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ITK、VTK 讀取 DiCOM 檔案資訊，并實作互動預覽

DICOM 檔案介紹

DICOM 全名叫 Digital Imaging and Communications in Medicine(醫學數字圖像與通信)，是醫學圖像和相關資訊的過節标準，也定義了臨床所需資料醫學圖像格式；

DICOM 資料格式包含大量屬性，例如病人名字、ID、年齡等基本資訊，這些資訊從儲存在 “頭檔案” 中，這種儲存方式避免了病人與圖像誤配；

一個病人樣本 包含多個 DICOM 子檔案，單個 DICOM 對象隻包含具有一幀像素資料，幀與幀之間以序列形式存在，可以來回切換形成類似于電影放映的情景，類似于把一個3D 圖像掃描成像，沿着垂直方向等厚度分割得到

ITK、VTK 讀取 DiCOM 檔案資訊，并實作互動預覽

ITK 對 DICOM 資料進行讀取

ITK 根據 DICOM 檔案讀取方式有兩種類型，單張 DICOM 讀取或 序列 DICOM 讀取

ITK 讀取單張 DICOM 檔案

  • itkImageSeriesReader;
  • itkGDCMImageIO;

讀取後可以通過 itkGCOMImageIO 中 Get*** 函數擷取病人相關資訊，并列印輸出，這裡需要注意一點，DICOM 對應的資料類型為 signed short；核心代碼：

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();// 讀取頭檔案資訊；

		//資訊指派
		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 讀取序列 DICOM 檔案

  • itkImageSeriesReader;
  • itkGDCMImageIO;
  • itkGDCMSeriesFileNames;

與單張讀取不同的是，多了一個 itkGDCMSeriesFileNames 類，用于打包 DICOM 序列檔案，再傳入 GDCMImageIO 進行讀取

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();// 讀取頭檔案資訊；

		//資訊指派
		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;
	}

運作結果如下：

ITK、VTK 讀取 DiCOM 檔案資訊，并實作互動預覽

除了上面病人年齡、性别、ID 基本資訊之外，用 itkGDCMImageIO 擷取更多病人相關資訊，這裡從itkGDCMImageIO.h 源碼中擷取到了下面函數，大家可以參考一下：

ITK、VTK 讀取 DiCOM 檔案資訊，并實作互動預覽

VTK 讀取 DICOM

vtk 讀取 DICOM 就比較簡單了，因為 VTK 封裝的有相關 DICOM 讀取類： vtkDICOMImageReader，可直接進行操作；

VTK讀取單張DICOM檔案并進行預覽

  • 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;
}

因為加入了一個互動視窗，是以可利用放大縮小

ITK、VTK 讀取 DiCOM 檔案資訊，并實作互動預覽

VTK讀取序列DICOM檔案并進行預覽

  • vtkDICOMImageReader

用法與單張讀取相似，差別是序列圖這裡讀取的檔案夾，而單張讀取的是單張 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;
}

代碼摘抄于官方，這裡定義了一個自定義互動類，可以通過滑動滑鼠或者按鍵來完成切片更換。并且通過類 vtkTextMapper 在界面上添加了兩個文本注釋，友善引導使用者

預覽效果如下：

ITK、VTK 讀取 DiCOM 檔案資訊，并實作互動預覽

（文章首發于公衆号：Z先生點記）

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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