DiffusionDICOMLoader.cpp File Reference

#include "mitkImage.h"
#include "mitkBaseData.h"
#include <mitkDiffusionPropertyHelper.h>
#include <mitkImageCast.h>
#include <mitkITKImageImport.h>
#include <itkImageFileWriter.h>
#include <itkNrrdImageIO.h>
#include "mitkCommandLineParser.h"
#include <itksys/SystemTools.hxx>
#include <itksys/Directory.hxx>
#include "mitkDiffusionDICOMFileReader.h"
#include "mitkSortByImagePositionPatient.h"
#include "mitkDICOMTagBasedSorter.h"
#include "mitkDICOMSortByTag.h"
#include "itkMergeDiffusionImagesFilter.h"
#include <mitkIOUtil.h>

Go to the source code of this file.

Typedefs
typedef short	DiffusionPixelType
typedef itk::VectorImage< DiffusionPixelType, 3 >	DwiImageType
typedef DwiImageType::PixelType	DwiPixelType
typedef DwiImageType::RegionType	DwiRegionType
typedef std::vector< DwiImageType::Pointer >	DwiImageContainerType
typedef mitk::Image	DiffusionImageType
typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType	GradientContainerType
typedef std::vector< GradientContainerType::Pointer >	GradientListContainerType

Functions
static mitk::StringList &	GetInputFilenames ()
void	SetInputFileNames (std::string input_directory)
mitk::Image::Pointer	ReadInDICOMFiles (mitk::StringList &input_files, std::string output_file)
void	SearchForInputInSubdirs (std::string root_directory, std::string subdir_prefix, std::vector< DiffusionImageType::Pointer > &output_container)
int	main (int argc, char *argv[])

Typedef Documentation

typedef mitk::Image DiffusionImageType

Definition at line 146 of file DiffusionDICOMLoader.cpp.

typedef short DiffusionPixelType

Definition at line 140 of file DiffusionDICOMLoader.cpp.

typedef std::vector< DwiImageType::Pointer > DwiImageContainerType

Definition at line 144 of file DiffusionDICOMLoader.cpp.

typedef itk::VectorImage<DiffusionPixelType,3> DwiImageType

Definition at line 141 of file DiffusionDICOMLoader.cpp.

typedef DwiImageType::PixelType DwiPixelType

Definition at line 142 of file DiffusionDICOMLoader.cpp.

typedef DwiImageType::RegionType DwiRegionType

Definition at line 143 of file DiffusionDICOMLoader.cpp.

typedef mitk::DiffusionPropertyHelper::GradientDirectionsContainerType GradientContainerType

Definition at line 147 of file DiffusionDICOMLoader.cpp.

typedef std::vector< GradientContainerType::Pointer > GradientListContainerType

Definition at line 148 of file DiffusionDICOMLoader.cpp.

Function Documentation

static mitk::StringList& GetInputFilenames ( )

static

Definition at line 39 of file DiffusionDICOMLoader.cpp.

Referenced by main(), SearchForInputInSubdirs(), and SetInputFileNames().

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

Read DICOM Files through the new (refactored) Diffusion DICOM Loader. It serves also as a first test of the new functionality, it will replace the current loading mechanism after the necessary parts are merged into the master branch.

Definition at line 198 of file DiffusionDICOMLoader.cpp.

References mitkCommandLineParser::addArgument(), us::any_cast(), mitkCommandLineParser::Bool, mitk::CastToItkImage(), mitk::DiffusionPropertyHelper::GetGradientContainer(), GetInputFilenames(), mitk::DiffusionPropertyHelper::GetReferenceBValue(), mitk::GrabItkImageMemory(), mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME, mitk::DiffusionPropertyHelper::InitializeImage(), mitkCommandLineParser::InputDirectory, mitk::DiffusionPropertyHelper::MEASUREMENTFRAMEPROPERTYNAME, MITK_ERROR, MITK_INFO, mitk::FloatProperty::New(), mitk::New(), mitk::Image::New(), mitkCommandLineParser::OutputFile, mitkCommandLineParser::parseArguments(), ReadInDICOMFiles(), mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME, mitk::IOUtil::Save(), SearchForInputInSubdirs(), mitkCommandLineParser::setArgumentPrefix(), mitkCommandLineParser::setCategory(), mitkCommandLineParser::setContributor(), mitkCommandLineParser::setDescription(), SetInputFileNames(), mitkCommandLineParser::setTitle(), and mitkCommandLineParser::String.

mitk::Image::Pointer ReadInDICOMFiles	(	mitk::StringList &	input_files,
		std::string	output_file
	)

Definition at line 77 of file DiffusionDICOMLoader.cpp.

References MITK_ERROR, and mitk::ClassicDICOMSeriesReader::New().

Referenced by main(), and SearchForInputInSubdirs().

void SearchForInputInSubdirs	(	std::string	root_directory,
		std::string	subdir_prefix,
		std::vector< DiffusionImageType::Pointer > &	output_container
	)

Definition at line 150 of file DiffusionDICOMLoader.cpp.

References GetInputFilenames(), MITK_INFO, ReadInDICOMFiles(), and SetInputFileNames().

Referenced by main().

void SetInputFileNames

(

std::string

input_directory

)

Definition at line 46 of file DiffusionDICOMLoader.cpp.

References GetInputFilenames(), and MITK_INFO.

Referenced by main(), and SearchForInputInSubdirs().