python处理DICOM并计算三维模型体积

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)

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