DICOM（Digital Imaging and Communications in Medicine）即医学数字成像和通信，是医学图像和相关信息的国际标准（ISO 12052）。它定义了质量能满足临床需要的可用于数据交换的医学图像格式，可用于处理、存储、打印和传输医学影像信息。DICOM可以便捷地交换于两个满足DICOM格式协议的工作站之间。目前该协议标准不仅广泛应用于大型医院，而且已成为小型诊所和牙科诊所医生办公室的标准影像阅读格式。
DICOM被广泛应用于放射医疗、心血管成像以及放射诊疗诊断设备（X射线，CT，核磁共振，超声等），并且在眼科和牙科等其它医学领域得到越来越深入广泛的应用。在数以万计的在用医学成像设备中，DICOM是部署最为广泛的医疗信息标准之一。当前大约有百亿级符合DICOM标准的医学图像用于临床使用。
目前，越来越多的DICOM应用程序和分析软件被运用于临床医学，促使越来越多的编程语言开发出支持DICOM API的框架。今天就让我来介绍一下Python语言下支持的DICOM模块，以及如何完成基本DICOM信息分析和处理的编程方法。
Pydicom
Pydicom是一个处理DICOM文件的纯Python软件包。它可以通过非常容易的“Pythonic”的方式来提取和修改DICOM数据，修改后的数据还会借此生成新的DICOM文件。作为一个纯Python包，Pydicom可以在Python解释器下任何平台运行，除了必须预先安装Numpy模块外，几乎无需其它任何配置要求。其局限性之一是无法处理压缩像素图像（如JPEG），其次是无法处理分帧动画图像（如造影电影）。
SimpleITK
Insight Segmentation and Registration Toolkit (ITK)是一个开源、跨平台的框架，可以提供给开发者增强功能的图像分析和处理套件。其中最为著名的就是SimpleITK，是一个简化版的、构建于ITK最顶层的模块。SimpleITK旨在易化图像处理流程和方法。
PIL
Python Image Library (PIL) 是在Python环境下不可缺少的图像处理模块，支持多种格式，并提供强大的图形与图像处理功能，而且API却非常简单易用。
OpenCV
OpenCV的全称是：Open Source Computer Vision Library。OpenCV是一个基于BSD许可（开源）发行的跨平台计算机视觉库，可以运行在Linux、Windows和Mac OS操作系统上。它轻量级而且高效——由一系列 C 函数和少量 C++ 类构成，同时提供了Python、Ruby、MATLAB等语言的接口，实现了图像处理和计算机视觉方面的很多通用算法。
下面就让我以实际Python代码来演示如何编程处理心血管冠脉造影DICOM图像信息。
1. 导入主要框架：SimpleITK、pydicom、PIL、cv2和numpy
import SimpleITK as sitk
from PIL import Image
import pydicom
import numpy as np
import cv2
2. 应用SimpleITK框架来读取DICOM文件的矩阵信息。如果DICOM图像是三维螺旋CT图像，则帧参数则代表CT扫描层数；而如果是造影动态电影图像，则帧参数就是15帧/秒的电影图像帧数。
def loadFile(filename):
ds = sitk.ReadImage(filename)
img_array = sitk.GetArrayFromImage(ds)
frame_num, width, height = img_array.shape
return img_array, frame_num, width, height
3. 应用pydicom来提取患者信息。
def loadFileInformation(filename):
information = {}
ds = pydicom.read_file(filename)
information['PatientID'] = ds.PatientID
information['PatientName'] = ds.PatientName
information['PatientBirthDate'] = ds.PatientBirthDate
information['PatientSex'] = ds.PatientSex
information['StudyID'] = ds.StudyID
information['StudyDate'] = ds.StudyDate
information['StudyTime'] = ds.StudyTime
information['InstitutionName'] = ds.InstitutionName
information['Manufacturer'] = ds.Manufacturer
information['NumberOfFrames'] = ds.NumberOfFrames
return information
4. 应用PIL来检查图像是否被提取。
def showImage(img_array, frame_num = 0):
img_bitmap = Image.fromarray(img_array[frame_num])
return img_bitmap
5. 采用CLAHE (Contrast Limited Adaptive Histogram Equalization)技术来优化图像。
def limitedEqualize(img_array, limit = 4.0):
img_array_list = []
for img in img_array:
clahe = cv2.createCLAHE(clipLimit = limit, tileGridSize = (8,8))
img_array_list.append(clahe.apply(img))
img_array_limited_equalized = np.array(img_array_list)
return img_array_limited_equalized
这一步对于整个图像处理起到很重要的作用，可以根据不同的原始DICOM图像的窗位和窗宽来进行动态调整，以达到最佳的识别效果。
原始图像：
经过自动窗位窗宽调节，生成：
再经过CLAHE优化，则生成：
最后应用OpenCV的Python框架cv2把每帧图像组合在一起，生成通用视频格式。
def writeVideo(img_array):
frame_num, width, height = img_array.shape
filename_output = filename.split('.')[0] + '.avi'
video = cv2.VideoWriter(filename_output, -1, 16, (width, height))
for img in img_array:
video.write(img)
video.release()
以下就是我基于上述的框架和算法设计的又一软件：Willowbend DICOM。该软件是图形界面，可以跨平台运行于Windows、Mac和Linux系统下。Willowbend DICOM可以快速进行DICOM-AVI转换，其间对每帧图像进行动态灰阶优化和自定义调节，并可迅速提取文件中的患者信息。该软件遵循MIT开源许可协议。
软件在GitHub中的链接：https://github.com/YangChuan80/WillowbendDICOM/blob/master/README.md
欢迎下载、应用并指正。以下就是Willowbend DICOM在我的GitHub程序库中的英文详细介绍，欢迎参阅。
Willowbend DICOM
A dialog-based DICOM to video converter.
Chuan Yang (yangc@sj-hospital.org)
Introduction
DICOM (Digital Imaging and Communications in Medicine) is a standard for handling, storing, printing, and transmitting information in medical imaging. DICOM files can be exchanged between two entities that are capable of receiving image and patient data in DICOM format by following network communications protocol. DICOM has been widely adopted by hospitals and is making inroads in smaller applications like dentists' and doctors' offices.
Willowbend DICOM is a dialog-based application performing the conversion from DICOM format to video format (avi) in order to meet the needs and requirements for universal computer systems (PC, Mac, Linux, etc.). So the ordinary users of such systems can use the converted file to present, communicate and store the universal files.
Medical imaging related staffs (including Interventional Cardiologists, Physicians of Peripheral Intervention, Neurointerventional Physicians, Medical Imaging Physicians and Radiological Technicians) can use it in medical conferences, educations and remote consultants of clinical medicine, and they will feel free to use universal video formats in the slide presentations in medical courses and case reports.
Furthermore, besides efficiently converting a file from DICOM to AVI format, Willowbend DICOM can implement auto grey-scale optimization and customization for every frame in a DICOM before conversion, and it's able to extract patient's information rapidly from the DICOM files.
Installation from Source
This option is only adopted by Python specialist. There are several dependencies necessarily preinstalled in your Python interpreter:
-
SimpleITK
conda install --channel https://conda.anaconda.org/SimpleITK SimpleITK
-
Pydicom 1.0
-
Download pydicom source from https://github.com/darcymason/pydicom
-
-
OpenCV
-
Download the wheel file from https://scivision.co/install-opencv-3-0-x-for-python-on-windows/
-
After you complete the WillowbendDICOM.py file download, run it:
python WillowbendDICOM.py
Python interpreter have to be Python 3.4 or later.
-
Setuptools & Pyinstaler
-
If you'd like to use PyInstaller, you should downgrade your setuptools module to 19.2.
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To perform frozen binary, do this:
pyinstaller WillowbendDICOM.py -w
Instructions
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Click Browse button to choose the DICOM file.
-
Load this chosen file. Don't forget to press Load button. When file successfully loaded, a information dialog will pop up to notice you.
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Click Convert button on the right to convert the currently loaded DICOM file to AVI file. During this session, you will be asked to specify the location you're going to output to. Next you are required to select the VIDEO COMPRESSION options, which the "Full Frames (Uncompressed)" is recommended. Click OK. You'll wait for about a second, and your AVI file is ready! Congratulations!
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Optionally, you can customize the value of the Clip Limit if you're not satisfied with your converted AVI file with the default value of 3.0. The higher value means the more contrast effect in the video file you'll get.
License
The MIT License (MIT)
Copyright (c) 2016 Chuan Yang
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Contributor List
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Wenzhe Xue, Ph.D., Mayo Clinic
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