tracking::Track_box Class Reference

Box class for dealing with tracks. More...

#include <track_box.h>

Collaboration diagram for tracking::Track_box:

Public Member Functions
const particle_track *	at (int n) const
	retruns the nth particle of the track. More...
particle_track *	get_first () const
	Returns a pointer to the first particle in the track. More...
particle_track *	get_last () const
	Returns a pointer to the last particle in the track. More...
void	extract_raw_pos (std::vector< float > &output, std::vector< unsigned int > &dims) const
	Extracts the raw posistion along the track. More...
void	extract_corrected_pos (std::vector< float > &output, std::vector< unsigned int > &dims) const
	gets the posistion corrected for drift More...
void	extract_raw_disp (std::vector< float > &output, std::vector< unsigned int > &dims) const
	Extracts the raw frame to frame displanement along the track. More...
void	extract_corrected_disp (std::vector< float > &output, std::vector< unsigned int > &dims) const
	gets the displacement corrected for drift More...
	Track_box (particle_track *first)
	Constructor. More...
	Track_box ()
virtual void	print ()
	Prints outs some representation of the track. More...
void	push_back (particle_track *next)
	adds the particle next the end of the track More...
unsigned int	get_id () const
	Return the track id. More...
virtual	~Track_box ()
	Destructor. More...
int	get_length () const
	Returns the length of the track. More...
void	output_to_wrapper (utilities::Wrapper_out &wrapper) const
	Outputs the particles in a track-centric format. More...
void	split_to_parts (Track_shelf &shelf)
	splits the track into segments that correspond to a single particle sliced in z. More...
void	average_cord (utilities::Tuple< float, 3 > &pos, float &I) const
	returns the intensity weighted average position used for link3D. More...
void	set_track_id (unsigned int in)
	Sets the track_id. More...

Protected Member Functions
particle_track *	at (int n)
	non-const version of at() More...
Track_box *	split_track (int indx)
	Splits the track at the given index and returns a pointer to the back half of the track. More...
void	trim_track (int ind_start, int length)
	Trims the track from the ind_start and keeps the next length particles. More...

Protected Attributes
particle_track *	t_first_
	Pointer to first particle in track. More...
particle_track *	t_last_
int	length_
	length of path More...
unsigned int	id_
	unique ID of the track More...

Static Protected Attributes
static int	running_count_ = 0
	the number of tracks identified used for unique id's More...

Detailed Description

Box class for dealing with tracks.

Essentially roling my own linked list class.

Constructor & Destructor Documentation

Track_box::Track_box

(

particle_track *

first)

Constructor.

References id_, length_, tracking::particle_track::reset_track(), running_count_, t_first_, and t_last_.

Track_box::Track_box

(

)

Referenced by split_track().

Track_box::~Track_box ( )

virtual

Destructor.

References tracking::particle_track::get_next(), and t_first_.

Member Function Documentation

const particle_track * Track_box::at

(

int

n)

const

retruns the nth particle of the track.

returns null if n > length

References length_, tracking::particle_track::step_backwards(), tracking::particle_track::step_forwards(), t_first_, and t_last_.

Referenced by split_track(), and trim_track().

particle_track * Track_box::at ( int  n)

protected

non-const version of at()

References length_, tracking::particle_track::step_backwards(), tracking::particle_track::step_forwards(), t_first_, and t_last_.

void Track_box::average_cord	(	utilities::Tuple< float, 3 > &	pos,
		float &	I
	)		const

returns the intensity weighted average position used for link3D.

This really should be sub-classed

References utilities::D_I, utilities::D_ZPOS, tracking::particle_track::get_value(), tracking::particle_track::next_, and t_first_.

Referenced by utilities::Wrapper_o_hdf::set_all_values().

void Track_box::extract_corrected_disp	(	std::vector< float > &	output,
		std::vector< unsigned int > &	dims
	)		const

gets the displacement corrected for drift

References tracking::particle_track::get_corrected_disp(), tracking::particle_track::get_next(), length_, and t_first_.

void Track_box::extract_corrected_pos	(	std::vector< float > &	output,
		std::vector< unsigned int > &	dims
	)		const

gets the posistion corrected for drift

References tracking::particle_track::get_corrected_pos(), tracking::particle_track::get_next(), length_, and t_first_.

void Track_box::extract_raw_disp	(	std::vector< float > &	output,
		std::vector< unsigned int > &	dims
	)		const

Extracts the raw frame to frame displanement along the track.

References tracking::particle_base::get_disp(), tracking::particle_track::get_next(), length_, and t_first_.

void Track_box::extract_raw_pos	(	std::vector< float > &	output,
		std::vector< unsigned int > &	dims
	)		const

Extracts the raw posistion along the track.

References tracking::particle_track::get_next(), tracking::particle_base::get_position(), length_, and t_first_.

particle_track* tracking::Track_box::get_first ( ) const

inline

Returns a pointer to the first particle in the track.

References t_first_.

Referenced by tracking::Track_shelf::output_to_wrapper().

unsigned int tracking::Track_box::get_id ( ) const

inline

Return the track id.

References id_.

Referenced by tracking::particle_track::get_track_id(), tracking::particle_track::get_value(), and tracking::Track_shelf::output_to_wrapper().

particle_track* tracking::Track_box::get_last ( ) const

inline

Returns a pointer to the last particle in the track.

References t_last_.

int tracking::Track_box::get_length ( ) const

inline

Returns the length of the track.

References length_.

Referenced by tracking::Track_shelf::output_to_wrapper().

void Track_box::output_to_wrapper

(

utilities::Wrapper_out &

wrapper)

const

Outputs the particles in a track-centric format.

References utilities::Wrapper_out::add_meta_data(), utilities::Wrapper_out::close_group(), tracking::particle_base::get_frame(), tracking::particle_track::get_next(), id_, length_, utilities::Wrapper_out::open_group(), utilities::Wrapper_out::set_all_values(), and t_first_.

void Track_box::print ( )

virtual

Prints outs some representation of the track.

References id_, length_, tracking::particle_track::print_t(), and t_first_.

Referenced by main().

void Track_box::push_back

(

particle_track *

next)

adds the particle next the end of the track

References length_, tracking::particle_track::reset_track(), tracking::particle_track::set_next(), tracking::particle_track::set_prev(), t_first_, and t_last_.

Referenced by tracking::hash_case::init(), tracking::Track_shelf::init(), and main().

void tracking::Track_box::set_track_id ( unsigned int  in)

inline

Sets the track_id.

References id_.

void Track_box::split_to_parts

(

Track_shelf &

shelf)

splits the track into segments that correspond to a single particle sliced in z.

The resulting new tracks are stored in the self

References tracking::Track_shelf::add_track(), utilities::D_I, tracking::particle_track::get_next(), tracking::particle_track::get_value(), length_, split_track(), t_first_, and trim_track().

Referenced by main().

Track_box * Track_box::split_track ( int  indx)

protected

Splits the track at the given index and returns a pointer to the back half of the track.

References at(), tracking::particle_track::clear_next(), tracking::particle_track::clear_prev(), tracking::particle_track::get_prev(), length_, t_first_, t_last_, and Track_box().

Referenced by split_to_parts().

void Track_box::trim_track ( int  ind_start, int  length  )

protected

Trims the track from the ind_start and keeps the next length particles.

Parameters

ind_start	first particle to keep
length	number of particles to keep

References at(), tracking::particle_track::clear_data_backward(), tracking::particle_track::clear_data_forward(), length_, tracking::particle_track::step_forwards(), t_first_, and t_last_.

Referenced by split_to_parts().

Member Data Documentation

unsigned int tracking::Track_box::id_

protected

unique ID of the track

Referenced by get_id(), output_to_wrapper(), print(), set_track_id(), and Track_box().

int tracking::Track_box::length_

protected

length of path

Referenced by at(), extract_corrected_disp(), extract_corrected_pos(), extract_raw_disp(), extract_raw_pos(), get_length(), output_to_wrapper(), print(), push_back(), split_to_parts(), split_track(), Track_box(), and trim_track().

int Track_box::running_count_ = 0

staticprotected

the number of tracks identified used for unique id's

Referenced by Track_box().

particle_track* tracking::Track_box::t_first_

protected

Pointer to first particle in track.

Referenced by at(), average_cord(), extract_corrected_disp(), extract_corrected_pos(), extract_raw_disp(), extract_raw_pos(), get_first(), output_to_wrapper(), print(), push_back(), split_to_parts(), split_track(), Track_box(), trim_track(), and ~Track_box().

particle_track* tracking::Track_box::t_last_

protected

Referenced by at(), get_last(), push_back(), split_track(), Track_box(), and trim_track().

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

• common_src/include/track_box.h
• common_src/cxx/function_cascades.cpp
• common_src/cxx/track_box.cpp