames()
    pimg_list = [(sitk.ReadImage(x).GetOrigin(), x) for x in image_list]
    s_img_list = [path for _, path in sorted(pimg_list, key = lambda x: x[0][2])]
    return s_img_list
#x_path是导入路径，完整的LIDC-IDRI-0应该如LIDC-IDRI-0001...LIDC-IDRI-0133，每个LIDC-IDRI-0文件夹下是study编号的文件夹，study 下是series文件夹，该文件夹下即为每个病例的所有.dcm文件
x_path = r'E:\zonghe_feijiejie\LIDC-IDRI\LIDC-IDRI-0'
#存储路径，为了与原先的路径匹配起来，路径从E:\zonghe_feijiejie\shunxu_LIDC-IDRI之后都是生成的
jieguo_path = r'E:\zonghe_feijiejie\shunxu_LIDC-IDRI\LIDC-IDRI-0'
for i in range(1,4):
    print('i',i)
    series1 = ''
    series2 = ''
    study1 = ''
    study2 = ''
    dst = ''
    jie = ''
    #给LIDC-IDRI-0补充
    if i <= 9:
        dst = os.path.join(x_path + str(0) + str(0) + str(i))
        jie = os.path.join(jieguo_path + str(0) + str(0) + str(i))
    elif i >= 10 and i <= 99:
        dst = os.path.join(x_path + str(0) + str(i))
        jie = os.path.join(jieguo_path + str(0) + str(i))
    else:
        dst = os.path.join(x_path + str(i))
        jie = os.path.join(jieguo_path + str(i))
     '''
	#path为完整的路径，例，E:\zonghe_feijiejie\LIDC-IDRI\LIDC-IDRI-	0001\1.3.6.1.4.1.14519.5.2.1.6279.6001.298806137288633453246975630178\1.3.6.1.4.1.14519.5.2.1.6279.6001.179049373636438705059720603192
	'''
    study1 = os.path.join(str(dst), str(os.listdir(dst)[0]))
    series1 = os.path.join(str(study1), str(os.listdir(study1)[0]))
    path = str(series1)
    print("path",path)
    z_sort = safe_sitk_read(path)
    study2 = os.path.join(str(jie), str(os.listdir(dst)[0]))
    series2 = study2 + '\\' + str(os.listdir(study1)[0])
    os.makedirs(series2)
    z_sort = safe_sitk_read(path)
    #存储新的数据
    #我这里z_sort是按照倒序排序的，即最后一张编号的.dcm图片排在第一位，因此输出反向
    j = len(z_sort)
    for img in z_sort:
        if j <=9:
            cunchu = os.path.join(series2+'\\'+str(0)+str(0)+str(0)+str(j)+'.dcm')
        elif  j>=10 and j<= 99:
            cunchu = os.path.join(series2+'\\'+str(0)+str(0)+ str(j) + '.dcm')
        else:
            cunchu = os.path.join(series2+'\\'+ str(0)+str(j) + '.dcm')
        shutil.copy(img, cunchu)
        j -=1