ITK配准：基于手动设置配准点的图像配准方法

本例子是通过手动设置定标点对待配准图像进行移动，使其与参考图像配准！

本文是基于位移场将图像进行wrap操作，以实现最终的配准！该实现是基于WarpImageFilter 进行操作的，WarpImageFilter 在给定的位移场的作用下将已有图像进行wrap（空间扭曲）操作。位移场可以看做是一张图像，其pixel type是长度至少为N的向量型（vector type）。其中N是输入图像的维数。位移场中每个向量表示输入空间中的几何点和输出空间上点的距离。P(in)=P(out)+d。

WarpImageFilter的输出是通过逆向映射实现的，输出像素被映射到输入图像。该方案避免了创建输出图像中的任何漏洞和重叠。在映射过程中存在不能映射到输入图像的整数位置，所以需要用到插值 函数 ，用以计算在非整数位置的像素值。默认的插值方式是 LinearInterpolateImageFunction，可以通过 SetInterpolator()来进行设置。

   映射到输入图像缓冲区的外部的位置，将分配一个边缘填充的值。

1、生成图像

参考图为：像素尺寸100X100，在以（40,40）和（60,60）为坐标所包围的区域像素值为255，其余区域像素值为0；

待配准图为：像素尺寸100X100，在以（20,20）和（80,80）为坐标所包围的区域像素值为100，其余区域像素值为0；

在配准的过程手动设置移动场源的定标点，即为配准导航点。

2、基于两个定标集合（即所谓的导航点，也称为简单称为配准点）产生位移场（displacement field）

1）设置形变场源对象的参数时，向参考图看起，如deformationFieldSource->SetOutputSpacing( fixedImage->GetSpacing() );等

2）生成参考图和待配准图的landmarks，即两者的地标！通过InsertElement( 2, sourcePoint );对地标点进行添加！

3）将地标点与形变场源进行关联

3、建立一个WarpImageFilterType的warpImageFilter。

1）需要设置其所对应的插值器

2）根据形变场源设置warpImageFilter的SetOutputSpacing和SetOutputOrigin

3）需要将其与2中的形变场源进行关联。warpImageFilter->SetDisplacementField( deformationFieldSource->GetOutput() );

同时也需要设置其待配准图像的输入：warpImageFilter->SetInput( movingImage );

4、输出配准结果

只需要利用一个writer将warpImageFilter的结果进行输出即可！

writer->SetInput (  warpImageFilter->GetOutput() );

#include "itkImageFileReader.h"#include "itkImageFileWriter.h"#include "itkImage.h"#include "itkVector.h"#if ITK_VERSION_MAJOR < 4#include "itkDeformationFieldSource.h"#else#include "itkLandmarkDisplacementFieldSource.h"#endif #include "itkWarpImageFilter.h" const     unsigned int   Dimension = 2;typedef   unsigned char  PixelType;typedef   itk::Image< PixelType, Dimension > ImageType; static void CreateFixedImage(ImageType::Pointer image);static void CreateMovingImage(ImageType::Pointer image); int main(int, char *[]){	typedef   float          VectorComponentType; 	typedef   itk::Vector< VectorComponentType, Dimension >    VectorType;	typedef   itk::Image< VectorType,  Dimension >   DeformationFieldType; 	ImageType::Pointer fixedImage =		ImageType::New();	CreateFixedImage(fixedImage); 	ImageType::Pointer movingImage =		ImageType::New();	CreateMovingImage(movingImage);//Computes a displacement field(位移场) from two sets of landmarks. #if ITK_VERSION_MAJOR < 4	typedef itk::DeformationFieldSource<DeformationFieldType>  DeformationFieldSourceType;#else	typedef itk::LandmarkDisplacementFieldSource<DeformationFieldType>  DeformationFieldSourceType;#endif	DeformationFieldSourceType::Pointer deformationFieldSource =		DeformationFieldSourceType::New();	//std::cout<<fixedImage->GetSpacing();	deformationFieldSource->SetOutputSpacing( fixedImage->GetSpacing() );//以参考图作为输入	deformationFieldSource->SetOutputOrigin(  fixedImage->GetOrigin() );	deformationFieldSource->SetOutputRegion(  fixedImage->GetLargestPossibleRegion() );	deformationFieldSource->SetOutputDirection( fixedImage->GetDirection() ); 	// Create source and target landmarks.	typedef DeformationFieldSourceType::LandmarkContainerPointer   LandmarkContainerPointer;	typedef DeformationFieldSourceType::LandmarkContainer          LandmarkContainerType;	typedef DeformationFieldSourceType::LandmarkPointType          LandmarkPointType; 	LandmarkContainerType::Pointer sourceLandmarks =		LandmarkContainerType::New();	LandmarkContainerType::Pointer targetLandmarks =		LandmarkContainerType::New(); 	LandmarkPointType sourcePoint;	LandmarkPointType targetPoint; 	//设置进行配准的起始位置	sourcePoint[0] = 40;//参考图像遍历的起始位置，坐标表示！	sourcePoint[1] = 40;	targetPoint[0] = 20;//待配准图像遍历的起始位置，坐标表示！	targetPoint[1] = 20;	sourceLandmarks->InsertElement( 0, sourcePoint );	targetLandmarks->InsertElement( 0, targetPoint ); 	sourcePoint[0] = 40;//设置第二个配准点	sourcePoint[1] = 60;	targetPoint[0] = 20;	targetPoint[1] = 80;	sourceLandmarks->InsertElement( 1, sourcePoint );	targetLandmarks->InsertElement( 1, targetPoint ); 	sourcePoint[0] = 60;//设置第3个配准点！	sourcePoint[1] = 40;	targetPoint[0] = 80;	targetPoint[1] = 20;	sourceLandmarks->InsertElement( 2, sourcePoint );	targetLandmarks->InsertElement( 2, targetPoint ); 	sourcePoint[0] = 60;//设置第4个配准点	sourcePoint[1] = 60;	targetPoint[0] = 80;	targetPoint[1] = 80;	sourceLandmarks->InsertElement( 3, sourcePoint );	targetLandmarks->InsertElement( 3, targetPoint );	//设置形变场场源！将其与配准点进行关联	deformationFieldSource->SetSourceLandmarks( sourceLandmarks.GetPointer() );	deformationFieldSource->SetTargetLandmarks( targetLandmarks.GetPointer() );	deformationFieldSource->UpdateLargestPossibleRegion(); 	// Write the deformation field	{		typedef itk::ImageFileWriter<  DeformationFieldType  > WriterType;		WriterType::Pointer writer =			WriterType::New();		writer->SetInput (  deformationFieldSource->GetOutput() );		writer->SetFileName( "deformation.mhd" );		writer->Update();	}  	typedef itk::WarpImageFilter< ImageType,		ImageType,		DeformationFieldType  >  WarpImageFilterType; 	WarpImageFilterType::Pointer warpImageFilter =		WarpImageFilterType::New();	//插值器类型	typedef itk::LinearInterpolateImageFunction<ImageType, double >  InterpolatorType;	InterpolatorType::Pointer interpolator =		InterpolatorType::New(); 	warpImageFilter->SetInterpolator( interpolator );	warpImageFilter->SetOutputSpacing( deformationFieldSource->GetOutput()->GetSpacing() );	warpImageFilter->SetOutputOrigin(  deformationFieldSource->GetOutput()->GetOrigin() );#if ITK_VERSION_MAJOR < 4	warpImageFilter->SetDeformationField( deformationFieldSource->GetOutput() );#else	warpImageFilter->SetDisplacementField( deformationFieldSource->GetOutput() );#endif	warpImageFilter->SetInput( movingImage );	warpImageFilter->Update(); 	// Write the output	typedef itk::ImageFileWriter<  ImageType  > WriterType;	WriterType::Pointer writer =		WriterType::New();	writer->SetInput (  warpImageFilter->GetOutput() );	writer->SetFileName( "output.png" );	writer->Update(); 	return EXIT_SUCCESS;} void CreateFixedImage(ImageType::Pointer image){	// Create a black image with a white square	//参考图像为（40,40）和（60,60）之间所包围的一个矩形框，且该区域灰度值为255	ImageType::IndexType start;	start.Fill(0); 	ImageType::SizeType size;	size.Fill(100); 	ImageType::RegionType region;	region.SetSize(size);	region.SetIndex(start); 	image->SetRegions(region);	image->Allocate();	image->FillBuffer(0); 	itk::ImageRegionIterator<ImageType> imageIterator(image,region); 	while(!imageIterator.IsAtEnd())	{		if(imageIterator.GetIndex()[0] > 40 && imageIterator.GetIndex()[0] < 60 &&			imageIterator.GetIndex()[1] > 40 && imageIterator.GetIndex()[1] < 60)		{			imageIterator.Set(255);		}		++imageIterator;	} 	// Write the deformation field	typedef itk::ImageFileWriter<  ImageType  > WriterType;	WriterType::Pointer writer =		WriterType::New();	writer->SetInput (  image );	writer->SetFileName( "fixed.png" );	writer->Update();}  void CreateMovingImage(ImageType::Pointer image){	// Create a black image with a white square	//待配准图像为(20,20)和（80,80）所围成的矩形框，且该区域灰度值为100	ImageType::IndexType start;	start.Fill(0); 	ImageType::SizeType size;	size.Fill(100); 	ImageType::RegionType region;	region.SetSize(size);	region.SetIndex(start); 	image->SetRegions(region);	image->Allocate();	image->FillBuffer(0); 	itk::ImageRegionIterator<ImageType> imageIterator(image,region); 	while(!imageIterator.IsAtEnd())	{		if(imageIterator.GetIndex()[0] > 20 && imageIterator.GetIndex()[0] < 80 &&			imageIterator.GetIndex()[1] > 20 && imageIterator.GetIndex()[1] < 80)		{			imageIterator.Set(100);		}		++imageIterator;	} 	// Write the deformation field	typedef itk::ImageFileWriter<  ImageType  > WriterType;	WriterType::Pointer writer =		WriterType::New();	writer->SetInput (  image );	writer->SetFileName( "moving.png" );	writer->Update();}结果图如下所示：
  

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