python处理DICOM并计算三维模型体积_Python

python处理DICOM并计算三维模型体积

2021-06-02 00:15qd_tudou Python

这篇文章主要为大家详细介绍了python处理DICOM，并计算三维模型体积，具有一定的参考价值，感兴趣的小伙伴们可以参考一下

在已知DICOM和三维模型对应掩膜的情况下，计算三维模型的体积。

思路：

1、计算每个体素的体积。每个体素为长方体，x，y为PixelSpacing，z为层间距

使用pydicom.read_file读取DICOM文件，dcm_tag.PixelSpacing获取像素间距，dcm_tag.SliceLocation 获取层间距

2、计算体素的个数

代码如下：

				?

									from PIL import Image

									import numpy as np

									import pydicom

									import os

									def get_pixels_No(bmp_data_dir):

									  pixels_No = 0

									  bmp_files = os.listdir(bmp_data_dir)

									  for bmp in bmp_files:

									    bmp_file = os.path.join(bmp_data_dir,bmp)

									    img = Image.open(bmp_file)

									    img_array = np.array(img)

									    # img_array.dtype为布尔类型，需要转换为Int类型，其累加和恰好为体素总和

									    img_array_int = img_array.astype(int)

									    pixels_No = pixels_No+img_array_int.sum()

									  return pixels_No

									def get_pixel_info(dcm_data_dir):

									  pixel_infos = []

									  dcm_files = os.listdir(dcm_data_dir)

									  dcm_file_1 = os.path.join(dcm_data_dir,dcm_files[0])

									  dcm_tag_1 = pydicom.read_file(dcm_file_1)

									  # 获取像素间距.

									  spacex, spacey = dcm_tag_1.PixelSpacing

									  # 获取层间距

									  # 有些 dcm图像并不是按照InstanceNumber进行排序的，不能直接用最后一张的slicelocation减去第一张，再除以张数

									  SliceLocations = []

									  ImagePositon_z = []

									  for dcm in dcm_files:

									    dcm_file = os.path.join(dcm_data_dir, dcm)

									    dcm_tag = pydicom.read_file(dcm_file)

									    SliceLocations.append(dcm_tag.SliceLocation)

									    ImagePositon_z.append(dcm_tag.ImagePositionPatient[2])

									  SliceLocations_max =max(SliceLocations)

									  SliceLocations_min =min(SliceLocations)

									  ImagePositon_z_max = max(ImagePositon_z)

									  ImagePositon_z_min = min(ImagePositon_z)

									  print(SliceLocations_max)

									  print(SliceLocations_min)

									  print(ImagePositon_z_max)

									  print(ImagePositon_z_min)

									  if SliceLocations_max - SliceLocations_min < 1e-10:

									    spacez = abs(ImagePositon_z_max - ImagePositon_z_min)/(len(dcm_files)-1)

									  else:

									    spacez = abs(SliceLocations_max - SliceLocations_min)/(len(dcm_files)-1)

									  pixel_infos = [spacex, spacey, spacez]

									  return pixel_infos

									def get_volume(dcm_data_dir,bmp_data_dir):

									  pixel_infos = get_pixel_info(dcm_data_dir)

									  pixels_No = get_pixels_No(bmp_data_dir)

									  volume=pixel_infos[0]*pixel_infos[1]*pixel_infos[2]*pixels_No/1000

									  return volume

									# dcm = pydicom.read_file(r"E:\20181210090945_LENG HONGYING F-44Y\Venous\0000.dcm")

									# print(dcm)

									# print(dcm.ImagePositionPatient[2])

									# print(dcm[0x0020, 0x0032].keyword,dcm[0x0020, 0x0032].value)

									volume=get_volume(r"E:\20181210090945_LENG HONGYING F-44Y\Venous",r"E:\20181210090945_LENG HONGYING F-44Y\Results\LungL")

									print("体积为%.1f"%volume)