Python处理医学影像学中的DICOM

DICOM 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_numwidthheight img_array.shape

      return img_arrayframe_numwidthheight


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_arrayframe_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_arraylimit 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, -116, (width, height))    

       for img in img_array:

                  video.write(img)

   video.release()

由于我没有数据,微信图片无法复制过来,只能看看代码了,详细图片请看参考。
======================================================================================================

VTK加载DICOM数据

import vtk
from vtk.util import numpy_support
import numpy

PathDicom = "./dir_with_dicom_files/"
reader = vtk.vtkDICOMImageReader()
reader.SetDirectoryName(PathDicom)
reader.Update()

# Load dimensions using `GetDataExtent`
_extent = reader.GetDataExtent()
ConstPixelDims = [_extent[1]-_extent[0]+1, _extent[3]-_extent[2]+1, _extent[5]-_extent[4]+1]

# Load spacing values
ConstPixelSpacing = reader.GetPixelSpacing()

# Get the 'vtkImageData' object from the reader
imageData = reader.GetOutput()
# Get the 'vtkPointData' object from the 'vtkImageData' object
pointData = imageData.GetPointData()
# Ensure that only one array exists within the 'vtkPointData' object
assert (pointData.GetNumberOfArrays()==1)
# Get the `vtkArray` (or whatever derived type) which is needed for the `numpy_support.vtk_to_numpy` function
arrayData = pointData.GetArray(0)

# Convert the `vtkArray` to a NumPy array
ArrayDicom = numpy_support.vtk_to_numpy(arrayData)
# Reshape the NumPy array to 3D using 'ConstPixelDims' as a 'shape'
ArrayDicom = ArrayDicom.reshape(ConstPixelDims, order='F')
PYDICOM加载DICOM数据:

可以在https://github.com/darcymason/pydicom的test里面看怎么用代码。

import dicom
import os
import numpy

PathDicom = "./dir_with_dicom_series/"
lstFilesDCM = []  # create an empty list
for dirName, subdirList, fileList in os.walk(PathDicom):
    for filename in fileList:
        if ".dcm" in filename.lower():  # check whether the file's DICOM
            lstFilesDCM.append(os.path.join(dirName,filename))
            
# Get ref file
RefDs = dicom.read_file(lstFilesDCM[0])

# Load dimensions based on the number of rows, columns, and slices (along the Z axis)
ConstPixelDims = (int(RefDs.Rows), int(RefDs.Columns), len(lstFilesDCM))

# Load spacing values (in mm)
ConstPixelSpacing = (float(RefDs.PixelSpacing[0]), float(RefDs.PixelSpacing[1]), float(RefDs.SliceThickness))

# The array is sized based on 'ConstPixelDims'
ArrayDicom = numpy.zeros(ConstPixelDims, dtype=RefDs.pixel_array.dtype)

# loop through all the DICOM files
for filenameDCM in lstFilesDCM:
    # read the file
    ds = dicom.read_file(filenameDCM)
    # store the raw image data
    ArrayDicom[:, :, lstFilesDCM.index(filenameDCM)] = ds.pixel_array
转换VTK built-in types to SimpleITK/ITK built-ins and vice-versa
import vtk
import SimpleITK

dctITKtoVTK = {SimpleITK.sitkInt8: vtk.VTK_TYPE_INT8,
               SimpleITK.sitkInt16: vtk.VTK_TYPE_INT16,
               SimpleITK.sitkInt32: vtk.VTK_TYPE_INT32,
               SimpleITK.sitkInt64: vtk.VTK_TYPE_INT64,
               SimpleITK.sitkUInt8: vtk.VTK_TYPE_UINT8,
               SimpleITK.sitkUInt16: vtk.VTK_TYPE_UINT16,
               SimpleITK.sitkUInt32: vtk.VTK_TYPE_UINT32,
               SimpleITK.sitkUInt64: vtk.VTK_TYPE_UINT64,
               SimpleITK.sitkFloat32: vtk.VTK_TYPE_FLOAT32,
               SimpleITK.sitkFloat64: vtk.VTK_TYPE_FLOAT64}
dctVTKtoITK = dict(zip(dctITKtoVTK.values(), 
                       dctITKtoVTK.keys()))
                       
def convertTypeITKtoVTK(typeITK):
    if typeITK in dctITKtoVTK:
        return dctITKtoVTK[typeITK]
    else:
        raise ValueError("Type not supported")

def convertTypeVTKtoITK(typeVTK):
    if typeVTK in dctVTKtoITK:
        return dctVTKtoITK[typeVTK]
    else:
        raise ValueError("Type not supported")
VTK-SimpleITK绘制数据

#!/usr/bin/python

import SimpleITK as sitk
import vtk
import numpy as np

from vtk.util.vtkConstants import *

def numpy2VTK(img,spacing=[1.0,1.0,1.0]):
    # evolved from code from Stou S.,
    # on http://www.siafoo.net/snippet/314
    importer = vtk.vtkImageImport()
    
    img_data = img.astype('uint8')
    img_string = img_data.tostring() # type short
    dim = img.shape
    
    importer.CopyImportVoidPointer(img_string, len(img_string))
    importer.SetDataScalarType(VTK_UNSIGNED_CHAR)
    importer.SetNumberOfScalarComponents(1)
    
    extent = importer.GetDataExtent()
    importer.SetDataExtent(extent[0], extent[0] + dim[2] - 1,
                           extent[2], extent[2] + dim[1] - 1,
                           extent[4], extent[4] + dim[0] - 1)
    importer.SetWholeExtent(extent[0], extent[0] + dim[2] - 1,
                            extent[2], extent[2] + dim[1] - 1,
                            extent[4], extent[4] + dim[0] - 1)

    importer.SetDataSpacing( spacing[0], spacing[1], spacing[2])
    importer.SetDataOrigin( 0,0,0 )

    return importer

def volumeRender(img, tf=[],spacing=[1.0,1.0,1.0]):
    importer = numpy2VTK(img,spacing)

    # Transfer Functions
    opacity_tf = vtk.vtkPiecewiseFunction()
    color_tf = vtk.vtkColorTransferFunction()

    if len(tf) == 0:
        tf.append([img.min(),0,0,0,0])
        tf.append([img.max(),1,1,1,1])

    for p in tf:
        color_tf.AddRGBPoint(p[0], p[1], p[2], p[3])
        opacity_tf.AddPoint(p[0], p[4])

    # working on the GPU
    # volMapper = vtk.vtkGPUVolumeRayCastMapper()
    # volMapper.SetInputConnection(importer.GetOutputPort())

    # # The property describes how the data will look
    # volProperty =  vtk.vtkVolumeProperty()
    # volProperty.SetColor(color_tf)
    # volProperty.SetScalarOpacity(opacity_tf)
    # volProperty.ShadeOn()
    # volProperty.SetInterpolationTypeToLinear()

    # working on the CPU
    volMapper = vtk.vtkVolumeRayCastMapper()
    compositeFunction = vtk.vtkVolumeRayCastCompositeFunction()
    compositeFunction.SetCompositeMethodToInterpolateFirst()
    volMapper.SetVolumeRayCastFunction(compositeFunction)
    volMapper.SetInputConnection(importer.GetOutputPort())

    # The property describes how the data will look
    volProperty =  vtk.vtkVolumeProperty()
    volProperty.SetColor(color_tf)
    volProperty.SetScalarOpacity(opacity_tf)
    volProperty.ShadeOn()
    volProperty.SetInterpolationTypeToLinear()
    
    # Do the lines below speed things up?
    # pix_diag = 5.0
    # volMapper.SetSampleDistance(pix_diag / 5.0)    
    # volProperty.SetScalarOpacityUnitDistance(pix_diag) 
    

    vol = vtk.vtkVolume()
    vol.SetMapper(volMapper)
    vol.SetProperty(volProperty)
    
    return [vol]


def vtk_basic( actors ):
    """
    Create a window, renderer, interactor, add the actors and start the thing
    
    Parameters
    ----------
    actors :  list of vtkActors
    
    Returns
    -------
    nothing
    """     
    
    # create a rendering window and renderer
    ren = vtk.vtkRenderer()
    renWin = vtk.vtkRenderWindow()
    renWin.AddRenderer(ren)
    renWin.SetSize(600,600)
    # ren.SetBackground( 1, 1, 1)
 
    # create a renderwindowinteractor
    iren = vtk.vtkRenderWindowInteractor()
    iren.SetRenderWindow(renWin)

    for a in actors:
        # assign actor to the renderer
        ren.AddActor(a )
    
    # render
    renWin.Render()
   
    # enable user interface interactor
    iren.Initialize()
    iren.Start()

        

#####

filename = 'toto.nii.gz'


img = sitk.ReadImage( filename ) # SimpleITK object
data = sitk.GetArrayFromImage( img ) # numpy array

from scipy.stats.mstats import mquantiles
q = mquantiles(data.flatten(),[0.7,0.98])
q[0]=max(q[0],1)
q[1] = max(q[1],1)
tf=[[0,0,0,0,0],[q[0],0,0,0,0],[q[1],1,1,1,0.5],[data.max(),1,1,1,1]]

actor_list = volumeRender(data, tf=tf, spacing=img.GetSpacing())

vtk_basic(actor_list)
下面一个不错的软件:

https://github.com/bastula/dicompyler
还有一个python的库mudicom,https://github.com/neurosnap/mudicom

import mudicom
mu = mudicom.load("mudicom/tests/dicoms/ex1.dcm")

# returns array of data elements as dicts
mu.read()

# returns dict of errors and warnings for DICOM
mu.validate()

# basic anonymization
mu.anonymize()
# save anonymization
mu.save_as("dicom.dcm")

# creates image object
img = mu.image # before v0.1.0 this was mu.image()
# returns numpy array
img.numpy # before v0.1.0 this was mu.numpy()

# using Pillow, saves DICOM image
img.save_as_pil("ex1.jpg")
# using matplotlib, saves DICOM image
img.save_as_plt("ex1_2.jpg")

参考:

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