BALL::Spectrum< DataT, PeakT, PositionT > Class Template Reference
[NMR spectra and related classes]

#include <BALL/NMR/spectrum.h>

Public Types


typedef DataT	DataType
	The datatype used to store the spectrum.
typedef PositionT	PositionType
	the data type used to store a position (for peaks and data)
typedef PeakT	PeakType
	The peak type.
typedef DataT::Iterator	Iterator
	An iterator.
typedef DataT::ConstIterator	ConstIterator
	A constant iterator.
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 vector< float >	computeHuInvariantsDifferences (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.
void	binaryRead (const String &filename)
	This function requires that DataT has a binaryRead method.


	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 vector< float > &	getHuInvariants () const
vector< float > &	getHuInvariants ()
Public Attributes
std::vector< float >	normal_moments
	precomputed normal moments
std::vector< float >	central_moments
	precomputed central moments
std::vector< float >	standardized_moments
	precomputed standardized moments
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 48 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 64 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 56 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 62 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 60 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 58 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 71 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 79 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 87 of file spectrum.h.

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

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

Destructor

Definition at line 92 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 ( ) [inline, virtual]

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

Definition at line 172 of file spectrum.h.

template<typename DataT , typename PeakT , typename PositionT >

void BALL::Spectrum< DataT, PeakT, PositionT >::clearSticks ( ) [inline, virtual]

Definition at line 179 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 ( ) [inline, virtual]

Definition at line 295 of file spectrum.h.

template<typename DataT , typename PeakT , typename PositionT >

vector< float > BALL::Spectrum< DataT, PeakT, PositionT >::computeHuInvariantsDifferences ( vector< Spectrum< DataT, PeakT, PositionT > > & spectra ) [inline, virtual]

Definition at line 302 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 [inline, virtual]

Calculate the difference between two spectra.

Definition at line 189 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
	)			`[inline, virtual]`

Definition at line 236 of file spectrum.h.

template<typename DataT , typename PeakT , typename PositionT >

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

Definition at line 272 of file spectrum.h.

template<typename DataT , typename PeakT , typename PositionT >

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

Definition at line 266 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`
	)			`[inline, 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 310 of file spectrum.h.

template<typename DataT , typename PeakT , typename PositionT >

vector< float > & BALL::Spectrum< DataT, PeakT, PositionT >::getHuInvariants ( ) [inline]

Definition at line 287 of file spectrum.h.

template<typename DataT , typename PeakT , typename PositionT >

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

Definition at line 281 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
	)			`[inline, 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 221 of file spectrum.h.

template<typename DataT , typename PeakT , typename PositionT >

Spectrum< DataT, PeakT, PositionT >::PositionType BALL::Spectrum< DataT, PeakT, PositionT >::getSpacing ( ) const [inline, virtual]

Return the spacing.

Definition at line 198 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
	)			`[inline, virtual]`

Definition at line 251 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 [inline, virtual]

Definition at line 123 of file spectrum.h.

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

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

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

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

Definition at line 122 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 149 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 160 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 165 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 164 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 163 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 147 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 162 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 151 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 161 of file spectrum.h.

BALL::Spectrum< DataT, PeakT, PositionT > Class Template Reference [NMR spectra and related classes]

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

BALL::Spectrum< DataT, PeakT, PositionT > Class Template Reference
[NMR spectra and related classes]

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