# -*-coding:utf-8-*-
import cv2
import numpy
import dicom
from matplotlib import pyplot as plt

dcm = dicom.read_file("dcm")
dcm.image = dcm.pixel_array * dcm.RescaleSlope + dcm.RescaleIntercept

slices = []
slices.append(dcm)
img = slices[int(len(slices) / 2)].image.copy()
ret, img = cv2.threshold(img, 90, 3071, cv2.THRESH_BINARY)
img = numpy.uint8(img)

im2, contours, _ = cv2.findContours(img, cv2.RETR_LIST, cv2.CHAIN_APPROX_SIMPLE)
mask = numpy.zeros(img.shape, numpy.uint8)
for contour in contours:
  cv2.fillPoly(mask, [contour], 255)
img[(mask > 0)] = 255

kernel = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (2, 2))
img = cv2.morphologyEx(img, cv2.MORPH_OPEN, kernel)

img2 = slices[int(len(slices) / 2)].image.copy()
img2[(img == 0)] = -2000

plt.figure(figsize=(12, 12))
plt.subplot(131)
plt.imshow(slices[int(len(slices) / 2)].image, 'gray')
plt.title('Original')
plt.subplot(132)
plt.imshow(img, 'gray')
plt.title('Mask')
plt.subplot(133)
plt.imshow(img2, 'gray')
plt.title('Result')
plt.show()

import pydicom
import os
import numpy
from matplotlib import pyplot, cm
# 用lstFilesDCM作为存放DICOM files的列表
PathDicom = "dicom/2" #与python文件同一个目录下的文件夹
lstFilesDCM = []
for dirName,subdirList,fileList in os.walk(PathDicom):
  for filename in fileList:
    if ".dcm" in filename.lower(): #判断文件是否为dicom文件
      print(filename)
      lstFilesDCM.append(os.path.join(dirName,filename)) # 加入到列表中
## 将第一张图片作为参考图
RefDs = pydicom.read_file(lstFilesDCM[0])  #读取第一张dicom图片
# 建立三维数组
ConstPixelDims = (int(RefDs.Rows),int(RefDs.Columns),len(lstFilesDCM)) # 得到spacing值 (mm为单位)
ConstPixelSpacing = (float(RefDs.PixelSpacing[0]), float(RefDs.PixelSpacing[1]), float(RefDs.SliceThickness))
# 三维数据
x = numpy.arange(0.0, (ConstPixelDims[0]+1)*ConstPixelSpacing[0], ConstPixelSpacing[0]) # 0到（第一个维数加一*像素间的间隔），步长为constpixelSpacing
y = numpy.arange(0.0, (ConstPixelDims[1]+1)*ConstPixelSpacing[1], ConstPixelSpacing[1]) #
z = numpy.arange(0.0, (ConstPixelDims[2]+1)*ConstPixelSpacing[2], ConstPixelSpacing[2]) #
ArrayDicom = numpy.zeros(ConstPixelDims, dtype=RefDs.pixel_array.dtype)
for filenameDCM in lstFilesDCM:
  ds = pydicom.read_file(filenameDCM)
  ArrayDicom[:, :, lstFilesDCM.index(filenameDCM)] = ds.pixel_array # 轴状面显示
  pyplot.figure(dpi=300)
  pyplot.axes().set_aspect('equal', 'datalim')
  pyplot.set_cmap(pyplot.gray())
  pyplot.pcolormesh(x, y, numpy.flipud(ArrayDicom[:, :, 2])) # 第三个维度表示现在展示的是第几层
  pyplot.show()