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python处理DICOM并计算三维模型体积

yipeiwu_com6年前 (2020-03-06)Python基础

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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