#include <BALL/NMR/spectrum.h>

Public Types

typedef DataT	DataType
	The datatype used to store the spectrum. More...

typedef PositionT	PositionType
	the data type used to store a position (for peaks and data) More...

typedef PeakT	PeakType
	The peak type. More...

typedef DataT::Iterator	Iterator
	An iterator. More...

typedef DataT::ConstIterator	ConstIterator
	A constant iterator. More...

Public Member Functions
virtual void	clear ()

virtual void	clearSticks ()

virtual double	difference (const Spectrum< DataT, PeakT, PositionT > &spectrum) const

virtual Spectrum< DataT, PeakT, PositionT >	differenceSpectrum (const Spectrum< DataT, PeakT, PositionT > &spectrum)

virtual double	earthMoversDistance (const Spectrum< DataT, PeakT, PositionT > &spectrum) const

virtual void	convertToGaussian ()

virtual void	convertToLorentzian ()

virtual void	computeAllMoments (int moment_number)

virtual void	setSpacing (const PositionType &spacing)

virtual PositionType	getSpacing () const

virtual void	setSticks (std::vector< PeakType > sticks)

virtual std::vector< PeakType >	getSticks () const

virtual double	getAbsIntegral () const

virtual void	computeHuInvariants ()

virtual std::vector< float >	computeHuInvariantsDifferences (std::vector< Spectrum< DataT, PeakT, PositionT > > &spectra)

virtual double	getFourierDifference (const Spectrum< DataT, PeakT, PositionT > &spectrum, float min_freq=1e6, float max_freq=-1e6)

virtual double	getNormalMomentsDifference (Spectrum< DataT, PeakT, PositionT > &spectrum, int moment_number)

virtual double	getCentralMomentsDifference (Spectrum< DataT, PeakT, PositionT > &spectrum, int moment_number)

virtual double	getStandardizedMomentsDifference (Spectrum< DataT, PeakT, PositionT > &spectrum, int moment_number)

void	binaryWrite (const String &filename)
	This function requires that DataT has a binaryWrite method. More...

void	binaryRead (const String &filename)
	This function requires that DataT has a binaryRead method. More...


	Spectrum ()

	Spectrum (const DataType &data)

	Spectrum (const std::vector< PeakType > &peaks, const PositionType &origin, const PositionType &dimension, const PositionType &spacing)

virtual	~Spectrum ()

Accessors
const DataType &	getData () const

DataType &	getData ()

const std::vector< float > &	getHuInvariants () const

std::vector< float > &	getHuInvariants ()

Public Attributes
std::vector< float >	normal_moments
	precomputed normal moments More...

std::vector< float >	central_moments
	precomputed central moments More...

std::vector< float >	standardized_moments
	precomputed standardized moments More...

Protected Attributes
DataType	data_

std::vector< PeakType >	sticks_

PositionType	spacing_

PositionType	min_

PositionType	max_

std::vector< float >	Hu_invariants_

Detailed Description

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>
class BALL::Spectrum< DataT, PeakT, PositionT >

A generic NMR spectrum class.

Definition at line 46 of file spectrum.h.

Member Typedef Documentation

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

typedef DataT::ConstIterator BALL::Spectrum< DataT, PeakT, PositionT >::ConstIterator

A constant iterator.

Definition at line 62 of file spectrum.h.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

typedef DataT BALL::Spectrum< DataT, PeakT, PositionT >::DataType

The datatype used to store the spectrum.

Typedefs

Definition at line 54 of file spectrum.h.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

typedef DataT::Iterator BALL::Spectrum< DataT, PeakT, PositionT >::Iterator

An iterator.

Definition at line 60 of file spectrum.h.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

typedef PeakT BALL::Spectrum< DataT, PeakT, PositionT >::PeakType

The peak type.

Definition at line 58 of file spectrum.h.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

typedef PositionT BALL::Spectrum< DataT, PeakT, PositionT >::PositionType

the data type used to store a position (for peaks and data)

Definition at line 56 of file spectrum.h.

Constructor & Destructor Documentation

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

BALL::Spectrum< DataT, PeakT, PositionT >::Spectrum ( )

inline

Constructors and Destructor

Definition at line 69 of file spectrum.h.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

BALL::Spectrum< DataT, PeakT, PositionT >::Spectrum ( const DataType & data )

inline

Definition at line 77 of file spectrum.h.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

BALL::Spectrum< DataT, PeakT, PositionT >::Spectrum	(	const std::vector< PeakType > &	peaks,
		const PositionType &	origin,
		const PositionType &	dimension,
		const PositionType &	spacing
	)

inline

Definition at line 85 of file spectrum.h.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

virtual BALL::Spectrum< DataT, PeakT, PositionT >::~Spectrum ( )

inlinevirtual

Destructor

Definition at line 90 of file spectrum.h.

Member Function Documentation

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

void BALL::Spectrum< DataT, PeakT, PositionT >::binaryRead ( const String & filename )

This function requires that DataT has a binaryRead method.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

void BALL::Spectrum< DataT, PeakT, PositionT >::binaryWrite ( const String & filename )

This function requires that DataT has a binaryWrite method.

template<typename DataT , typename PeakT , typename PositionT >

void BALL::Spectrum< DataT, PeakT, PositionT >::clear ( )

virtual

Clear the spectrum. Sets all data to zero. // TODO: what about the spacing?

Definition at line 170 of file spectrum.h.

template<typename DataT , typename PeakT , typename PositionT >

void BALL::Spectrum< DataT, PeakT, PositionT >::clearSticks ( )

virtual

Definition at line 177 of file spectrum.h.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

virtual void BALL::Spectrum< DataT, PeakT, PositionT >::computeAllMoments ( int moment_number )

virtual

template<typename DataT , typename PeakT , typename PositionT >

void BALL::Spectrum< DataT, PeakT, PositionT >::computeHuInvariants ( )

virtual

Definition at line 293 of file spectrum.h.

template<typename DataT , typename PeakT , typename PositionT >

std::vector< float > BALL::Spectrum< DataT, PeakT, PositionT >::computeHuInvariantsDifferences ( std::vector< Spectrum< DataT, PeakT, PositionT > > & spectra )

virtual

Definition at line 300 of file spectrum.h.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

virtual void BALL::Spectrum< DataT, PeakT, PositionT >::convertToGaussian ( )

virtual

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

virtual void BALL::Spectrum< DataT, PeakT, PositionT >::convertToLorentzian ( )

virtual

template<typename DataT , typename PeakT , typename PositionT >

double BALL::Spectrum< DataT, PeakT, PositionT >::difference ( const Spectrum< DataT, PeakT, PositionT > & spectrum ) const

virtual

Calculate the difference between two spectra.

Definition at line 187 of file spectrum.h.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

virtual Spectrum<DataT, PeakT, PositionT> BALL::Spectrum< DataT, PeakT, PositionT >::differenceSpectrum ( const Spectrum< DataT, PeakT, PositionT > & spectrum )

virtual

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

virtual double BALL::Spectrum< DataT, PeakT, PositionT >::earthMoversDistance ( const Spectrum< DataT, PeakT, PositionT > & spectrum ) const

virtual

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

virtual double BALL::Spectrum< DataT, PeakT, PositionT >::getAbsIntegral ( ) const

virtual

template<typename DataT , typename PeakT , typename PositionT >

double BALL::Spectrum< DataT, PeakT, PositionT >::getCentralMomentsDifference	(	Spectrum< DataT, PeakT, PositionT > &	spectrum,
		int	moment_number
	)

virtual

Definition at line 234 of file spectrum.h.

template<typename DataT , typename PeakT , typename PositionT >

const DataT & BALL::Spectrum< DataT, PeakT, PositionT >::getData ( ) const

Definition at line 264 of file spectrum.h.

template<typename DataT , typename PeakT , typename PositionT >

DataT & BALL::Spectrum< DataT, PeakT, PositionT >::getData ( )

Definition at line 270 of file spectrum.h.

template<typename DataT , typename PeakT , typename PositionT >

double BALL::Spectrum< DataT, PeakT, PositionT >::getFourierDifference	(	const Spectrum< DataT, PeakT, PositionT > &	spectrum,
		float	min_freq = `1e6`,
		float	max_freq = `-1e6`
	)

virtual

Computes the difference between the spectra in Fourier space. max_freq and min_freq can be used to include only a certain range into the comparison. In this case, we only use the positive frequencies (the negative ones are redundant anyhow) and assume that 0<=min_freq<max_freq<=1, where min_freq and max_freq are interpreted as percentages, e.g. calling this function with min_freq=0 and max_freq=0.5 would include the lower half of the positive frequencies.

Definition at line 308 of file spectrum.h.

template<typename DataT , typename PeakT , typename PositionT >

const std::vector< float > & BALL::Spectrum< DataT, PeakT, PositionT >::getHuInvariants ( ) const

Definition at line 279 of file spectrum.h.

template<typename DataT , typename PeakT , typename PositionT >

std::vector< float > & BALL::Spectrum< DataT, PeakT, PositionT >::getHuInvariants ( )

Definition at line 285 of file spectrum.h.

template<typename DataT , typename PeakT , typename PositionT >

double BALL::Spectrum< DataT, PeakT, PositionT >::getNormalMomentsDifference	(	Spectrum< DataT, PeakT, PositionT > &	spectrum,
		int	moment_number
	)

virtual

Computes the difference according to the precomputed normal moments up to moment_number. If the values have not been precomputed so far, we regenerate them.

Definition at line 219 of file spectrum.h.

template<typename DataT , typename PeakT , typename PositionT >

Spectrum< DataT, PeakT, PositionT >::PositionType BALL::Spectrum< DataT, PeakT, PositionT >::getSpacing ( ) const

virtual

Return the spacing.

Definition at line 196 of file spectrum.h.

template<typename DataT , typename PeakT , typename PositionT >

double BALL::Spectrum< DataT, PeakT, PositionT >::getStandardizedMomentsDifference	(	Spectrum< DataT, PeakT, PositionT > &	spectrum,
		int	moment_number
	)

virtual

Definition at line 249 of file spectrum.h.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

virtual std::vector<PeakType> BALL::Spectrum< DataT, PeakT, PositionT >::getSticks ( ) const

inlinevirtual

Definition at line 121 of file spectrum.h.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

void BALL::Spectrum< DataT, PeakT, PositionT >::setSpacing ( const PositionType & spacing )

virtual

Set the spacing.

Definition at line 204 of file spectrum.h.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

virtual void BALL::Spectrum< DataT, PeakT, PositionT >::setSticks ( std::vector< PeakType > sticks )

inlinevirtual

Definition at line 120 of file spectrum.h.

Member Data Documentation

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

std::vector<float> BALL::Spectrum< DataT, PeakT, PositionT >::central_moments

precomputed central moments

Definition at line 147 of file spectrum.h.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

DataType BALL::Spectrum< DataT, PeakT, PositionT >::data_

protected

Definition at line 158 of file spectrum.h.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

std::vector<float> BALL::Spectrum< DataT, PeakT, PositionT >::Hu_invariants_

protected

Definition at line 163 of file spectrum.h.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

PositionType BALL::Spectrum< DataT, PeakT, PositionT >::max_

protected

Definition at line 162 of file spectrum.h.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

PositionType BALL::Spectrum< DataT, PeakT, PositionT >::min_

protected

Definition at line 161 of file spectrum.h.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

std::vector<float> BALL::Spectrum< DataT, PeakT, PositionT >::normal_moments

precomputed normal moments

Definition at line 145 of file spectrum.h.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

PositionType BALL::Spectrum< DataT, PeakT, PositionT >::spacing_

protected

Definition at line 160 of file spectrum.h.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

std::vector<float> BALL::Spectrum< DataT, PeakT, PositionT >::standardized_moments

precomputed standardized moments

Definition at line 149 of file spectrum.h.

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>

std::vector<PeakType> BALL::Spectrum< DataT, PeakT, PositionT >::sticks_

protected

Definition at line 159 of file spectrum.h.

Public Types

Public Member Functions

Public Attributes

Protected Attributes

Detailed Description

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position> class BALL::Spectrum< DataT, PeakT, PositionT >

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template<typename DataT, typename PeakT, typename PositionT = typename PeakT::Position>
class BALL::Spectrum< DataT, PeakT, PositionT >