Top level class for holding the track boxes. More...

#include <track_shelf.h>

Collaboration diagram for tracking::Track_shelf:

Public Member Functions
void	add_new_track (particle_track *first_part)
	Add a track to the shelf starting from a particle. More...

void	add_track (Track_box *track)
	adds a pointer to a track_box to the shelf. More...

void	remove_short_tracks (int min_length)
	Removes all tracks from the shelf that are shorter than n. More...

void	print ()
	Print Track_shelf to stdout. More...

void	set_shelf ()
	Sets all of the particles in shelf to their respective wrappers. More...

void	track_length_histogram (utilities::Histogram &in)
	Generates a histogram of the lengths of all the tracks in the Track_shelf. More...

void	msd (std::vector< double > &msd_vec, std::vector< int > &entry_count) const
	Generates the MSD plot for all the tarcks in this shelf. More...

void	msd_corrected (utilities::Counted_vector &msd) const
	Generates the corrected MSD plot for all the tarcks in this shelf. More...

void	msd_corrected (utilities::Counted_vector &md, utilities::Counted_vector &msd, utilities::Counted_vector &msd_sq) const
	Generates the corrected MSD, mean displacement and <\|d\|^4> plot for all the tarcks in this shelf. More...

void	disp_sq_hist (int time_step, utilities::Histogram &disp_sq_hist) const
	generates a histogram of the squared displacement of the specified time step More...

void	set_raw_disp_to_cell (utilities::Cell &output) const
	sets the tracks into the cell that is passed in More...

void	set_corrected_disp_to_cell (utilities::Cell &output) const
	sets the corrected tracks into the cell that is passed in More...

unsigned int	get_track_count () const
	returns the number of tracks in shelf More...

void	pass_fun_to_track (void(Track_box::*fun)() const) const
	Pass a function to all of the Track_box objects contained. More...

void	output_to_wrapper (utilities::Wrapper_out &wrapper) const
	Outputs the particles in a track-centric format. More...

void	output_to_wrapper (utilities::Generic_wrapper &wrapper, const utilities::Md_store *md_store) const
	This function assumes that the tracks have been renumbered, such that the pigeon hole principle applies. More...

void	output_link_to_wrapper (utilities::Wrapper_out &wrapper, const utilities::Tuple< float, 3 > &scale_t, const utilities::Tuple< float, 3 > &dim) const
	outputs the contents of the shelf treating each track as a single particle. More...

void	split_to_parts (Track_shelf &out_put_shelf)
	Splits all the tracks in the self in to sections that represent single particles when the tracking is linking between z-planes. More...

void	renumber ()
	Renumbers the tracks sequentially. More...

void	init (Master_box &mb)
	Initializes the tracks in the track shelf based on read in trakid. More...

void	init (hash_case &hc)
	Initializes the tracks in the track shelf based on read in trakid. More...

void	compute_corrected_TA (Trk_accumulator &ta) const
	Shove data in to a track accumulator. More...

void	compute_corrected_TA_ncuts (Trk_accumulator &ta, int min_neighbors, int max_neighbors) const
	Shove data in to a track accumulator, makes cuts based on the number of neighbors a particles has. More...

Track_box *	get_track (unsigned int track_id) const
	Returns a pointer to track with id track_id. More...

	Track_shelf ()
	Constructor. More...

	~Track_shelf ()
	Destructor. Destroys all of the tracks contained in the shelf. More...

Protected Member Functions
void	remove_track_internal_ (std::list< Track_box * >::iterator it)
	internal private function to do track removal to make maintianign code simpler More...

Protected Attributes
std::list< Track_box * >	tracks_
	list to keep track of all the created tracks. More...

unsigned int	track_count_
	number of tracks in the self More...

Detailed Description

Top level class for holding the track boxes.

(which are the head of the linked lists made of particle_track objects).

Constructor & Destructor Documentation

tracking::Track_shelf::Track_shelf ( )

inline

Constructor.

Track_shelf::~Track_shelf ( )

Destructor. Destroys all of the tracks contained in the shelf.

References tracks_.

Member Function Documentation

void Track_shelf::add_new_track ( particle_track * first_part)

Add a track to the shelf starting from a particle.

Parameters

first_part The first particle in the track

References track_count_, and tracks_.

Referenced by tracking::hash_case::link(), tracking::track_list::link_pairs(), and tracking::track_list::trivial_bonds().

void Track_shelf::add_track ( Track_box * track)

adds a pointer to a track_box to the shelf.

The shelf takes responsibility for deleting the track when done.

References track_count_, and tracks_.

Referenced by tracking::hash_case::init(), init(), and tracking::Track_box::split_to_parts().

void Track_shelf::compute_corrected_TA ( Trk_accumulator & ta) const

Shove data in to a track accumulator.

References tracking::Trk_accumulator::add_disp(), tracking::particle_track::get_corrected_disp(), tracking::Trk_accumulator::max_step(), tracking::particle_track::step_forwards(), and tracks_.

Referenced by main().

void Track_shelf::compute_corrected_TA_ncuts	(	Trk_accumulator &	ta,
		int	min_neighbors,
		int	max_neighbors
	)		const

Shove data in to a track accumulator, makes cuts based on the number of neighbors a particles has.

References tracking::Trk_accumulator::add_disp(), tracking::particle_track::get_corrected_disp(), tracking::particle_base::get_neighborhood_size(), tracking::Trk_accumulator::max_step(), tracking::particle_track::step_forwards(), and tracks_.

Referenced by main().

void Track_shelf::disp_sq_hist	(	int	time_step,
		utilities::Histogram &	disp_sq_hist
	)		const

generates a histogram of the squared displacement of the specified time step

Parameters

time_step	integer greater than zero less than maximum track length
disp_sq_hist	histogram to be filled. Is not cleared.

Deprecated:: This computation should be done with a Trk_accumulator

References utilities::Histogram::add_data_point(), tracking::particle_track::distancesq_corrected(), tracking::particle_track::step_forwards(), and tracks_.

Referenced by main().

Track_box * Track_shelf::get_track ( unsigned int track_id) const

Returns a pointer to track with id track_id.

raises runtime_error of track not found

Parameters

[in] track_id the id of the track to return

References tracks_.

unsigned int tracking::Track_shelf::get_track_count ( ) const

inline

returns the number of tracks in shelf

References track_count_.

Referenced by main().

void Track_shelf::init ( Master_box & mb)

Initializes the tracks in the track shelf based on read in trakid.

References add_track(), utilities::D_TRACKID, tracking::Master_box::get_particle(), tracking::particle_base::get_wrapper_value(), tracking::Track_box::push_back(), tracking::Master_box::size(), track_count_, and tracks_.

Referenced by main().

void Track_shelf::init ( hash_case & hc)

Initializes the tracks in the track shelf based on read in trakid.

References add_track(), utilities::D_TRACKID, tracking::hash_case::get_num_frames(), tracking::particle_base::get_wrapper_value(), tracking::Track_box::push_back(), tracking::hash_case::return_shelf(), tracking::Hash_shelf::shelf_to_list(), track_count_, and tracks_.

void Track_shelf::msd	(	std::vector< double > &	msd_vec,
		std::vector< int > &	entry_count
	)		const

Generates the MSD plot for all the tarcks in this shelf.

Deprecated:: This computation should be done with a Trk_accumulator

References tracking::particle_base::distancesq(), tracking::particle_track::step_forwards(), and tracks_.

void Track_shelf::msd_corrected ( utilities::Counted_vector & msd) const

Generates the corrected MSD plot for all the tarcks in this shelf.

Deprecated:: This computation should be done with a Trk_accumulator

References utilities::Counted_vector::batch_add_to_element(), tracking::particle_track::distancesq_corrected(), utilities::Counted_vector::get_length(), tracking::particle_track::step_forwards(), and tracks_.

void Track_shelf::msd_corrected	(	utilities::Counted_vector &	md,
		utilities::Counted_vector &	msd,
		utilities::Counted_vector &	msd_sq
	)		const

Generates the corrected MSD, mean displacement and <|d|^4> plot for all the tarcks in this shelf.

Deprecated:: This computation should be done with a Trk_accumulator

References utilities::Counted_vector::batch_add_to_element(), tracking::particle_track::distancesq_corrected(), utilities::Counted_vector::get_length(), tracking::particle_track::step_forwards(), and tracks_.

void Track_shelf::output_link_to_wrapper	(	utilities::Wrapper_out &	wrapper,
		const utilities::Tuple< float, 3 > &	scale_t,
		const utilities::Tuple< float, 3 > &	dim
	)		const

outputs the contents of the shelf treating each track as a single particle.

for use with 3D linking. This should be sub-classed

References utilities::Wrapper_out::add_meta_data_root(), utilities::Wrapper_out::close_group(), utilities::Wrapper_out::open_group(), utilities::Wrapper_out::set_all_values(), track_count_, and tracks_.

Referenced by main().

void Track_shelf::output_to_wrapper ( utilities::Wrapper_out & wrapper) const

Outputs the particles in a track-centric format.

Assumes that the wrapper is already initialized.

Parameters

wrapper output wrapper, already initialized

References tracks_.

Referenced by main().

void Track_shelf::output_to_wrapper	(	utilities::Generic_wrapper &	wrapper,
		const utilities::Md_store *	md_store
	)		const

This function assumes that the tracks have been renumbered, such that the pigeon hole principle applies.

If not, it will throw an error. It also assumes that the tracks are in order in the shelf.

Parameters

wrapper	where to dump the data to.
md_store	meta data store object

References utilities::Generic_wrapper::add_dset(), utilities::Generic_wrapper::add_meta_data(), utilities::Generic_wrapper::close_group(), utilities::Generic_wrapper::close_wrapper(), utilities::format_name(), tracking::Track_box::get_first(), tracking::particle_base::get_frame(), tracking::Track_box::get_id(), tracking::particle_base::get_ind(), tracking::Track_box::get_length(), utilities::Md_store::get_value(), utilities::Generic_wrapper::is_open(), utilities::Generic_wrapper::open_group(), utilities::Generic_wrapper::open_wrapper(), track_count_, tracks_, and utilities::V_UINT.

void Track_shelf::pass_fun_to_track ( void(Track_box::*)() const fun) const

Pass a function to all of the Track_box objects contained.

References tracks_.

void Track_shelf::print ( )

Print Track_shelf to stdout.

References tracks_.

Referenced by main().

void Track_shelf::remove_short_tracks ( int min_length)

Removes all tracks from the shelf that are shorter than n.

This does not clear the link information in the particle_track objects.

Parameters

min_length the minimum length of tracks left in the shelf after

References remove_track_internal_(), and tracks_.

Referenced by main().

void Track_shelf::remove_track_internal_ ( std::list< Track_box * >::iterator it)

protected

internal private function to do track removal to make maintianign code simpler

References track_count_, and tracks_.

Referenced by remove_short_tracks().

void Track_shelf::renumber ( )

Renumbers the tracks sequentially.

Track id numbers are only used when outputting the tracks.

References tracks_.

Referenced by main().

void tracking::Track_shelf::set_corrected_disp_to_cell ( utilities::Cell & output) const

sets the corrected tracks into the cell that is passed in

void tracking::Track_shelf::set_raw_disp_to_cell ( utilities::Cell & output) const

sets the tracks into the cell that is passed in

void tracking::Track_shelf::set_shelf ( )

Sets all of the particles in shelf to their respective wrappers.

void Track_shelf::split_to_parts ( Track_shelf & out_put_shelf)

Splits all the tracks in the self in to sections that represent single particles when the tracking is linking between z-planes.

References tracks_.

Referenced by main().

void Track_shelf::track_length_histogram ( utilities::Histogram & in)

Generates a histogram of the lengths of all the tracks in the Track_shelf.

References utilities::Histogram::add_data_point(), and tracks_.

Referenced by main().

Member Data Documentation

unsigned int tracking::Track_shelf::track_count_

protected

number of tracks in the self

Referenced by add_new_track(), add_track(), get_track_count(), init(), output_link_to_wrapper(), output_to_wrapper(), and remove_track_internal_().

std::list<Track_box*> tracking::Track_shelf::tracks_

protected

list to keep track of all the created tracks.

The shelf is responsible for cleaning up the tracks at the end. A list is used so that addition/removal is fast. Random access isn't important. Tracks can now be renumbered.

Referenced by add_new_track(), add_track(), compute_corrected_TA(), compute_corrected_TA_ncuts(), disp_sq_hist(), get_track(), init(), msd(), msd_corrected(), output_link_to_wrapper(), output_to_wrapper(), pass_fun_to_track(), print(), remove_short_tracks(), remove_track_internal_(), renumber(), split_to_parts(), track_length_histogram(), and ~Track_shelf().

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

common_src/include/track_shelf.h
common_src/cxx/function_cascades.cpp
common_src/cxx/track_shelf.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation