【Python医学影像从超详细入门】2.NII NII.GZ NRRD DICOM JPG文件格式转换

【Python医学影像从超详细入门】2.NII NII.GZ NRRD DICOM文件格式转换

NII NII.GZ NRRD DICOM是医学影像常用的四种存储格式。
为了实现可视化，通常还需要将其转换为JPG格式。

其之间的相互转换需要使用到以下库：
SimpleITK
nibabel
cv2
numpy

首先您需要在控制台安装缺少的库(只需要安装提示缺少的库)

#SimpleITK:
pip install --user -i https://pypi.tuna.tsinghua.edu.cn/simple SimpleITK
#nibabel:
pip install --user -i https://pypi.tuna.tsinghua.edu.cn/simple nibabel
#cv2:
pip install -i https://pypi.tuna.tsinghua.edu.cn/simple opencv-python
#numpy:
pip install numpy

dicom转nii nii.gz nrrd方法：

#dicom即文件夹存储的dcm后缀文件转为nii或nii.gz或nrrd格式
#dicom文件夹目录  niipath:要保存的文件名
def dcm2niigz(dcmpath, niipath):
    reader = sitk.ImageSeriesReader()
    dicom_names = reader.GetGDCMSeriesFileNames(dcmpath)
    reader.SetFileNames(dicom_names)
    image2 = reader.Execute() 

    image_array = sitk.GetArrayFromImage(image2)
    origin = image2.GetOrigin()
    spacing = image2.GetSpacing()
    direction = image2.GetDirection()
    image3 = sitk.GetImageFromArray(image_array)
    
    image3.SetSpacing(spacing)
    image3.SetDirection(direction)
    image3.SetOrigin(origin)
    
    sitk.WriteImage(image3, niipath)  

nii nii.gz nrrd互相转换方法：

#nii nii.gz nrrd格式之间互相转换
def nii2nii(oripath,savepath):
    data = sitk.ReadImage(oripath)
    img = sitk.GetArrayFromImage(data)
    out = sitk.GetImageFromArray(img)
    sitk.WriteImage(out,savepath)

nii nii.gz nrrd 原始影像转换为jpg的方法:
(请注意 原始影像与勾画文件转换为JPG方式略有不同)

#转换为jpg图像时,调整窗位窗宽
def window_transform(img, windowWidth, windowCenter):
    minWindow = float(windowCenter) - 0.5*float(windowWidth)
    img = (img - minWindow) / float(windowWidth)
    img[img < 0] = 0
    img[img > 1] = 1
    img = (img * 255).astype('float32')
    return img

#nii nii.gz nrrd的原始影像文件(非勾画)转换为jpg
#file_path应该是nii nii.gz nrrd文件  to_path应该是一个文件夹
def Niigz2jpg(file_path,to_path,cwckON,cwckcenter,cwckwidth):
    
    n1 = nib.load(file_path)
    n1 = n1.get_fdata()
    
    if(cwckON):
        n1 = window_transform(n1,cwckwidth,cwckcenter)

    if(os.path.exists(to_path)):#若已存在文件夹
        shutil.rmtree(to_path)#则删除文件夹
    os.mkdir(to_path)#重新创建文件夹
    
    
    for i in range(n1.shape[2]):
        out_path = to_path + '\\' + str(i) + ".jpg"
        nt=cv2.flip(np.rot90(n1[:,:,i],3),1)
        nt = nt.astype('float32')
        cv2.imwrite(out_path,nt)

nii nii.gz nrrd勾画文件转换为jpg方法：

#nii nii.gz nrrd勾画文件转jpg  需要像素值X255
def Nii2jpg_x255(file_path,to_path):
    n1 = nib.load(file_path)
    n1 = n1.get_fdata()
    n1 = np.array(n1,dtype=np.uint8)
    n1 = n1 * 255
    if(os.path.exists(to_path)):
        shutil.rmtree(to_path)
    if(not os.path.exists(to_path)):
        os.mkdir(to_path)
    for i in range(n1.shape[2]):
        out_path = to_path + '\\' + str(i) + ".jpg"
        nt=cv2.flip(np.rot90(n1[:,:,i],3),1)
        cv2.imwrite(out_path,nt)

勾画jpg覆盖到原始影像jpg的方法：

#orijpgpath:原始影像的jpg图像所在文件夹
#maskjpgpath:勾画文件的jpg图像所在文件夹
#alpha:勾画覆盖强度
#savepath:文件保存目录
def ori_mask_2jpg(orijpgpath,maskjpgpath,alpha,savepath):
    names1 = os.listdir(orijpgpath)
    names1.sort(key=lambda x:int(x.split('.')[0]))
    names2 = os.listdir(maskjpgpath)
    names2.sort(key=lambda x:int(x.split('.')[0]))
    
    if(os.path.exists(savepath)):
        shutil.rmtree(savepath)
    os.mkdir(savepath)
    
    for i in range(len(names1)):
        im1 = cv2.imread(orijpgpath + '\\' + names1[i])
        im2 = cv2.imread(maskjpgpath + '\\' + names2[i])
        im3 = np.concatenate([im1, cv2.addWeighted(im2, alpha, im1, 1,0,0)], axis=1)
        cv2.imwrite(savepath+'\\'+names1[i],im3)

您可以前往此文章以获取使用实例：
【Python医学影像从超详细入门】1.医学影像与勾画文件查看(NII NII.GZ NRRD转JPG)