svkQuantifyMetabolites Class Reference

#include <svkQuantifyMetabolites.h>

Inheritance diagram for svkQuantifyMetabolites:

Public Member Functions
	vtkTypeMacro (svkQuantifyMetabolites, svkImageAlgorithm)
void	SetXMLFileName (vtkstd::string xmlFileName)
vtkstd::string	GetXMLFileName ()
void	ClearXMLFile ()
void	SetVerbose (bool isVerbose)
vtkstd::vector < svkMriImageData * > *	GetMetMaps ()
void	LimitToSelectedVolume (float fraction=0.5001)
vtkstd::vector< vtkstd::vector < vtkstd::string > >	GetRegionNameVector ()
int	GetIntFromString (vtkstd::string stringVal)
float	GetFloatFromString (vtkstd::string stringVal)
void	ModifyRegion (int regionID, float peakPPM, float widthPPM)
void	SetAnatomyType (svkTypes::AnatomyType anatomyType)
Public Member Functions inherited from svkImageAlgorithm
	vtkTypeMacro (svkImageAlgorithm, vtkImageAlgorithm)
svkImageData *	GetOutput ()
svkImageData *	GetOutput (int port)
svkImageData *	GetImageDataInput (int port)

Static Public Member Functions
static svkQuantifyMetabolites *	New ()
static void	WriteDefaultXMLTemplate (string fileName, bool clobber=false)
static string	GetDefaultXMLFileName ()
static bool	ShouldUpgradeXML ()
static string	GetOldVersionName ()
static void	SaveOldVersion ()

Protected Member Functions
	svkQuantifyMetabolites ()
	~svkQuantifyMetabolites ()
virtual int	RequestInformation (vtkInformation *request, vtkInformationVector **inputVector, vtkInformationVector *outputVector)
virtual int	RequestData (vtkInformation *request, vtkInformationVector **inputVector, vtkInformationVector *outputVector)
virtual int	FillInputPortInformation (int vtkNotUsed(port), vtkInformation *info)
virtual int	FillOutputPortInformation (int vtkNotUsed(port), vtkInformation *info)
Protected Member Functions inherited from svkImageAlgorithm
	svkImageAlgorithm ()
	~svkImageAlgorithm ()

Static Protected Member Functions
static void	GetCurrentXMLVersion (string *v1, string *v2, string *v3)

Detailed Description

Class to generate a set of metabolite maps representing quantified peak regions, ratios or z-scores. This class uses other algorithms to perform the necessary quantification and outputs an array of metabolilte maps (svkMriImageData objects).

Requires an XML input file specifying the regions to quantify.

Constructor & Destructor Documentation

svkQuantifyMetabolites ( )

protected

References svkTypes::ANATOMY_BRAIN, and svkQuantifyMetabolites::GetDefaultXMLFileName().

~svkQuantifyMetabolites ( )

protected

Member Function Documentation

void ClearXMLFile

(

)

Sets the current XML data to NULL so the file will be re-read.

Referenced by svkQuantifyMetabolites::SetXMLFileName().

int FillInputPortInformation ( int   vtkNotUsedport, vtkInformation *  info  )

protectedvirtual

Default input type is svkImageData base class. Override with a specific concrete type in sub class if necessary.

Reimplemented from svkImageAlgorithm.

int FillOutputPortInformation ( int   vtkNotUsedport, vtkInformation *  info  )

protectedvirtual

Output from this algo is an svkMriImageData object.

Reimplemented from svkImageAlgorithm.

void GetCurrentXMLVersion ( string *  v1, string *  v2, string *  v3  )

staticprotected

References svkQuantifyMetabolites::GetDefaultXMLFileName().

Referenced by svkQuantifyMetabolites::GetOldVersionName(), and svkQuantifyMetabolites::ShouldUpgradeXML().

string GetDefaultXMLFileName ( )

static

gets the default xml quantification template filename $HOME/.SIVICQuant.xml

References svkUtils::GetHomeDirectory().

Referenced by svkQuantifyMetabolites::GetCurrentXMLVersion(), svkQuantifyMetabolites::GetOldVersionName(), svkQuantifyMetabolites::SaveOldVersion(), svkQuantifyMetabolites::svkQuantifyMetabolites(), and svkQuantifyMetabolites::WriteDefaultXMLTemplate().

float GetFloatFromString

(

vtkstd::string

stringVal

)

int GetIntFromString

(

vtkstd::string

stringVal

)

vtkstd::vector< svkMriImageData * > * GetMetMaps

(

)

string GetOldVersionName ( )

static

References svkQuantifyMetabolites::GetCurrentXMLVersion(), and svkQuantifyMetabolites::GetDefaultXMLFileName().

Referenced by svkQuantifyMetabolites::SaveOldVersion().

vtkstd::vector< vtkstd::vector< vtkstd::string > > GetRegionNameVector

(

)

Returns an stl map containing the region name, with a vector of 2 floats that store the region peak ppm and width in ppm. All info parsed from the xml config file.

References svkTypes::GetAnatomyTypeString(), svkImageData::GetDcmHeader(), svkImageAlgorithm::GetImageDataInput(), and svkDcmHeader::GetStringValue().

string GetXMLFileName

(

)

Get the path to the current XML file

void LimitToSelectedVolume

(

float

fraction = 0.5001

)

void ModifyRegion	(	int	regionID,
		float	peakPPM,
		float	widthPPM
	)

Modify a region's peak and width.

References svkImageData::GetDcmHeader(), svkImageAlgorithm::GetImageDataInput(), and svkDcmHeader::GetStringValue().

static svkQuantifyMetabolites* New ( )

static

int RequestData ( vtkInformation *  request, vtkInformationVector **  inputVector, vtkInformationVector *  outputVector  )

protectedvirtual

Copy the Dcm Header and Provenance from the input to the output.

int RequestInformation ( vtkInformation *  request, vtkInformationVector **  inputVector, vtkInformationVector *  outputVector  )

protectedvirtual

Resets the origin and extent for correct initialization of output svkMriImageData object from input svkMrsImageData object.

void SaveOldVersion ( )

static

References svkUtils::CopyFile(), svkQuantifyMetabolites::GetDefaultXMLFileName(), and svkQuantifyMetabolites::GetOldVersionName().

void SetAnatomyType

(

svkTypes::AnatomyType

anatomyType

)

void SetVerbose

(

bool

isVerbose

)

Write the integrals for each voxel to stdout. Default is false.

void SetXMLFileName

(

vtkstd::string

xmlFileName

)

set the path/name to xml file.

References svkQuantifyMetabolites::ClearXMLFile().

bool ShouldUpgradeXML ( )

static

References svkQuantifyMetabolites::GetCurrentXMLVersion(), and svkTypeUtils::StringToInt().

vtkTypeMacro	(	svkQuantifyMetabolites	,
		svkImageAlgorithm
	)

void WriteDefaultXMLTemplate ( string  fileName, bool  clobber = false  )

static

Print out a template xml config file: if fileName is "", then use default filename ( $HOME/.SIVICQuant.xml) if clober is false, will not overwrite existing file.

References svkQuantifyMetabolites::GetDefaultXMLFileName().

---

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

• svkQuantifyMetabolites.h
• svkQuantifyMetabolites.cc