Public Types
enum	RegistrationMode { ALADIN_RIGID =0, ITK_RIGID =1, ALADIN_AFFINE =2, ITK_AFFINE =3, ALADIN_DIFFDEMONS =4, ITK_AFFINEBSPLINE =5, ALIBABA_RIGID =6, ALIBABA_AFFINE =7, ALADIN_MILXBSPLINE =8, NIFTI_REG =9, NIFTI_ALADIN_REG =10, ITK_AFFINE_DIFFDEMONS =11, ITKALADIN_DIFFDEMONS =12, DIFFDEMONS =13 }

enum	InterpolateMode { INTERP_NEAREST =0, INTERP_LINEAR =1, INTERP_BSPLINE =2, INTERP_BSPLINE5 =3 }

enum	ConsensusMode { VOTING =0, MULTISTAPLE =1 }

typedef float	InputPixelType

typedef float	OutputPixelType

typedef itk::Vector< InputPixelType, 3 >	VectorPixelType

typedef itk::Image< VectorPixelType, 3 >	DemonsDeformationFieldType

typedef itk::Image< InputPixelType, 3 >	InputImageType

typedef itk::Image< OutputPixelType, 3 >	OutputImageType

typedef itk::NearestNeighborInterpolateImageFunction< InputImageType, double >	NearestNeighborInterpolatorType

typedef itk::LinearInterpolateImageFunction< InputImageType, double >	LinearInterpolatorType

typedef itk::BSplineInterpolateImageFunction< InputImageType, double, double >	BsplineInterpolatorType

typedef itk::Vector< float, 3 >	VectorType

typedef itk::OrientedImage< InputPixelType, 3 >	FixedImageType

typedef itk::OrientedImage< InputPixelType, 3 >	MovingImageType

typedef itk::OrientedImage< VectorType, 3 >	FieldType

typedef itk::NearestNeighborInterpolateImageFunction< FixedImageType, double >	NearestNeighborOrientatedInterpolatorType

typedef itk::LinearInterpolateImageFunction< FixedImageType, double >	LinearOrientatedInterpolatorType

typedef itk::BSplineInterpolateImageFunction< FixedImageType, double, double >	BsplineOrientatedInterpolatorType

Public Member Functions
void	writeFile3D (FixedImageType::Pointer image, std::string outputFileName)

FixedImageType::Pointer	readFile3D (std::string fileName)

bool	LoadSettings (std::string)

int	GetNumberOfCases ()

int	GetNumberOfCases2 ()

int	GetNumberOfAtlases ()

int	GetNumberOfLabellings ()

std::vector< int >	GetCaseIDs ()

std::vector< std::string >	GetCaseFileNames ()

std::vector< std::string >	GetCaseFileNames2 ()

std::string	GetCaseFileName (int caseID)

std::string	GetCaseFileName2 (int caseID)

std::vector< int >	GetAtlasIDs ()

std::vector< std::string >	GetAtlasFileNames ()

std::string	GetAtlasFileName (int caseID)

std::vector< int >	GetLabellingIDs ()

std::vector< std::string >	GetLabellingFileNames ()

std::vector< std::string >	GetLabellingFileNames (int caseID)

std::vector< std::string >	GetPropagatedOutputAtlases ()

std::vector< std::string >	GetPropagatedOutputTransforms ()

std::string	GetPropagatedOutputAtlases (int caseID)

std::vector< std::string >	GetPropagatedOutputLabels ()

std::vector< std::string >	GetPropagatedOutputLabels (int caseID)

bool	ClearPropagatedOutputAtlasesLabels ()

bool	SetCase (int caseID, std::string filenames)

bool	SetCases (std::vector< int > caseIDs, std::vector< std::string > caseFilenames)

bool	SetCasePair (int caseID, std::string filenames, std::string filenames2)

bool	SetCasesPair (std::vector< int > caseIDs, std::vector< std::string > caseFilenames, std::vector< std::string > caseFilenames2)

bool	ClearCases ()

bool	SetAtlases (std::vector< int > atlasIDs, std::vector< std::string > atlasFilenames)

bool	SetAtlas (int atlasIDs, std::string atlasFilenames)

bool	SetAtlases (std::vector< int > atlasIDs, std::vector< std::string > atlasFilenames, std::vector< int > labellingIDs, std::vector< std::string > labellingFilenames)

bool	SetAtlases (std::vector< int > atlasIDs, std::vector< std::string > atlasFilenames, std::vector< int > labellingIDs, std::vector< std::string > labellingFilenames, std::vector< int > maskIDs, std::vector< std::string > maskFilenames)

bool	SetAtlases (std::vector< int > atlasIDs, std::vector< std::string > atlasFilenames, std::vector< int > labellingIDs, std::vector< std::string > labellingFilenames, std::vector< int > maskIDs, std::vector< std::string > maskFilenames, std::vector< std::string > maskFilenames2)

bool	SetAtlas (int atlasIDs, std::string atlasFilenames, std::vector< std::string > labellingFilenames)

bool	ClearAtlases ()

void	SetOutputPrefix (std::string prefix)

std::string	GetOutputPrefix ()

bool	SetRegistrationInterpolation (InterpolateMode mode)

bool	SetAtlasInterpolation (InterpolateMode mode)

bool	SetLabelledImageInterpolation (InterpolateMode mode)

bool	SetLabelledImageInterpolation (std::vector< InterpolateMode > modes)

void	SetUseConsensus (bool flag)

bool	GetUseConsensus ()

bool	SetRegistrationMode (int registrationScheme, std::string configFilename="NULL")

bool	SetRegistrationMode (RegistrationMode registrationScheme, std::string)

RegistrationMode	GetRegistrationMode ()

bool	SetConsensusMode (int consensusScheme, std::string configFilename="NULL")

bool	SetConsensusMode (ConsensusMode consensusScheme, std::string)

ConsensusMode	GetConsensusMode ()

bool	ConfigureRegistration (RegistrationMode, std::string)

void	SetFilesToSave (int value)

void	UpdatePipeline ()

void	Voting (std::vector< std::string > inputFilenames, std::string outputFilename, int modulo, int N, ConsensusMode consensusMode)

bool	RegisterRigidITK (std::string dataFile, std::string atlasFile, std::string outputPrefix, bool Invert, std::string dataMaskFile, std::string atlasMaskFile)

bool	RegisterMilxNonRigid (std::string dataFile, std::string atlasFile, std::string outputName, bool Invert)

bool	RegisterAffineITK (std::string dataFile, std::string atlasFile, std::string outputPrefix, bool Invert, std::string dataMaskFile, std::string atlasMaskFile)

bool	RegisterNonRigidBsplineITK (std::string dataFile, std::string atlasFile, std::string outputPrefix, bool Invert, std::string dataMaskFile, std::string atlasMaskFile)

double	NmiITK (std::string dataFile, std::string atlasFile)

void	LoadTRSF (std::string filename1, std::string filename2, double *array, bool invert)

void	LoadTRSF (std::string filename, double *array, bool invert)

bool	PropagateAffine (std::string dataFile, std::string outFile, std::string targetFile, double *array, InterpolateMode mode, itk::SpatialOrientation::ValidCoordinateOrientationFlags &flag, itk::SpatialOrientationAdapter::DirectionType &dir)

bool	PropagateITKRigid (std::string dataFile, std::string outFile, std::string targetFile, std::string transformFile, InterpolateMode mode)

bool	PropagateITKAffine (std::string dataFile, std::string outFile, std::string targetFile, std::string transformFile, InterpolateMode mode)

bool	PropagateITKAffineBspline (std::string inputImage, std::string targetFile, std::string outputFilename, std::string inputTransform, std::string inputBsplineTransform, InterpolateMode mode)

unsigned int	StringToCharArray (std::string &cmdline, char **argument)

Public Attributes
std::vector< int >	m_AtlasIDs

std::vector< std::string >	m_AtlasFilenames

std::vector< int >	m_LabellingIDs

std::vector< std::string >	m_LabellingFilenames

std::vector< int >	m_MaskIDs

std::vector< std::string >	m_MaskFilenames

std::vector< std::string >	m_MaskFilenames2

std::vector< int >	m_CaseIDs

std::vector< std::string >	m_CaseFilenames

std::vector< std::string >	m_CaseFilenames2

std::string	m_OutputPrefix

std::vector< std::string >	m_PropagatedAtlases

std::vector< std::string >	m_PropagatedLabelling

std::vector< std::string >	m_PropagatedTransforms

InterpolateMode	m_RegistrationInterpolation

InterpolateMode	m_AtlasInterpolation

InterpolateMode	m_LabelledImageInterpolation

std::vector< InterpolateMode >	m_MultipleLabelledImageInterpolation

RegistrationMode	m_RegistrationMode

bool	m_UseConsensus

ConsensusMode	m_ConsensusMode

int	m_SaveFiles

NearestNeighborInterpolatorType::Pointer	m_NearestNeighborInterpolator

LinearInterpolatorType::Pointer	m_LinearInterpolator

BsplineInterpolatorType::Pointer	m_BsplineInterpolator

NearestNeighborOrientatedInterpolatorType::Pointer	m_NearestNeighborOrientatedInterpolator

LinearOrientatedInterpolatorType::Pointer	m_LinearOrientatedInterpolator

BsplineOrientatedInterpolatorType::Pointer	m_BsplineOrientatedInterpolator

Detailed Description

Definition at line 70 of file milxRegistration.h.

Member Function Documentation

◆ ConfigureRegistration()

bool milx::Registration::ConfigureRegistration	(	RegistrationMode	,
		std::string
	)

inline

Options to configure individual schemes (ie if not using config file).

Definition at line 606 of file milxRegistration.h.

◆ GetNumberOfCases()

int milx::Registration::GetNumberOfCases ( )

inline

Various Get Calls

Definition at line 144 of file milxRegistration.h.

◆ GetPropagatedOutputAtlases()

std::vector<std::string> milx::Registration::GetPropagatedOutputAtlases ( )

inline

Return the list of final output filenames for the propagated atlases and labels

As multiple

Definition at line 250 of file milxRegistration.h.

◆ LoadSettings()

bool milx::Registration::LoadSettings ( std::string )

inline

Configure registration class

Allows everything to be configured via one txt file.
ie load IDs, images, atlases, labellings, RegistrationMode, Registration Setting filename

Definition at line 136 of file milxRegistration.h.

◆ readFile3D()

Registration::FixedImageType::Pointer milx::Registration::readFile3D ( std::string fileName )

readFile3D reads in a 3D file of the specified name

Parameters

fileName the path of the file

Returns: an ITK smart pointer to the image

Definition at line 2648 of file milxRegistration.cxx.

◆ RegisterRigidITK()

bool milx::Registration::RegisterRigidITK	(	std::string	dataFile,
		std::string	atlasFile,
		std::string	outputPrefix,
		bool	Invert,
		std::string	dataMaskFile,
		std::string	atlasMaskFile
	)

Various code that requires refactoring

Note: In the future, the below should probably be implemented in a factory !

Definition at line 729 of file milxRegistration.cxx.

◆ SetAtlases()

bool milx::Registration::SetAtlases	(	std::vector< int >	atlasIDs,
		std::vector< std::string >	atlasFilenames
	)

inline

Set/Clear list of atlases, labellings and IDs

Case IDs should be unique.
Note: Labelling IDs are assumed to correspond to caseIDs
Previous Atlases will be removed.

Definition at line 339 of file milxRegistration.h.

◆ SetCase()

bool milx::Registration::SetCase	(	int	caseID,
		std::string	filenames
	)

inline

Set/Clear list of images to register or co-register

Definition at line 295 of file milxRegistration.h.

◆ SetConsensusMode()

bool milx::Registration::SetConsensusMode	(	int	consensusScheme,
		std::string	configFilename = `"NULL"`
	)

inline

Set Consensus Mode

Definition at line 577 of file milxRegistration.h.

◆ SetFilesToSave()

void milx::Registration::SetFilesToSave ( int value )

inline

Options to enable the amount of files to remain

5 or more saves all files (default)
4 do not save deformation fields
3 do not save propagated atlases
2 do not save transforms
1 do not save propagated labels
0 should save nothing

Definition at line 620 of file milxRegistration.h.

◆ SetOutputPrefix()

void milx::Registration::SetOutputPrefix ( std::string prefix )

inline

Set Output prefix

Note: this supports the use of /tmp/CASEID/case_CASEID_with_ATLASID_

Definition at line 430 of file milxRegistration.h.

◆ SetRegistrationInterpolation()

bool milx::Registration::SetRegistrationInterpolation ( InterpolateMode mode )

inline

SetInterpolation used for each step

Definition at line 443 of file milxRegistration.h.

◆ SetRegistrationMode()

bool milx::Registration::SetRegistrationMode	(	int	registrationScheme,
		std::string	configFilename = `"NULL"`
	)

inline

Set Registration scheme to use.

Definition at line 482 of file milxRegistration.h.

◆ SetUseConsensus()

void milx::Registration::SetUseConsensus ( bool flag )

inline

Enable/Disable the use of Voting

By default disabled

Definition at line 470 of file milxRegistration.h.

◆ UpdatePipeline()

void milx::Registration::UpdatePipeline ( )

inline

Not used in this code

Definition at line 628 of file milxRegistration.h.

◆ writeFile3D()

void milx::Registration::writeFile3D	(	FixedImageType::Pointer	image,
		std::string	outputFileName
	)

writeFile outputs a 3D image

Parameters

image	an ITK smart pointer to the image
outputFileName	the path of the file

Definition at line 2626 of file milxRegistration.cxx.

Member Data Documentation

◆ m_AtlasIDs

std::vector<int> milx::Registration::m_AtlasIDs

Variables used by this class;

Definition at line 628 of file milxRegistration.h.

◆ m_NearestNeighborInterpolator

NearestNeighborInterpolatorType::Pointer milx::Registration::m_NearestNeighborInterpolator

Declare interpolators

Definition at line 666 of file milxRegistration.h.

The documentation for this class was generated from the following files:

plugin/registration/itk/milxRegistration.h
plugin/registration/itk/milxRegistration.cxx

Public Types

Public Member Functions

Public Attributes

Detailed Description

Member Function Documentation

◆ ConfigureRegistration()

◆ GetNumberOfCases()

◆ GetPropagatedOutputAtlases()

◆ LoadSettings()

◆ readFile3D()

◆ RegisterRigidITK()

◆ SetAtlases()

◆ SetCase()

◆ SetConsensusMode()

◆ SetFilesToSave()

◆ SetOutputPrefix()

◆ SetRegistrationInterpolation()

◆ SetRegistrationMode()

◆ SetUseConsensus()

◆ UpdatePipeline()

◆ writeFile3D()

Member Data Documentation

◆ m_AtlasIDs

◆ m_NearestNeighborInterpolator