phase_encoding.h File Reference

#include <Eigen/Dense>
#include "app.h"
#include "axes.h"
#include "header.h"
#include "file/nifti_utils.h"
#include "file/ofstream.h"

Go to the source code of this file.

Namespaces
namespace	MR
namespace	MR::PhaseEncoding

Functions
template<class MatrixType >
void	MR::PhaseEncoding::check (const MatrixType &PE)
	check that a phase-encoding table is valid More...
template<class MatrixType , class HeaderType >
void	MR::PhaseEncoding::check (const MatrixType &PE, const HeaderType &header)
	check that the PE scheme matches the DWI data in header More...
template<class MatrixType >
void	MR::PhaseEncoding::set_scheme (Header &header, const MatrixType &PE)
	store the phase encoding matrix in a header More...
void	MR::PhaseEncoding::clear_scheme (Header &header)
	clear the phase encoding matrix from a header More...
Eigen::MatrixXd	MR::PhaseEncoding::parse_scheme (const Header &)
	parse the phase encoding matrix from a header More...
Eigen::MatrixXd	MR::PhaseEncoding::get_scheme (const Header &)
	get a phase encoding matrix More...
template<class MatrixType >
void	MR::PhaseEncoding::scheme2eddy (const MatrixType &PE, Eigen::MatrixXd &config, Eigen::Array< int, Eigen::Dynamic, 1 > &indices)
	Convert a phase-encoding scheme into the EDDY config / indices format. More...
Eigen::MatrixXd	MR::PhaseEncoding::eddy2scheme (const Eigen::MatrixXd &, const Eigen::Array< int, Eigen::Dynamic, 1 > &)
	Convert phase-encoding infor from the EDDY config / indices format into a standard scheme. More...
template<class MatrixType , class HeaderType >
Eigen::MatrixXd	MR::PhaseEncoding::transform_for_image_load (const MatrixType &pe_scheme, const HeaderType &H)
	Modifies a phase encoding scheme if being imported alongside a non-RAS image. More...
template<class MatrixType , class HeaderType >
Eigen::MatrixXd	MR::PhaseEncoding::transform_for_nifti_write (const MatrixType &pe_scheme, const HeaderType &H)
	Modifies a phase encoding scheme if being exported alongside a NIfTI image. More...
template<class MatrixType , class HeaderType >
void	MR::PhaseEncoding::save (const MatrixType &PE, const HeaderType &header, const std::string &path)
	Save a phase-encoding scheme to file. More...
template<class MatrixType , class HeaderType >
void	MR::PhaseEncoding::save_eddy (const MatrixType &PE, const HeaderType &header, const std::string &config_path, const std::string &index_path)
	Save a phase-encoding scheme to EDDY format config / index files. More...
void	MR::PhaseEncoding::export_commandline (const Header &)
	Save the phase-encoding scheme from a header to file depending on command-line options. More...
template<class HeaderType >
Eigen::MatrixXd	MR::PhaseEncoding::load (const std::string &path, const HeaderType &header)
	Load a phase-encoding scheme from a matrix text file. More...
template<class HeaderType >
Eigen::MatrixXd	MR::PhaseEncoding::load_eddy (const std::string &config_path, const std::string &index_path, const HeaderType &header)
	Load a phase-encoding scheme from an EDDY-format config / indices file pair. More...

Variables
const App::OptionGroup	MR::PhaseEncoding::ImportOptions
const App::OptionGroup	MR::PhaseEncoding::SelectOptions
const App::OptionGroup	MR::PhaseEncoding::ExportOptions