Represents a range of TTTR indices. More...

#include <TTTRRange.h>

Inheritance diagram for TTTRRange:

Public Member Functions
	TTTRRange (int start, int stop)
	Constructs a TTTRRange with the specified start and stop indices.

	TTTRRange (int start=-1, int stop=-1, TTTRRange *other=nullptr)
	Constructs a TTTRRange.

virtual size_t	size ()
	Gets the number of TTTR indices in the range.

	TTTRRange (const TTTRRange &p2)
	Copy constructor.

std::vector< int >	get_tttr_indices ()
	Gets the vector of TTTR indices assigned to the range.

int	get_start () const
	Gets the start index of the TTTR range.

int	get_stop () const
	Gets the stop index of the TTTR range.

std::vector< int >	get_start_stop ()
	Gets a vector of the start and stop TTTR indices of the range.

unsigned long	get_stop_time (TTTR *tttr) const
	Gets the stop time of the TTTR range.

unsigned long	get_start_time (TTTR *tttr) const
	Gets the start time of the TTTR range.

std::vector< unsigned long >	get_start_stop_time (TTTR *tttr)
	Gets a vector of the start and stop times of the TTTR range.

unsigned int	get_duration (TTTR *tttr)
	Gets the duration between the start and stop times of the TTTR range.

void	insert (int idx)
	Inserts an index into the TTTR index vector.

void	clear ()
	Clears the TTTR index set.

int	strip (const std::vector< int > &tttr_indices, int offset=0)
	Strips TTTR indices from a range starting at tttr_indices[offset].

double	get_mean_microtime (TTTR *tttr_data, double microtime_resolution=-1.0, int minimum_number_of_photons=1)
	Computes the mean microtime in units of the microtime resolution.

void	get_microtime_histogram (std::shared_ptr< TTTR > tttr, double *histogram, int n_histogram, double *time, int n_time, unsigned short micro_time_coarsening)
	Gets the microtime histogram for the TTTRRange.

double	get_mean_lifetime (TTTR tttr_data, int minimum_number_of_photons=3, TTTR tttr_irf=nullptr, double m0_irf=1.0, double m1_irf=1.0, double dt=1.0, std::vector< double > *background=nullptr, double m0_bg=0.0, double m1_bg=0.0, double background_fraction=-1.0)
	Computes the mean lifetime for the TTTRRange.

bool	operator== (const TTTRRange &other) const
	Equality operator.

bool	operator!= (const TTTRRange &other) const
	Inequality operator.

TTTRRange &	operator+= (const TTTRRange &rhs)
	Compound assignment addition operator.

Static Public Member Functions
static double	compute_mean_lifetime (std::vector< int > &tttr_indices, TTTR tttr_data, int minimum_number_of_photons=3, TTTR tttr_irf=nullptr, double m0_irf=1.0, double m1_irf=1.0, double dt=1.0, std::vector< double > *background=nullptr, double m0_bg=0.0, double m1_bg=0.0, double background_fraction=-1.0)
	Computes the mean lifetime for a set of TTTR indices.

Protected Attributes
itlib::flat_set< int >	_tttr_indices {}
	Set of TTTR indices in the range.

Detailed Description

Represents a range of TTTR indices.

Constructor & Destructor Documentation

◆ TTTRRange() [1/3]

TTTRRange::TTTRRange	(	int	start,
		int	stop )

Constructs a TTTRRange with the specified start and stop indices.

Parameters

start	The start index of the range.
stop	The stop index of the range.

◆ TTTRRange() [2/3]

TTTRRange::TTTRRange	(	int	start = -1,
		int	stop = -1,
		TTTRRange *	other = nullptr )

inline

Constructs a TTTRRange.

If both start and stop are non-negative, inserts them into the _tttr_indices set. If other is not nullptr, inserts its start and stop indices into the set.

Parameters

start	The start index of the range.
stop	The stop index of the range.
other	Pointer to another TTTRRange (optional).

◆ TTTRRange() [3/3]

TTTRRange::TTTRRange ( const TTTRRange & p2 )

Copy constructor.

Parameters

p2	Reference to another TTTRRange to copy.

Member Function Documentation

◆ clear()

void TTTRRange::clear ( )

inline

Clears the TTTR index set.

◆ compute_mean_lifetime()

static double TTTRRange::compute_mean_lifetime	(	std::vector< int > &	tttr_indices,
		TTTR *	tttr_data,
		int	minimum_number_of_photons = 3,
		TTTR *	tttr_irf = nullptr,
		double	m0_irf = 1.0,
		double	m1_irf = 1.0,
		double	dt = 1.0,
		std::vector< double > *	background = nullptr,
		double	m0_bg = 0.0,
		double	m1_bg = 0.0,
		double	background_fraction = -1.0 )

static

Computes the mean lifetime for a set of TTTR indices.

The average lifetimes are computed (not fitted) by the methods of moments (Irvin Isenberg, 1973, Biophysical journal).

If a TTTRRange has not enough photons, it is filled with zeros.

By default, fluorescence lifetimes are computed in units of the micro time if no dt is provided.

Parameters

tttr_indices	Vector of TTTR indices.
tttr_data	Pointer to a TTTR object.
minimum_number_of_photons	Minimum number of photons in a micro time.
tttr_irf	Pointer to a TTTR object of the IRF.
m0_irf	Zero moment of the IRF (optional, default=1).
m1_irf	First moment of the IRF (optional, default=1).
dt	Time resolution of the micro time.
background	Vector of background values (optional).
m0_bg	Zero moment of the background (optional, default=0).
m1_bg	First moment of the background (optional, default=0).
background_fraction	Fraction of background pattern in data (if negative, no background).

Returns: The mean lifetime.

◆ get_duration()

unsigned int TTTRRange::get_duration ( TTTR * tttr )

inline

Gets the duration between the start and stop times of the TTTR range.

Parameters

tttr	Pointer to a TTTR object.

Returns: The duration or 0 if tttr is nullptr or the set is empty.

◆ get_mean_lifetime()

double TTTRRange::get_mean_lifetime	(	TTTR *	tttr_data,
		int	minimum_number_of_photons = 3,
		TTTR *	tttr_irf = nullptr,
		double	m0_irf = 1.0,
		double	m1_irf = 1.0,
		double	dt = 1.0,
		std::vector< double > *	background = nullptr,
		double	m0_bg = 0.0,
		double	m1_bg = 0.0,
		double	background_fraction = -1.0 )

Computes the mean lifetime for the TTTRRange.

If a TTTRRange has not enough photons, returns -1.

By default, fluorescence lifetimes are computed in units of the micro time if no dt is provided.

Parameters

tttr_data	Pointer to a TTTR object.
minimum_number_of_photons	Minimum number of photons in a micro time.
tttr_irf	Pointer to a TTTR object of the IRF.
m0_irf	Zero moment of the IRF (optional, default=1).
m1_irf	First moment of the IRF (optional, default=1).
dt	Time resolution of the micro time.
background	Vector of background values (optional).
m0_bg	Zero moment of the background (optional, default=0).
m1_bg	First moment of the background (optional, default=0).
background_fraction	Fraction of background pattern in data (if negative, no background).

Returns: The mean lifetime.

◆ get_mean_microtime()

double TTTRRange::get_mean_microtime	(	TTTR *	tttr_data,
		double	microtime_resolution = -1.0,
		int	minimum_number_of_photons = 1 )

inline

Computes the mean microtime in units of the microtime resolution.

If there are fewer than the minimum number of photons in a TTTRRange, the function returns zero.

Parameters

tttr_data	Pointer to a TTTR object.
microtime_resolution	Microtime resolution.
minimum_number_of_photons	Minimum number of photons in a micro time.

Returns: The mean microtime.

◆ get_microtime_histogram()

void TTTRRange::get_microtime_histogram	(	std::shared_ptr< TTTR >	tttr,
		double **	histogram,
		int *	n_histogram,
		double **	time,
		int *	n_time,
		unsigned short	micro_time_coarsening )

inline

Gets the microtime histogram for the TTTRRange.

Parameters

tttr	Pointer to a TTTR object.
histogram	Pointer to the histogram array.
n_histogram	Pointer to the size of the histogram array.
time	Pointer to the time array.
n_time	Pointer to the size of the time array.
micro_time_coarsening	Microtime coarsening factor.

◆ get_start()

int TTTRRange::get_start ( ) const

inline

Gets the start index of the TTTR range.

Returns: The start index or -1 if the set is empty.

◆ get_start_stop()

std::vector< int > TTTRRange::get_start_stop ( )

inline

Gets a vector of the start and stop TTTR indices of the range.

Returns: A vector containing the start and stop indices.

◆ get_start_stop_time()

std::vector< unsigned long > TTTRRange::get_start_stop_time ( TTTR * tttr )

inline

Gets a vector of the start and stop times of the TTTR range.

Parameters

tttr	Pointer to a TTTR object.

Returns: A vector containing the start and stop times.

◆ get_start_time()

unsigned long TTTRRange::get_start_time ( TTTR * tttr ) const

inline

Gets the start time of the TTTR range.

Parameters

tttr	Pointer to a TTTR object.

Returns: The start time or 0 if tttr is nullptr or the set is empty.

◆ get_stop()

int TTTRRange::get_stop ( ) const

inline

Gets the stop index of the TTTR range.

Returns: The stop index or -1 if the set is empty.

◆ get_stop_time()

unsigned long TTTRRange::get_stop_time ( TTTR * tttr ) const

inline

Gets the stop time of the TTTR range.

Parameters

tttr	Pointer to a TTTR object.

Returns: The stop time or 0 if tttr is nullptr or the set is empty.

◆ get_tttr_indices()

std::vector< int > TTTRRange::get_tttr_indices ( )

inline

Gets the vector of TTTR indices assigned to the range.

Returns: A vector containing the TTTR indices in the set.

◆ insert()

void TTTRRange::insert ( int idx )

inline

Inserts an index into the TTTR index vector.

Parameters

idx	The index to insert.

◆ operator!=()

bool TTTRRange::operator!= ( const TTTRRange & other ) const

inline

Inequality operator.

Parameters

other Another TTTRRange to compare.

Returns: True if the two TTTRRanges are not equal, false otherwise.

◆ operator+=()

TTTRRange & TTTRRange::operator+= ( const TTTRRange & rhs )

inline

Compound assignment addition operator.

Parameters

rhs	Another TTTRRange to add.

Returns: Reference to the modified TTTRRange.

◆ operator==()

bool TTTRRange::operator== ( const TTTRRange & other ) const

inline

Equality operator.

Parameters

other Another TTTRRange to compare.

Returns: True if the two TTTRRanges are equal, false otherwise.

◆ size()

virtual size_t TTTRRange::size ( )

inlinevirtual

Gets the number of TTTR indices in the range.

Returns: The size of the tttr_indices set.

Reimplemented in CLSMFrame, and CLSMLine.

◆ strip()

int TTTRRange::strip	(	const std::vector< int > &	tttr_indices,
		int	offset = 0 )

inline

Strips TTTR indices from a range starting at tttr_indices[offset].

The tttr_indices need to be sorted in ascending size.

Parameters

tttr_indices	Vector of TTTR indices.
offset	Offset index.

Returns: Updated offset index.

Member Data Documentation

◆ _tttr_indices

itlib::flat_set<int> TTTRRange::_tttr_indices {}

protected

Set of TTTR indices in the range.

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

/builds/skf/tttrlib/include/TTTRRange.h

Public Member Functions

Static Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ TTTRRange() [1/3]

◆ TTTRRange() [2/3]

◆ TTTRRange() [3/3]

Member Function Documentation

◆ clear()

◆ compute_mean_lifetime()

◆ get_duration()

◆ get_mean_lifetime()

◆ get_mean_microtime()

◆ get_microtime_histogram()

◆ get_start()

◆ get_start_stop()

◆ get_start_stop_time()

◆ get_start_time()

◆ get_stop()

◆ get_stop_time()

◆ get_tttr_indices()

◆ insert()

◆ operator!=()

◆ operator+=()

◆ operator==()

◆ size()

◆ strip()

Member Data Documentation

◆ _tttr_indices