Registration.cpp File Reference

#include "mitkCommandLineParser.h"
#include <mitkIOUtil.h>
#include <mitkRegistrationWrapper.h>
#include <mitkImage.h>
#include <mitkImageCast.h>
#include <mitkITKImageImport.h>
#include <mitkImageTimeSelector.h>
#include <itkImageFileWriter.h>
#include <itksys/SystemTools.hxx>
#include <itkDirectory.h>
#include "itkLinearInterpolateImageFunction.h"
#include "itkWindowedSincInterpolateImageFunction.h"
#include "itkIdentityTransform.h"
#include "itkResampleImageFilter.h"
#include "itkNrrdImageIO.h"

Go to the source code of this file.

Typedefs
typedef std::vector< std::string >	FileListType
typedef itk::Image< double, 3 >	InputImageType

Functions
static mitk::Image::Pointer	ExtractFirstTS (mitk::Image *image, std::string fileType)
static std::vector< std::string > &	split (const std::string &s, char delim, std::vector< std::string > &elems)
static std::vector< std::string >	split (const std::string &s, char delim)
static FileListType	CreateFileList (std::string folder, std::string postfix)
	Create list of all files in provided folder ending with same postfix. More...
static std::string	GetSavePath (std::string outputFolder, std::string fileName)
static mitk::Image::Pointer	ResampleBySpacing (mitk::Image *input, float *spacing, bool useLinInt=false)
static FileListType	CreateDerivedFileList (std::string baseFN, std::string baseSuffix, std::vector< std::string > derivedPatterns)
	Build a derived file name from moving images e.g. xxx_T2.nrrd becomes xxx_GTV.nrrd. More...
static void	SaveImage (std::string fileName, mitk::Image *image, std::string fileType)
	Save images according to file type. More...
static void	CopyResources (FileListType fileList, std::string outputPath)
	Copy derived resources from first time step. Append _reg tag, but leave data untouched. More...
int	main (int argc, char *argv[])

Typedef Documentation

typedef std::vector<std::string> FileListType

Definition at line 39 of file Registration.cpp.

typedef itk::Image<double, 3> InputImageType

Definition at line 40 of file Registration.cpp.

Function Documentation

static void CopyResources ( FileListType  fileList, std::string  outputPath  )

static

Copy derived resources from first time step. Append _reg tag, but leave data untouched.

Definition at line 217 of file Registration.cpp.

References ExtractFirstTS(), mitk::IOUtil::LoadImage(), MITK_INFO, and mitk::IOUtil::SaveImage().

Referenced by main().

static FileListType CreateDerivedFileList ( std::string  baseFN, std::string  baseSuffix, std::vector< std::string >  derivedPatterns  )

static

Build a derived file name from moving images e.g. xxx_T2.nrrd becomes xxx_GTV.nrrd.

Definition at line 189 of file Registration.cpp.

References MITK_INFO.

Referenced by main().

static FileListType CreateFileList ( std::string  folder, std::string  postfix  )

static

Create list of all files in provided folder ending with same postfix.

Definition at line 73 of file Registration.cpp.

References filename, and mitk::New().

Referenced by main().

static mitk::Image::Pointer ExtractFirstTS ( mitk::Image *  image, std::string  fileType  )

static

Definition at line 42 of file Registration.cpp.

References mitk::ImageTimeSelector::New().

Referenced by CopyResources(), and main().

static std::string GetSavePath ( std::string  outputFolder, std::string  fileName  )

static

Definition at line 98 of file Registration.cpp.

Referenced by main().

int main	(	int	argc,
		char *	argv[]
	)

Definition at line 231 of file Registration.cpp.

References mitkCommandLineParser::addArgument(), us::any_cast(), mitk::RegistrationWrapper::ApplyTransformationToImage(), mitkCommandLineParser::Bool, CopyResources(), CreateDerivedFileList(), CreateFileList(), ExtractFirstTS(), GetSavePath(), mitk::RegistrationWrapper::GetTransformation(), mitkCommandLineParser::helpText(), mitkCommandLineParser::InputDirectory, mitk::IOUtil::LoadImage(), MITK_ERROR, MITK_INFO, MITK_WARN, offset, mitkCommandLineParser::OutputDirectory, mitkCommandLineParser::parseArguments(), ResampleBySpacing(), mitk::IOUtil::Save(), mitk::IOUtil::SaveImage(), mitkCommandLineParser::setArgumentPrefix(), mitkCommandLineParser::setCategory(), mitkCommandLineParser::setContributor(), mitkCommandLineParser::setDescription(), mitkCommandLineParser::setTitle(), split(), and mitkCommandLineParser::String.

static mitk::Image::Pointer ResampleBySpacing ( mitk::Image *  input, float *  spacing, bool  useLinInt = false  )

static

1) Resampling

Definition at line 109 of file Registration.cpp.

References mitk::CastToItkImage(), mitk::GrabItkImageMemory(), mitk::New(), and mitk::Image::New().

Referenced by main().

static void SaveImage ( std::string  fileName, mitk::Image *  image, std::string  fileType  )

static

Save images according to file type.

Definition at line 209 of file Registration.cpp.

References MITK_INFO, and mitk::IOUtil::Save().

static std::vector<std::string>& split ( const std::string &  s, char  delim, std::vector< std::string > &  elems  )

static

Definition at line 55 of file Registration.cpp.

Referenced by main(), and split().

static std::vector<std::string> split ( const std::string &  s, char  delim  )

static

Definition at line 66 of file Registration.cpp.

References split().