#include <CLSMImage.h>

Public Member Functions
std::shared_ptr< TTTR >	get_tttr ()

void	set_tttr (std::shared_ptr< TTTR > v)

const CLSMSettings *	get_settings ()

size_t	size ()
	Get the number of frames in the CLSMImage.

void	fill (TTTR *tttr_data=nullptr, std::vector< int > channels=std::vector< int >(), bool clear=true, const std::vector< std::pair< int, int > > &micro_time_ranges=std::vector< std::pair< int, int > >())
	Fills the time-tagged time-resolved (TTTR) indices of the pixels with the indices of the photons that fall within each pixel.

void	fill_pixels (TTTR *tttr_data, std::vector< int > channels, bool clear_pixel=true, std::vector< std::pair< int, int > > micro_time_ranges=std::vector< std::pair< int, int > >())
	Fills the time-tagged time-resolved (TTTR) indices of the pixels with the indices of the channels that fall within each pixel.

void	clear ()
	Clears the time-tagged time-resolved (TTTR) indices stored in the pixels.

void	clear_pixels ()
	Clears the time-tagged time-resolved (TTTR) indices stored in the pixels.

void	strip (const std::vector< int > &tttr_indices, int offset=0)
	Strips time-tagged time-resolved (TTTR) indices from all pixels in the image.

void	get_fcs_image (float *output, int dim1, int dim2, int dim3, int dim4, std::shared_ptr< TTTR > tttr, CLSMImage clsm_other=nullptr, std::string correlation_method="default", int n_bins=50, int n_casc=1, bool stack_frames=false, bool normalized_correlation=false, int min_photons=2)
	Computes an image where pixels represent correlation curves.

std::vector< CLSMFrame * >	get_frames ()
	Retrieves the frames stored in the CLSMImage.

void	get_intensity (unsigned short *output, int dim1, int dim2, int dim3)
	Computes an intensity image.

void	get_fluorescence_decay (TTTR tttr_data, unsigned char output, int dim1, int dim2, int dim3, int *dim4, int micro_time_coarsening=1, bool stack_frames=false)
	Computes an image stack where the value of each pixel corresponds to a histogram of micro times in each pixel. The micro times can be coarsened by integer numbers.

void	get_decay_of_pixels (TTTR tttr_data, uint8_t mask, int dmask1, int dmask2, int dmask3, unsigned int *output, int dim1, int *dim2, int tac_coarsening, bool stack_frames)
	Computes micro time histograms for the stacks of images and a selection of pixels. Photons in pixels that are selected by the selection array contribute to the returned array of micro time histograms.

void	get_mean_micro_time (TTTR tttr_data, double output, int dim1, int dim2, int dim3, double microtime_resolution=-1.0, int minimum_number_of_photons=2, bool stack_frames=false)
	Calculates an image stack where the value of each pixel corresponds to the mean micro time (in units of the micro channel resolution).

void	get_phasor (float *output, int dim1, int dim2, int dim3, int dim4, TTTR tttr_data, TTTR *tttr_irf=nullptr, double frequency=-1, int minimum_number_of_photons=2, bool stack_frames=false)
	Computes the phasor values for every pixel.

void	get_mean_lifetime (TTTR tttr_data, double output, int dim1, int dim2, int dim3, int minimum_number_of_photons=3, TTTR *tttr_irf=nullptr, double m0_irf=1.0, double m1_irf=1.0, bool stack_frames=false, std::vector< double > background=std::vector< double >(), double m0_bg=0.0, double m1_bg=0.0, double background_fraction=-1.0)
	Computes an image of average lifetimes.

int	to1D (int frame, int line, int pixel)
	Convert three-dimensional coordinates (frame, line, pixel) to a one-dimensional index.

std::vector< int >	to3D (int idx)
	Convert a one-dimensional index to three-dimensional coordinates (frame, line, pixel).

CLSMPixel *	getPixel (unsigned int idx)
	Get a pointer to a CLSMPixel object based on a one-dimensional index.

int	get_n_frames () const
	Get the number of frames in the CLSM image.

int	get_n_lines () const
	Get the number of lines per frame in the CLSMImage.

int	get_n_pixel () const
	Get the number of pixels per line in a frame of the CLSMImage.

void	copy (const CLSMImage &p2, bool fill=false)
	Copy information from another CLSMImage object.

void	append (CLSMFrame *frame)
	Append a CLSMFrame to the CLSM image.

void	transform (unsigned int *input, int n_input)
	Move the content of the Pixels based on source and target pixel indices.

void	rebin (int bin_line, int bin_pixel)
	Rebin a CLSMImage.

void	distribute (unsigned int pixel_id, CLSMImage *target, std::vector< int > &target_pixel_ids, std::vector< int > &target_probabilities)
	Distribute the photons of a pixel_id to a set of pixel ids in a target image according to provided probabilities.

void	crop (int frame_start, int frame_stop, int line_start, int line_stop, int pixel_start, int pixel_stop)
	Crop the CLSMImage.

void	stack_frames ()
	Stack frames in the CLSMImage.

	CLSMImage (const CLSMImage &p2, bool fill=false)
	Copy constructor for CLSMImage.

	CLSMImage (std::shared_ptr< TTTR > tttr_data=nullptr, CLSMSettings settings=CLSMSettings(), CLSMImage *source=nullptr, bool fill=true, std::vector< int > channels=std::vector< int >(), std::vector< std::pair< int, int > > micro_time_ranges=std::vector< std::pair< int, int > >())
	Constructs a CLSMImage object from TTTR data.

virtual	~CLSMImage ()
	Destructor for CLSMImage.

CLSMFrame *	operator[] (unsigned int i_frame)
	Accessor for CLSMFrame at the specified index in CLSMImage.

double	get_line_duration (int frame=0, int line=0)
	Obtains the duration of a line (in milliseconds) for a specified frame and line.

double	get_pixel_duration (int frame=0, int line=0)
	Obtains the duration of a pixel (in milliseconds) for a specified frame and line.

Static Public Member Functions
static void	compute_ics (double *output, int dim1, int dim2, int dim3, std::shared_ptr< TTTR > tttr_data=nullptr, CLSMImage clsm=nullptr, double images=nullptr, int input_frames=-1, int input_lines=-1, int input_pixel=1, std::vector< int > x_range=std::vector< int >({0, -1}), std::vector< int > y_range=std::vector< int >({0, -1}), std::vector< std::pair< int, int > > frames_index_pairs=std::vector< std::pair< int, int > >(), std::string subtract_average="", uint8_t *mask=nullptr, int dmask1=-1, int dmask2=-1, int dmask3=-1)
	Performs an image correlation spectroscopy analysis via FFTs for a set of frames.

static void	get_roi (double *output, int dim1, int dim2, int dim3, CLSMImage clsm=nullptr, std::vector< int > x_range=std::vector< int >({0,-1}), std::vector< int > y_range=std::vector< int >({0,-1}), std::string subtract_average="", double background=0.0, bool clip=false, double clip_max=1e6, double clip_min=-1e6, double images=nullptr, int n_frames=-1, int n_lines=-1, int n_pixels=1, uint8_t *mask=nullptr, int dmask1=-1, int dmask2=-1, int dmask3=-1, std::vector< int > selected_frames=std::vector< int >())
	Copies a region of interest (ROI) from the input images, performs background correction, and stores the result in a new array.

static std::vector< int >	get_frame_edges (TTTR *tttr=nullptr, int start_event=0, int stop_event=-1, std::vector< int > marker_frame_start=std::vector< int >({4, 6}), int marker_event_type=15, int reading_routine=CLSM_SP8, bool skip_before_first_frame_marker=false, bool skip_after_last_frame_marker=false)
	Retrieves the time-tagged time-resolved (TTTR) indices of frame markers for a Leica SP8 microscope.

static std::vector< int >	get_line_edges (TTTR *tttr, int start_event, int stop_event, int marker_line_start=1, int marker_line_stop=2, int marker_event_type=15, int reading_routine=CLSM_SP8)
	Identifies line edges by reading start and stop markers in a time-tagged time-resolved (TTTR) dataset.

static std::vector< int >	get_line_edges_by_duration (TTTR *tttr, int start_event, int stop_event, int marker_line_start=1, int line_duration=2, int marker_event_type=15, int reading_routine=CLSM_SP8)
	Identifies line edges by reading a start marker and using line duration as the stop criterion in a time-tagged time-resolved (TTTR) dataset.

Public Attributes
std::vector< int >	marker_frame
	Vector containing the tttr indices of the frame markers.

int	marker_line_start
	Defines the marker for a line start.

int	marker_line_stop
	Defines the marker for a line stop.

int	marker_event
	The event type used for the marker.

std::string	reading_routine = "default"

bool	skip_before_first_frame_marker = false

bool	skip_after_last_frame_marker = false

Protected Member Functions
void	create_frames (bool clear_first=true)

void	create_lines ()

void	determine_number_of_lines ()

Protected Attributes
size_t	n_frames = 0
	The number of frames in an CLSMImage.

size_t	n_lines = 0
	The number of lines per frames.

size_t	n_pixel = 0
	The number if pixels per line.

std::shared_ptr< TTTR >	tttr = nullptr
	Pointer to tttr data that used to construct the Image.

Friends
class	Correlator

class	CLSMFrame

class	CLSMLine

class	CLSMPixel

Constructor & Destructor Documentation

◆ CLSMImage() [1/2]

CLSMImage::CLSMImage	(	const CLSMImage &	p2,
		bool	fill = false )

Copy constructor for CLSMImage.

Constructs a new CLSMImage by copying the content of another CLSMImage.

Parameters

p2	[in] The CLSMImage object from which the content is copied.
fill	[in] If set to true (default is false), the time-tagged time-resolved indices of the pixels are copied.

◆ CLSMImage() [2/2]

CLSMImage::CLSMImage	(	std::shared_ptr< TTTR >	tttr_data = nullptr,
		CLSMSettings	settings = CLSMSettings(),
		CLSMImage *	source = nullptr,
		bool	fill = true,
		std::vector< int >	channels = std::vector< int >(),
		std::vector< std::pair< int, int > >	micro_time_ranges = std::vector< std::pair< int, int > >() )

explicit

Constructs a CLSMImage object from TTTR data.

Constructs a CLSMImage object from Time-Tagged Time-Resolved (TTTR) data, using specified markers, settings, and optional source CLSMImage.

Parameters

tttr_data	[in] Pointer to TTTR object containing the raw data.
settings	[in] CLSMSettings object specifying parameters for image construction.
source	[in] A CLSMImage object used as a template. All frames and lines are copied, and empty pixels are created. If fill is set to true (default), the content of the pixels is copied.
fill	[in] If set to true (default), the lines are filled with pixels containing either the photons of the specified channels or the photons from the source CLSMImage instance.
channels	[in] The channel number of the events used to fill the pixels.
micro_time_ranges	[in] Vector of pairs specifying the micro time ranges.

See also: CLSMSettings for more details on available settings.

◆ ~CLSMImage()

virtual CLSMImage::~CLSMImage ( )

inlinevirtual

Destructor for CLSMImage.

Frees memory by deleting dynamically allocated CLSMFrame objects in the frames vector. It ensures proper cleanup of resources when a CLSMImage object is destroyed.

Member Function Documentation

◆ append()

void CLSMImage::append ( CLSMFrame * frame )

Append a CLSMFrame to the CLSM image.

Appends a CLSMFrame to the CLSM image.

Parameters

frame The CLSMFrame to be appended.

◆ clear()

void CLSMImage::clear ( )

Clears the time-tagged time-resolved (TTTR) indices stored in the pixels.

◆ clear_pixels()

void CLSMImage::clear_pixels ( )

inline

Clears the time-tagged time-resolved (TTTR) indices stored in the pixels.

Deprecated: Use the 'clear' function instead.

This function is deprecated in favor of 'clear'. It removes the stored TTTR indices from the pixels.

◆ compute_ics()

static void CLSMImage::compute_ics	(	double **	output,
		int *	dim1,
		int *	dim2,
		int *	dim3,
		std::shared_ptr< TTTR >	tttr_data = nullptr,
		CLSMImage *	clsm = nullptr,
		double *	images = nullptr,
		int	input_frames = -1,
		int	input_lines = -1,
		int	input_pixel = 1,
		std::vector< int >	x_range = std::vector< int >({0, -1}),
		std::vector< int >	y_range = std::vector< int >({0, -1}),
		std::vector< std::pair< int, int > >	frames_index_pairs = std::vector< std::pair< int, int > >(),
		std::string	subtract_average = "",
		uint8_t *	mask = nullptr,
		int	dmask1 = -1,
		int	dmask2 = -1,
		int	dmask3 = -1 )

static

Performs an image correlation spectroscopy analysis via FFTs for a set of frames.

This function computes the image correlation for a set of frames, either specified by an array or a CLSMImage object. It can compute image cross-correlation and image auto-correlations based on the type of correlation specified by a vector of pairs.

Parameters

output	[out] Array that will contain the Image Correlation Spectrscopy analysis (ICS).
dim1	[out] Number of frames in the ICS.
dim2	[out] Number of lines (line shifts) in the ICS.
dim3	[out] Number of pixels (pixel shifts) in the ICS.
tttr_data	[in] Pointer to TTTR object containing the raw data (optional).
clsm	[in] Optional pointer to a CLSMImage object.
images	[in] Optional pointer to an image array.
input_frames	[in] Number of frames in the image array.
input_lines	[in] Number of lines in the image array.
input_pixel	[in] Number of pixels per line in the image array.
x_range	[in] Defines the region of interest (ROI) in the image (pixel).
y_range	[in] Defines the ROI in y-direction (lines).
frames_index_pairs	[in] Vector of integer pairs corresponding to frame numbers used for cross-correlation (default computes auto-correlation).
subtract_average	[in] Specifies background correction: "stack" subtracts the average over all frames, "frame" subtracts the average of each frame. Default is no correction.
mask	[in] Stack of images used as a mask to select pixels (optional).
dmask1	[in] Number of frames in the mask.
dmask2	[in] Number of lines in the mask.
dmask3	[in] Number of pixels per line in the mask.

◆ copy()

void CLSMImage::copy	(	const CLSMImage &	p2,
		bool	fill = false )

Copy information from another CLSMImage object.

Copies the information from another CLSMImage object, including pixel indices, if the fill parameter is set to true (default is false).

Parameters

p2	The CLSMImage object from which information is copied.
fill	If set to true (default is false), the time-tagged time-resolved indices of the pixels are copied.

◆ create_frames()

void CLSMImage::create_frames ( bool clear_first = true )

protected

◆ create_lines()

void CLSMImage::create_lines ( )

protected

◆ crop()

void CLSMImage::crop	(	int	frame_start,
		int	frame_stop,
		int	line_start,
		int	line_stop,
		int	pixel_start,
		int	pixel_stop )

Crop the CLSMImage.

Crop the image by specifying the range of frames, lines, and pixels to keep.

Parameters

frame_start	[in] Starting frame index for cropping.
frame_stop	[in] Stopping frame index for cropping.
line_start	[in] Starting line index for cropping.
line_stop	[in] Stopping line index for cropping.
pixel_start	[in] Starting pixel index for cropping.
pixel_stop	[in] Stopping pixel index for cropping.

◆ determine_number_of_lines()

void CLSMImage::determine_number_of_lines ( )

protected

◆ distribute()

void CLSMImage::distribute	(	unsigned int	pixel_id,
		CLSMImage *	target,
		std::vector< int > &	target_pixel_ids,
		std::vector< int > &	target_probabilities )

Distribute the photons of a pixel_id to a set of pixel ids in a target image according to provided probabilities.

This function distributes the photons of a specified pixel_id to a set of pixel_ids in a target CLSMImage based on the provided probabilities.

Parameters

pixel_id	[in] The source pixel_id whose photons will be distributed.
target	[in] Pointer to the target CLSMImage.
target_pixel_ids	[in] Vector of target pixel_ids to which photons will be distributed.
target_probabilities	[in] Vector of probabilities corresponding to each target pixel_id.

◆ fill()

void CLSMImage::fill	(	TTTR *	tttr_data = nullptr,
		std::vector< int >	channels = std::vector< int >(),
		bool	clear = true,
		const std::vector< std::pair< int, int > > &	micro_time_ranges = std::vector< std::pair< int, int > >() )

Fills the time-tagged time-resolved (TTTR) indices of the pixels with the indices of the photons that fall within each pixel.

This function processes the TTTR data to associate routing channels with pixels based on specified criteria. The TTTR indices of the channels within each pixel are stored.

Parameters

tttr_data	Pointer to the TTTR object containing the data to be processed (default is nullptr).
channels	List of routing channels. Events that have routing channels in this vector are added to pixels of corresponding time.
clear	If set to true (default), the pixels are cleared before being filled. If set to false, new TTTR indices are added to the pixels.
micro_time_ranges	List of pairs representing micro-time ranges. If provided, only events within these ranges are considered.

◆ fill_pixels()

void CLSMImage::fill_pixels	(	TTTR *	tttr_data,
		std::vector< int >	channels,
		bool	clear_pixel = true,
		std::vector< std::pair< int, int > >	micro_time_ranges = std::vector<std::pair<int,int>>() )

inline

Fills the time-tagged time-resolved (TTTR) indices of the pixels with the indices of the channels that fall within each pixel.

Deprecated: Use the 'fill' function instead.

This function is deprecated in favor of 'fill'. It processes the TTTR data to associate routing channels with pixels based on specified criteria. The TTTR indices of the channels within each pixel are stored.

Parameters

tttr_data	Pointer to the TTTR object containing the data to be processed.
channels	List of routing channels. Events that have routing channels in this vector are added to pixels of corresponding time.
clear_pixel	If set to true (default), the pixels are cleared before being filled. If set to false, new TTTR indices are added to the pixels.
micro_time_ranges	List of pairs representing micro-time ranges. If provided, only events within these ranges are considered.

◆ get_decay_of_pixels()

void CLSMImage::get_decay_of_pixels	(	TTTR *	tttr_data,
		uint8_t *	mask,
		int	dmask1,
		int	dmask2,
		int	dmask3,
		unsigned int **	output,
		int *	dim1,
		int *	dim2,
		int	tac_coarsening,
		bool	stack_frames )

Computes micro time histograms for the stacks of images and a selection of pixels. Photons in pixels that are selected by the selection array contribute to the returned array of micro time histograms.

This function calculates micro time histograms for selected pixels in the image stack, based on a provided mask. The resulting micro time histograms are stored in the provided output array, and the dimensions of the output array are returned in the output parameters.

Parameters

tttr_data	Pointer to a TTTR object.
mask	A stack of images used as a mask to select pixels.
dmask1	Number of frames in the mask.
dmask2	Number of lines in the mask.
dmask3	Number of pixels per line in the mask.
output	Pointer to the output array of unsigned int that contains the micro time histograms. The array is allocated by the function.
dim1	Dimension of the output array, i.e., the number of stacks.
dim2	Dimension of the output array, i.e., the number of micro time channels.
tac_coarsening	Constant used to coarsen the micro times.
stack_frames	If true, the frames are stacked.

◆ get_fcs_image()

void CLSMImage::get_fcs_image	(	float **	output,
		int *	dim1,
		int *	dim2,
		int *	dim3,
		int *	dim4,
		std::shared_ptr< TTTR >	tttr,
		CLSMImage *	clsm_other = nullptr,
		std::string	correlation_method = "default",
		int	n_bins = 50,
		int	n_casc = 1,
		bool	stack_frames = false,
		bool	normalized_correlation = false,
		int	min_photons = 2 )

Computes an image where pixels represent correlation curves.

This function calculates a correlation image where each pixel corresponds to a correlation curve. The resulting image is determined by the specified parameters and is stored in the provided output array.

Parameters

output	Pointer to the array that will contain the correlation image. The array is allocated by the function.
dim1	Number of correlation curves in the image (frames or time bins).
dim2	Number of lines per frame in the correlation image.
dim3	Number of pixels per line in the correlation image.
dim4	Number of cascades in the correlation image.
tttr	Shared pointer to the TTTR object containing the data.
clsm_other	Pointer to another CLSMImage object (default is nullptr).
correlation_method	Method used for correlation computation (default is "default").
n_bins	Number of bins used for correlation computation (default is 50).
n_casc	Number of cascades in the correlation image (default is 1).
stack_frames	If true, correlation curves are stacked into a single image (default is false).
normalized_correlation	If true, correlation curves are normalized (default is false).
min_photons	Minimum number of photons required for correlation computation (default is 2).

◆ get_fluorescence_decay()

void CLSMImage::get_fluorescence_decay	(	TTTR *	tttr_data,
		unsigned char **	output,
		int *	dim1,
		int *	dim2,
		int *	dim3,
		int *	dim4,
		int	micro_time_coarsening = 1,
		bool	stack_frames = false )

Computes an image stack where the value of each pixel corresponds to a histogram of micro times in each pixel. The micro times can be coarsened by integer numbers.

This function calculates an image stack where each pixel represents a histogram of micro times. The resulting image stack is stored in the provided output array, and the dimensions of the image stack are returned in the output parameters.

Parameters

tttr_data	Pointer to a TTTR object.
output	Pointer to the output array of unsigned chars that will contain the image stack. The array is allocated by the function.
dim1	Number of frames in the image stack.
dim2	Number of lines per frame in the image stack.
dim3	Number of pixels per line in the image stack.
dim4	Number of micro time channels in the histogram.
micro_time_coarsening	Constant used to coarsen the micro times. The default value is 1, and the micro times are binned without coarsening.
stack_frames	If true, the frames are stacked.

◆ get_frame_edges()

static std::vector< int > CLSMImage::get_frame_edges	(	TTTR *	tttr = nullptr,
		int	start_event = 0,
		int	stop_event = -1,
		std::vector< int >	marker_frame_start = std::vector< int >({4, 6}),
		int	marker_event_type = 15,
		int	reading_routine = CLSM_SP8,
		bool	skip_before_first_frame_marker = false,
		bool	skip_after_last_frame_marker = false )

static

Retrieves the time-tagged time-resolved (TTTR) indices of frame markers for a Leica SP8 microscope.

This function analyzes a TTTR object to extract frame marker information. The frame markers are identified by specified parameters, and the corresponding TTTR indices are returned as a vector.

Parameters

tttr	Pointer to the TTTR object that is inspected (default is nullptr).
start_event	Starting event index for analysis (default is 0).
stop_event	Stopping event index for analysis (default is -1, indicating the end of the TTTR data).
marker_frame_start	Vector specifying the frame markers to consider (default is {4, 6}).
marker_event_type	Event type associated with frame markers (default is 15).
reading_routine	Type of reading routine, e.g., CLSM_SP8 (default is CLSM_SP8).
skip_before_first_frame_marker	If true, skip events before the first frame marker (default is false).
skip_after_last_frame_marker	If true, skip events after the last frame marker (default is false).

Returns: Vector of TTTR indices corresponding to frame markers.

◆ get_frames()

std::vector< CLSMFrame * > CLSMImage::get_frames ( )

inline

Retrieves the frames stored in the CLSMImage.

Returns: Vector of CLSMFrame pointers representing the frames in the CLSMImage.

◆ get_intensity()

void CLSMImage::get_intensity	(	unsigned short **	output,
		int *	dim1,
		int *	dim2,
		int *	dim3 )

Computes an intensity image.

This function calculates an intensity image and stores it in the provided output array. The dimensions of the intensity image are returned in the output parameters.

Parameters

output	Pointer to the array that will contain the intensity image. The array is allocated by the function.
dim1	Number of frames in the intensity image.
dim2	Number of lines per frame in the intensity image.
dim3	Number of pixels per line in the intensity image.

◆ get_line_duration()

double CLSMImage::get_line_duration	(	int	frame = 0,
		int	line = 0 )

inline

Obtains the duration of a line (in milliseconds) for a specified frame and line.

This function calculates the duration of a line in milliseconds for a given frame and line based on the time-tagged time-resolved (TTTR) data and header information.

Parameters

frame	Number of the frame in the image (default is 0).
line	Number of the line in the image (default is 0).

Returns: Duration of the line in the selected frame in milliseconds. Returns -1.0 if the TTTR object is not initialized or if frame and line indices are out of bounds.

◆ get_line_edges()

static std::vector< int > CLSMImage::get_line_edges	(	TTTR *	tttr,
		int	start_event,
		int	stop_event,
		int	marker_line_start = 1,
		int	marker_line_stop = 2,
		int	marker_event_type = 15,
		int	reading_routine = CLSM_SP8 )

static

Identifies line edges by reading start and stop markers in a time-tagged time-resolved (TTTR) dataset.

This function analyzes a TTTR object to extract line edges based on specified start and stop markers. The corresponding TTTR indices are returned as a vector.

Parameters

tttr	Pointer to the TTTR object that is inspected.
start_event	Starting event index for analysis.
stop_event	Stopping event index for analysis.
marker_line_start	Marker value indicating the start of a line (default is 1).
marker_line_stop	Marker value indicating the stop of a line (default is 2).
marker_event_type	Event type associated with line markers (default is 15).
reading_routine	Type of reading routine, e.g., CLSM_SP8 (default is CLSM_SP8).

Returns: Vector of TTTR indices corresponding to line edges.

◆ get_line_edges_by_duration()

static std::vector< int > CLSMImage::get_line_edges_by_duration	(	TTTR *	tttr,
		int	start_event,
		int	stop_event,
		int	marker_line_start = 1,
		int	line_duration = 2,
		int	marker_event_type = 15,
		int	reading_routine = CLSM_SP8 )

static

Identifies line edges by reading a start marker and using line duration as the stop criterion in a time-tagged time-resolved (TTTR) dataset.

This function analyzes a TTTR object to extract line edges based on a specified start marker and line duration. The corresponding TTTR indices are returned as a vector.

Parameters

tttr	Pointer to the TTTR object that is inspected.
start_event	Starting event index for analysis.
stop_event	Stopping event index for analysis.
marker_line_start	Marker value indicating the start of a line (default is 1).
line_duration	Duration of a line, used as the stop criterion (default is 2).
marker_event_type	Event type associated with line markers (default is 15).
reading_routine	Type of reading routine, e.g., CLSM_SP8 (default is CLSM_SP8).

Returns: Vector of TTTR indices corresponding to line edges.

◆ get_mean_lifetime()

void CLSMImage::get_mean_lifetime	(	TTTR *	tttr_data,
		double **	output,
		int *	dim1,
		int *	dim2,
		int *	dim3,
		int	minimum_number_of_photons = 3,
		TTTR *	tttr_irf = nullptr,
		double	m0_irf = 1.0,
		double	m1_irf = 1.0,
		bool	stack_frames = false,
		std::vector< double >	background = std::vector< double >(),
		double	m0_bg = 0.0,
		double	m1_bg = 0.0,
		double	background_fraction = -1.0 )

Computes an image of average lifetimes.

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

Pixels with few photons can be discriminated. Discriminated pixels are filled with zeros.

By default, the fluorescence lifetimes of the pixels are computed in units of nanoseconds.

Parameters

tttr_data	Pointer to a TTTR object.
output	Pointer to the output array that will contain the image stack. The array is allocated by the function.
dim1	Returns the number of frames.
dim2	Returns the number of lines.
dim3	Returns the number of pixels per line.
minimum_number_of_photons	The minimum number of photons in a micro time (default is 3).
tttr_irf	Pointer to a TTTR object of the Instrument Response Function (IRF) (default is nullptr).
m0_irf	The zero moment of the IRF (optional, default is 1.0).
m1_irf	The first moment of the IRF (optional, default is 1.0).
stack_frames	If true, the frames are stacked (default is false).
background	Vector of background values (optional, default is an empty vector).
m0_bg	The zero moment of the background (optional, default is 0.0).
m1_bg	The first moment of the background (optional, default is 0.0).
background_fraction	Background fraction used for discrimination (default is -1.0, which disables discrimination).

◆ get_mean_micro_time()

void CLSMImage::get_mean_micro_time	(	TTTR *	tttr_data,
		double **	output,
		int *	dim1,
		int *	dim2,
		int *	dim3,
		double	microtime_resolution = -1.0,
		int	minimum_number_of_photons = 2,
		bool	stack_frames = false )

Calculates an image stack where the value of each pixel corresponds to the mean micro time (in units of the micro channel resolution).

Pixels with few photons can be discriminated. Discriminated pixels will be filled with zeros.

Parameters

tttr_data	Pointer to a TTTR object.
output	Pointer to the output array that will contain the image stack. The array is allocated by the function.
dim1	Returns the number of frames.
dim2	Returns the number of lines.
dim3	Returns the number of pixels per line.
microtime_resolution	Micro channel resolution (default is -1.0, which means it will be obtained from the TTTR object).
minimum_number_of_photons	The minimum number of photons in a micro time (default is 2).
stack_frames	If true, the frames are stacked (default is false). If stack frames is set to true, the mean arrival time is computed using the TTTR indices of all pixels (corresponding to the photon-weighted mean arrival time).

◆ get_n_frames()

int CLSMImage::get_n_frames ( ) const

inline

Get the number of frames in the CLSM image.

This member function returns the number of frames in the CLSM image.

Returns: The number of frames in the CLSM image.

◆ get_n_lines()

int CLSMImage::get_n_lines ( ) const

inline

Get the number of lines per frame in the CLSMImage.

This member function returns the number of lines per frame in the CLSMImage.

Returns: The number of lines per frame in the CLSMImage.

◆ get_n_pixel()

int CLSMImage::get_n_pixel ( ) const

inline

Get the number of pixels per line in a frame of the CLSMImage.

This member function returns the number of pixels per line in a frame of the CLSMImage.

Returns: The number of pixels per line in a frame of the CLSMImage.

◆ get_phasor()

void CLSMImage::get_phasor	(	float **	output,
		int *	dim1,
		int *	dim2,
		int *	dim3,
		int *	dim4,
		TTTR *	tttr_data,
		TTTR *	tttr_irf = nullptr,
		double	frequency = -1,
		int	minimum_number_of_photons = 2,
		bool	stack_frames = false )

Computes the phasor values for every pixel.

Pixels with few photons can be discriminated. Discriminated pixels will be filled with zeros.

Parameters

output	Pointer to the output array that will contain the image stack. The array is allocated by the function.
dim1	Returns the number of frames.
dim2	Returns the number of lines.
dim3	Returns the number of pixels per line.
dim4	Returns 2 (first is the g phasor value (cos), second the s phasor (sin)).
tttr_data	Pointer to a TTTR object.
tttr_irf	Pointer to a TTTR object representing the Instrument Response Function (IRF) (default is nullptr).
frequency	Modulation frequency for phasor computation (default is -1, which means it will be obtained from the TTTR object).
minimum_number_of_photons	The minimum number of photons in a micro time (only used if frames are not stacked, default is 2).
stack_frames	If true, the frames are stacked (default is false). If stack frames is set to true, the mean arrival time is computed using the TTTR indices of all pixels (corresponding to the photon-weighted mean arrival time).

◆ get_pixel_duration()

double CLSMImage::get_pixel_duration	(	int	frame = 0,
		int	line = 0 )

inline

Obtains the duration of a pixel (in milliseconds) for a specified frame and line.

This function calculates the duration of a pixel in milliseconds for a given frame and line, based on the time-tagged time-resolved (TTTR) data, header information, and the number of pixels per line.

Parameters

frame	Selected frame number (default is 0).
line	Selected line number (default is 0).

Returns: Duration of the pixel in the selected frame in milliseconds. Returns -1.0 if the TTTR object is not initialized, or if frame and line indices are out of bounds.

◆ get_roi()

static void CLSMImage::get_roi	(	double **	output,
		int *	dim1,
		int *	dim2,
		int *	dim3,
		CLSMImage *	clsm = nullptr,
		std::vector< int >	x_range = std::vector< int >({0,-1}),
		std::vector< int >	y_range = std::vector< int >({0,-1}),
		std::string	subtract_average = "",
		double	background = 0.0,
		bool	clip = false,
		double	clip_max = 1e6,
		double	clip_min = -1e6,
		double *	images = nullptr,
		int	n_frames = -1,
		int	n_lines = -1,
		int	n_pixels = 1,
		uint8_t *	mask = nullptr,
		int	dmask1 = -1,
		int	dmask2 = -1,
		int	dmask3 = -1,
		std::vector< int >	selected_frames = std::vector< int >() )

static

Copies a region of interest (ROI) from the input images, performs background correction, and stores the result in a new array.

The ROI is defined by specifying ranges for pixels and lines. The function supports various correction options, such as subtracting a constant background value, clipping output values, and correcting by the mean intensity of frames.

Parameters

output	Pointer to the array that will contain the ROI. The array is allocated by the function.
dim1	Number of frames in the output ROI.
dim2	Number of lines per frame in the output ROI.
dim3	Number of pixels per line in the output ROI.
clsm	Pointer to a CLSMImage object (default is nullptr).
x_range	Range (selection) of pixels for the ROI.
y_range	Range (selection) of lines for the ROI.
subtract_average	If set to "stack," the mean image of the ROIs computed by averaging over all frames is subtracted from each frame, and the mean intensity of all frames and pixels is added to the pixels. If set to "frame," the average of each frame is subtracted from that frame. Default is no correction.
background	Constant number subtracted from each pixel.
clip	If true, values in the ROI are clipped to the range [clip_min, clip_max] (default is false).
clip_max	Maximum value when output ROIs are clipped.
clip_min	Minimum value when output ROIs are clipped.
images	Input array of images used to define ROIs (default is nullptr).
n_frames	Number of frames in the input array images.
n_lines	Number of lines in the input array images.
n_pixels	Number of pixels per line in the input array images.
mask	Stack of images used to select pixels (default is nullptr).
dmask1	Number of frames; if smaller than ROI, the first mask frame is applied to all ROI frames greater than dmask1.
dmask2	Number of lines; if smaller than ROI, the outside region is selected, and the mask is applied to all lines smaller than dmask2.
dmask3	Number of pixels per line in the mask.
selected_frames	List of frames used to define the ROIs. If empty, all frames in the input are used.

◆ get_settings()

const CLSMSettings * CLSMImage::get_settings ( )

inline

◆ get_tttr()

std::shared_ptr< TTTR > CLSMImage::get_tttr ( )

inline

◆ getPixel()

CLSMPixel * CLSMImage::getPixel ( unsigned int idx )

inline

Get a pointer to a CLSMPixel object based on a one-dimensional index.

This member function calculates the three-dimensional coordinates (frame, line, pixel) corresponding to a given one-dimensional index and returns a pointer to the corresponding CLSMPixel object.

Parameters

idx	One-dimensional index to determine the CLSMPixel.

Returns: Pointer to the CLSMPixel object.

◆ operator[]()

CLSMFrame * CLSMImage::operator[] ( unsigned int i_frame )

inline

Accessor for CLSMFrame at the specified index in CLSMImage.

Returns a pointer to the CLSMFrame located at the given index in the frames vector.

Parameters

i_frame [in] Index of the desired CLSMFrame.

Returns: Pointer to the CLSMFrame at the specified index.

◆ rebin()

void CLSMImage::rebin	(	int	bin_line,
		int	bin_pixel )

Rebin a CLSMImage.

Rebinning redistributes photons and macro times in pixels.

Note: Rebinning may alter the distribution of photons and macro times in the image.

Parameters

bin_line	[in] Binning factor for lines.
bin_pixel	[in] Binning factor for pixels within lines.

◆ set_tttr()

void CLSMImage::set_tttr ( std::shared_ptr< TTTR > v )

inline

◆ size()

size_t CLSMImage::size ( )

inline

Get the number of frames in the CLSMImage.

◆ stack_frames()

void CLSMImage::stack_frames ( )

inline

Stack frames in the CLSMImage.

This function stacks the frames in the CLSMImage by summing the pixel values of each corresponding pixel in all frames.

◆ strip()

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

Strips time-tagged time-resolved (TTTR) indices from all pixels in the image.

This function removes specified TTTR indices from all pixels in the image. It assumes that each TTTR index is present only once in the image.

Parameters

tttr_indices	List of TTTR indices to be removed from the pixels.
offset	Offset value added to the TTTR indices before removal (default is 0).

◆ to1D()

int CLSMImage::to1D	(	int	frame,
		int	line,
		int	pixel )

inline

Convert three-dimensional coordinates (frame, line, pixel) to a one-dimensional index.

This inline function calculates a unique one-dimensional index for a given set of three-dimensional coordinates representing a position in an array.

Parameters

frame	Index of the frame.
line	Index of the line within the frame.
pixel	Index of the pixel within the line.

Returns: One-dimensional index corresponding to the input coordinates.

◆ to3D()

std::vector< int > CLSMImage::to3D ( int idx )

inline

Convert a one-dimensional index to three-dimensional coordinates (frame, line, pixel).

This inline function calculates the three-dimensional coordinates (frame, line, pixel) corresponding to a given one-dimensional index in an array.

Parameters

idx	One-dimensional index to be converted.

Returns: Vector containing frame, line, and pixel indices in that order.

◆ transform()

void CLSMImage::transform	(	unsigned int *	input,
		int	n_input )

Move the content of the Pixels based on source and target pixel indices.

The input is an interleaved array of source and target pixel indices. A pixel index is a mapping from frames, lines, and pixel combination to an index.

Parameters

input	[in] Pointer to an interleaved array containing source and target pixel indices.
n_input	[in] Number of elements in the input array.

Friends And Related Symbol Documentation

◆ CLSMFrame

friend class CLSMFrame

friend

◆ CLSMLine

friend class CLSMLine

friend

◆ CLSMPixel

friend class CLSMPixel

friend

◆ Correlator

friend class Correlator

friend

Member Data Documentation

◆ marker_event

int CLSMImage::marker_event

The event type used for the marker.

◆ marker_frame

std::vector<int> CLSMImage::marker_frame

Vector containing the tttr indices of the frame markers.

◆ marker_line_start

int CLSMImage::marker_line_start

Defines the marker for a line start.

◆ marker_line_stop

int CLSMImage::marker_line_stop

Defines the marker for a line stop.

◆ n_frames

size_t CLSMImage::n_frames = 0

protected

The number of frames in an CLSMImage.

◆ n_lines

size_t CLSMImage::n_lines = 0

protected

The number of lines per frames.

◆ n_pixel

size_t CLSMImage::n_pixel = 0

protected

The number if pixels per line.

◆ reading_routine

std::string CLSMImage::reading_routine = "default"

◆ skip_after_last_frame_marker

bool CLSMImage::skip_after_last_frame_marker = false

◆ skip_before_first_frame_marker

bool CLSMImage::skip_before_first_frame_marker = false

CLSM TTTR data starts can have incomplete frame. Thus skipping data can make sense

◆ tttr

std::shared_ptr<TTTR> CLSMImage::tttr = nullptr

protected

Pointer to tttr data that used to construct the Image.

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

/builds/skf/tttrlib/include/CLSMImage.h

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Friends

Constructor & Destructor Documentation

◆ CLSMImage() [1/2]

◆ CLSMImage() [2/2]

◆ ~CLSMImage()

Member Function Documentation

◆ append()

◆ clear()

◆ clear_pixels()

◆ compute_ics()

◆ copy()

◆ create_frames()

◆ create_lines()

◆ crop()

◆ determine_number_of_lines()

◆ distribute()

◆ fill()

◆ fill_pixels()

◆ get_decay_of_pixels()

◆ get_fcs_image()

◆ get_fluorescence_decay()

◆ get_frame_edges()

◆ get_frames()

◆ get_intensity()

◆ get_line_duration()

◆ get_line_edges()

◆ get_line_edges_by_duration()

◆ get_mean_lifetime()

◆ get_mean_micro_time()

◆ get_n_frames()

◆ get_n_lines()

◆ get_n_pixel()

◆ get_phasor()

◆ get_pixel_duration()

◆ get_roi()

◆ get_settings()

◆ get_tttr()

◆ getPixel()

◆ operator[]()

◆ rebin()

◆ set_tttr()

◆ size()

◆ stack_frames()

◆ strip()

◆ to1D()

◆ to3D()

◆ transform()

Friends And Related Symbol Documentation

◆ CLSMFrame

◆ CLSMLine

◆ CLSMPixel

◆ Correlator

Member Data Documentation

◆ marker_event

◆ marker_frame

◆ marker_line_start

◆ marker_line_stop

◆ n_frames

◆ n_lines

◆ n_pixel

◆ reading_routine

◆ skip_after_last_frame_marker

◆ skip_before_first_frame_marker

◆ tttr