ITK、VTK 读取 DiCOM 文件信息，并实现交互预览

其他 2021-01-22 21:52:05 阅读次数: 0

DICOM 文件介绍

DICOM 全名叫 Digital Imaging and Communications in Medicine(医学数字图像与通信)，是医学图像和相关信息的过节标准，也定义了临床所需数据医学图像格式；

DICOM 数据格式包含大量属性，例如病人名字、ID、年龄等基本信息，这些信息从储存在 “头文件” 中，这种储存方式避免了病人与图像误配；

一个病人样本 包含多个 DICOM 子文件，单个 DICOM 对象只包含具有一帧像素数据，帧与帧之间以序列形式存在，可以来回切换形成类似于电影放映的情景，类似于把一个3D 图像扫描成像，沿着垂直方向等厚度分割得到

Snipaste_2020-07-11_11-25-24.png

ITK 对 DICOM 数据进行读取

ITK 根据 DICOM 文件读取方式有两种类型，单张 DICOM 读取或 序列 DICOM 读取

ITK 读取单张 DICOM 文件

  • itkImageSeriesReader;
  • itkGDCMImageIO;

读取后可以通过 itkGCOMImageIO 中 Get*** 函数获取病人相关信息，并打印输出，这里需要注意一点，DICOM 对应的数据类型为 signed short；核心代码：

	string DirectoryPath = "D:/Data_Training/Dicom_data/215020265/AT000002.152046493.dcm";
	

	typedef signed short InternalPixelType;
	const unsigned int  Dimension = 2;
	using InternalImageType = itk::Image<InternalPixelType, Dimension>;

	typedef itk::Image<InternalPixelType, Dimension> ImageType;
	typedef itk::ImageSeriesReader<ImageType> ReaderType;
	
	typedef itk::GDCMImageIO ImageIOType;
	
	ImageIOType::Pointer gdcmIO = ImageIOType::New();
	
	ReaderType::Pointer reader = ReaderType::New();
	reader->SetImageIO(gdcmIO);
	reader->SetFileNames(DirectoryPath);

	// Reading Data;
	try
	{
		reader->Update();
		reader->GetMetaDataDictionary();
		gdcmIO->GetMetaDataDictionary();// 读取头文件信息；

		//信息赋值
		char* name = new char[50];
		char* patientID = new char[50];
		char* time = new char[50];
		char* manufacture = new char[50];
		char* modility = new char[50];
		char* hospital = new char[50];
		char* sex = new char[50];
		char* age = new char[50];
		char* description = new char[100];
		

		
		
		int pixelType = gdcmIO->GetPixelType();
		int componentType = gdcmIO->GetComponentType();
		int fileType = gdcmIO->GetFileType();
		ImageIOType::ByteOrder byteOrder;
		byteOrder = gdcmIO->GetByteOrder();
		
		unsigned int dim = 0;
		gdcmIO->GetDimensions(dim);
		ImageIOType::SizeType imgsize;
		imgsize = gdcmIO->GetImageSizeInPixels();
		int componetSize = gdcmIO->GetComponentSize();
		int dimension = gdcmIO->GetNumberOfDimensions();
		int ori = 0;
	
		gdcmIO->GetOrigin(ori);
		int spa = 0;

		gdcmIO->GetPatientSex(sex);
		gdcmIO->GetPatientAge(age);
		gdcmIO->GetStudyDescription(description);
		gdcmIO->GetSpacing(spa);
		gdcmIO->GetPatientName(name);
		gdcmIO->GetModality(modility);
		gdcmIO->GetPatientID(patientID);
		gdcmIO->GetManufacturer(manufacture);
		gdcmIO->GetStudyDate(time);
		ImageIOType::TCompressionType compressType;
		compressType = gdcmIO->GetCompressionType();
		gdcmIO->GetInstitution(hospital);
		ImageType::SpacingType spacetype;
		spacetype = reader->GetOutput()->GetSpacing();
		ImageType::PointType origin;
		origin = reader->GetOutput()->GetOrigin();
		
		
		
		cout << "name:" << name << endl;
		cout << "age:" << age << endl;
		cout << "sex:" << sex << endl;
		cout << "description:" << description << endl;
		cout << "hospital:" << hospital << endl;
		cout << "modility:" << modility << endl;
		cout << "manfacture:" << manufacture << endl;
		cout << "dim:" << dim << endl;
		cout << "origin：" << origin << endl;
		cout << "Time:" << time << endl;
		cout << "patientID:" << patientID << endl;
		
	}
	catch (const itk::ExceptionObject& excp)
	{
		cout << " Reading Exceptaion Caught" << endl;
		cout << excp.what() << endl;
		
		return EXIT_FAILURE;
	}

ITK 读取序列 DICOM 文件

  • itkImageSeriesReader;
  • itkGDCMImageIO;
  • itkGDCMSeriesFileNames;

与单张读取不同的是，多了一个 itkGDCMSeriesFileNames 类，用于打包 DICOM 序列文件，再传入 GDCMImageIO 进行读取

	string DirectoryPath = "D:/Data_Training/Dicom_data/215020265";

	typedef signed short InternalPixelType;
	const unsigned int  Dimension = 3;
	using InternalImageType = itk::Image<InternalPixelType, Dimension>;

	typedef itk::Image<InternalPixelType, Dimension> ImageType;
	typedef itk::ImageSeriesReader<ImageType> ReaderType;
	
	typedef itk::GDCMImageIO ImageIOType;
	typedef itk::GDCMSeriesFileNames NamesGeneratorType;
	
	ImageIOType::Pointer gdcmIO = ImageIOType::New();
	NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New();
	
	namesGenerator->SetInputDirectory(DirectoryPath);
	
	const ReaderType::FileNamesContainer & filenames =
		namesGenerator->GetInputFileNames();

	std::size_t numberOfFileNames = filenames.size();
	std::cout << numberOfFileNames << std::endl;
	
	
	ReaderType::Pointer reader = ReaderType::New();
	reader->SetImageIO(gdcmIO);
	reader->SetFileNames(filenames);
	

	// Reading Data;
	try
	{
		reader->Update();
		reader->GetMetaDataDictionary();
		gdcmIO->GetMetaDataDictionary();// 读取头文件信息；

		//信息赋值
		char* name = new char[50];
		char* patientID = new char[50];
		char* time = new char[50];
		char* manufacture = new char[50];
		char* modility = new char[50];
		char* hospital = new char[50];
		char* sex = new char[50];
		char* age = new char[50];
		char* description = new char[100];
		

		
		
		int pixelType = gdcmIO->GetPixelType();
		int componentType = gdcmIO->GetComponentType();
		int fileType = gdcmIO->GetFileType();
		ImageIOType::ByteOrder byteOrder;
		byteOrder = gdcmIO->GetByteOrder();
		
		unsigned int dim = 0;
		gdcmIO->GetDimensions(dim);
		ImageIOType::SizeType imgsize;
		imgsize = gdcmIO->GetImageSizeInPixels();
		int componetSize = gdcmIO->GetComponentSize();
		int dimension = gdcmIO->GetNumberOfDimensions();
		int ori = 0;
	
		gdcmIO->GetOrigin(ori);
		int spa = 0;

		gdcmIO->GetPatientSex(sex);
		gdcmIO->GetPatientAge(age);
		gdcmIO->GetStudyDescription(description);
		gdcmIO->GetSpacing(spa);
		gdcmIO->GetPatientName(name);
		gdcmIO->GetModality(modility);
		gdcmIO->GetPatientID(patientID);
		gdcmIO->GetManufacturer(manufacture);
		gdcmIO->GetStudyDate(time);
		ImageIOType::TCompressionType compressType;
		compressType = gdcmIO->GetCompressionType();
		gdcmIO->GetInstitution(hospital);
		ImageType::SpacingType spacetype;
		spacetype = reader->GetOutput()->GetSpacing();
		ImageType::PointType origin;
		origin = reader->GetOutput()->GetOrigin();
		
		
		
		cout << "name:" << name << endl;
		cout << "age:" << age << endl;
		cout << "sex:" << sex << endl;
		cout << "description:" << description << endl;
		cout << "hospital:" << hospital << endl;
		cout << "modility:" << modility << endl;
		cout << "manfacture:" << manufacture << endl;
		cout << "dim:" << dim << endl;
		cout << "origin：" << origin << endl;
		cout << "Time:" << time << endl;
		cout << "patientID:" << patientID << endl;
		
	}
	catch (const itk::ExceptionObject& excp)
	{
		cout << " Reading Exceptaion Caught" << endl;
		cout << excp.what() << endl;
		
		return EXIT_FAILURE;
	}

运行结果如下：

Snipaste_2020-07-11_10-42-43.png

除了上面病人年龄、性别、ID 基本信息之外，用 itkGDCMImageIO 获取更多病人相关信息，这里从itkGDCMImageIO.h 源码中获取到了下面函数，大家可以参考一下：

Snipaste_2020-07-11_11-54-48.png

VTK 读取 DICOM

vtk 读取 DICOM 就比较简单了，因为 VTK 封装的有相关 DICOM 读取类： vtkDICOMImageReader，可直接进行操作；

VTK读取单张DICOM文件并进行预览

  • vtkDICOMImageReader
#include<vtkSmartPointer.h>
#include<vtkImageViewer2.h>
#include<vtkDICOMImageReader.h>
#include<vtkRenderWindow.h>
#include<vtkRenderWindowInteractor.h>
#include<vtkRenderer.h>
#include<iostream>
#include<string.h>
#include<vtkAutoInit.h>


VTK_MODULE_INIT(vtkRenderingOpenGL2);
VTK_MODULE_INIT(vtkInteractionStyle);


int main()
{
	using namespace std;
	
	string OpenPath = "D:/Data_Training/Dicom_data/215020265/AT000001.151955287.dcm";
	
	vtkSmartPointer<vtkDICOMImageReader> reader =
		vtkSmartPointer<vtkDICOMImageReader>::New();
	reader->SetFileName(OpenPath.c_str());
	reader->Update();


	vtkSmartPointer<vtkImageViewer2> imageViewer =
		vtkSmartPointer<vtkImageViewer2>::New();
	imageViewer->SetInputConnection(reader->GetOutputPort());

	vtkSmartPointer<vtkRenderWindowInteractor> renWin =
		vtkSmartPointer<vtkRenderWindowInteractor>::New();
	imageViewer->SetupInteractor(renWin);
	imageViewer->Render();
	imageViewer->GetRenderer()->ResetCamera();
	imageViewer->Render();

	renWin->Start();

	return EXIT_SUCCESS;
}

因为加入了一个交互窗口，因此可利用放大缩小

VTKiMAge1.gif

VTK读取序列DICOM文件并进行预览

  • vtkDICOMImageReader

用法与单张读取相似，区别是序列图这里读取的文件夹，而单张读取的是单张 DICOM;

#include<vtkSmartPointer.h>
#include<vtkImageViewer2.h>
#include<vtkDICOMImageReader.h>
#include<vtkRenderWindow.h>
#include<vtkRenderWindowInteractor.h>
#include<vtkRenderer.h>
#include<vtkTextProperty.h>
#include<vtkTextMapper.h>
#include<vtkActor2D.h>
#include<vtkInteractorStyleImage.h>
#include<vtkObjectFactory.h>
#include<iostream>
#include<string.h>
#include<vtkAutoInit.h>
#include<sstream>


VTK_MODULE_INIT(vtkRenderingOpenGL2);
VTK_MODULE_INIT(vtkInteractionStyle);
VTK_MODULE_INIT(vtkRenderingFreeType)

using namespace std;
class StatusMessage{
    
    
public:
	static std::string Format(int slice, int maxSlice)
	{
    
    
		std::stringstream tmp;
		tmp << "Slice Number  " << slice + 1 << "/" << maxSlice + 1;
		
		return tmp.str();
	}

};

// Define own interation style;
class myVtkInteractorStyleImage : public vtkInteractorStyleImage
{
    
    
public:
	static myVtkInteractorStyleImage* New();
	vtkTypeMacro(myVtkInteractorStyleImage, vtkInteractorStyleImage);
	
protected:
	vtkImageViewer2* _ImageViewer;
	vtkTextMapper* _StatusMapper;
	int _Slice;
	int _MinSlice;
	int _MaxSlice;
	
public:
	void SetImageViewer(vtkImageViewer2* imageViwer)
	{
    
    
		_ImageViewer = imageViwer;
		_MinSlice = imageViwer->GetSliceMin();
		_MaxSlice = imageViwer->GetSliceMax();
		_Slice = _MinSlice;
		
		cout << "Slice : Min = " << _MinSlice << ", Max = " << _MaxSlice << endl;

	}
	
	void SetStatusMapper(vtkTextMapper* statusMapper)
	{
    
    
		_StatusMapper = statusMapper;
	}
	
protected:
	void MoveSliceForward()
	{
    
    
		if (_Slice<_MaxSlice)
		{
    
    
			_Slice += 1;
			cout << " MoveSliceForward::Slice = " << _Slice << endl;
			_ImageViewer->SetSlice(_Slice);
			std::string msg = StatusMessage::Format(_Slice, _MaxSlice);
			_StatusMapper->SetInput(msg.c_str());
			_ImageViewer->Render();

		}
	}

	void MoveSliceBackward()
	{
    
    
		if(_Slice>_MinSlice)
		{
    
    
			_Slice -= 1;
			cout << "MoveSliceBackward::Slice = " << _Slice << endl;
			_ImageViewer->SetSlice(_Slice);
			std::string msg = StatusMessage::Format(_Slice, _MaxSlice);
			_StatusMapper->SetInput(msg.c_str());
			_ImageViewer->Render();

		}
	}

	virtual void OnKeyDown()
	{
    
    
		string key = this->GetInteractor()->GetKeySym();
		if (key.compare("Up") == 0)
		{
    
    
			MoveSliceForward();
		}
		else if (key.compare("Down") == 0)
		{
    
    
			MoveSliceBackward();
		}
		vtkInteractorStyleImage::OnKeyDown();
		
	}

	virtual void OnMouseWheelForward()
	{
    
    
		MoveSliceForward();
	}
	
	virtual void OnMouseWheelBackward()
	{
    
    
		if (_Slice > _MinSlice)
		{
    
    
			MoveSliceBackward();
		}
	}
};


vtkStandardNewMacro(myVtkInteractorStyleImage);



int main()
{
    
    
	using namespace std;
	
	string OpenPath = "D:/Data_Training/Dicom_data/215020265/";
	
	vtkSmartPointer<vtkDICOMImageReader> reader =
		vtkSmartPointer<vtkDICOMImageReader>::New();
	reader->SetDirectoryName(OpenPath.c_str());
	reader->Update();
	

	vtkSmartPointer<vtkImageViewer2> imageViewer =
		vtkSmartPointer<vtkImageViewer2>::New();
	imageViewer->SetInputConnection(reader->GetOutputPort());



	//Slice Status
	vtkSmartPointer<vtkTextProperty> sliceTextProp =
		vtkSmartPointer<vtkTextProperty>::New();
	sliceTextProp->SetFontFamilyToCourier();
	sliceTextProp->SetFontSize(20);
	sliceTextProp->SetVerticalJustificationToBottom();
	sliceTextProp->SetJustificationToLeft();

	vtkSmartPointer<vtkTextMapper> sliceTextMapper =
		vtkSmartPointer<vtkTextMapper>::New();
	string msg = StatusMessage::Format(imageViewer->GetSliceMin(), imageViewer->GetSliceMax());
	sliceTextMapper->SetInput(msg.c_str());
	cout << "msg" << msg.c_str() << endl;

	sliceTextMapper->SetTextProperty(sliceTextProp);
	
	vtkSmartPointer<vtkActor2D> sliceTextActor =
		vtkSmartPointer<vtkActor2D>::New();
	sliceTextActor->SetMapper(sliceTextMapper);
	sliceTextActor->SetPosition(15, 10);
	

	//usage hint message;
	vtkSmartPointer<vtkTextProperty> usageTextProp =
		vtkSmartPointer<vtkTextProperty>::New();
	usageTextProp->SetFontFamilyToCourier();
	usageTextProp->SetFontSize(14);
	usageTextProp->SetVerticalJustificationToTop();
	usageTextProp->SetJustificationToLeft();
	
	vtkSmartPointer<vtkTextMapper> usageTextMapper =
		vtkSmartPointer<vtkTextMapper>::New();
	usageTextMapper->SetInput("Slice with mouse wheel\n or Up/Down-Key\n =Zoom weh pressed right\n mouse button while dragging");
	usageTextMapper->SetTextProperty(usageTextProp);
	
	vtkSmartPointer<vtkActor2D> usageTextActor =
		vtkSmartPointer <vtkActor2D>::New();
	usageTextActor->SetMapper(usageTextMapper);
	usageTextActor->GetPositionCoordinate()->SetCoordinateSystemToNormalizedDisplay();
	usageTextActor->GetPositionCoordinate()->SetValue(0.05, 0.95);


	vtkSmartPointer<myVtkInteractorStyleImage> myInteractorStyle =
		vtkSmartPointer<myVtkInteractorStyleImage>::New();
	
	myInteractorStyle->SetImageViewer(imageViewer);
	myInteractorStyle->SetStatusMapper(sliceTextMapper);


	vtkSmartPointer<vtkRenderWindowInteractor> renWin =
		vtkSmartPointer<vtkRenderWindowInteractor>::New();
	imageViewer->SetupInteractor(renWin);
	renWin->SetInteractorStyle(myInteractorStyle);

	imageViewer->GetRenderer()->AddActor2D(sliceTextActor);
	imageViewer->GetRenderer()->AddActor2D(usageTextActor);


	imageViewer->Render();
	imageViewer->GetRenderer()->ResetCamera();
	imageViewer->Render();

	renWin->Start();

	return EXIT_SUCCESS;
}

代码摘抄于官方，这里定义了一个自定义交互类，可以通过滑动鼠标或者按键来完成切片更换。并且通过类 vtkTextMapper 在界面上添加了两个文本注释，方便引导用户

预览效果如下：

VTKimage2.gif
（文章首发于公众号：Z先生点记）

Reference:

1，https://itk.org/Doxygen/html/classitk_1_1ImageSeriesReader.html

2，https://lorensen.github.io/VTKExamples/site/Cxx/IO/ReadDICOMSeries/`

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