Class for particles that are aware of tracking. More...

#include <particle_track.h>

Inheritance diagram for tracking::particle_track:

Collaboration diagram for tracking::particle_track:

Public Member Functions
	particle_track (int i_ind, int frame)

	particle_track (int i_ind, utilities::Tuplef pos, unsigned int frame)
	constructor that does not require any calls to the wrapper to get set up. More...

	~particle_track ()
	Destructor. More...

void	print_t (int more) const
	recursive print function for printing out the sequence of a track. More...

const particle_track *	get_next () const
	Returns a pointer to the next particle in the track. More...

particle_track *	get_next ()
	Returns a pointer to the next particle in the track. More...

const particle_track *	get_prev () const
	Returns a pointer to the previous particle in the track. More...

particle_track *	get_prev ()
	Returns a pointer to the previous particle in the track. More...

const utilities::Tuplef	get_corrected_disp (const particle_track *part_in) const
	Returns the corrected forward displacement. More...

bool	step_forwards (int n, const particle_track *&next) const
	Returns true if there is a particle n steps forward and passes a pointer to it out as a reference, if there is not a particle, returns false. More...

bool	step_backwards (int n, const particle_track *&next) const
	Returns true if there is a particle n steps backwards and passes a pointer to it out as a reference, if there is not a particle, returns false. More...

Track_box *	get_track () const
	get what track the particle belongs to. More...

int	get_track_id () const
	Retruns the identifer of the Track_box the particle is in. More...

const Hash_shelf *	get_shelf () const
	Returns pointer to the shelf the particle resides in. More...

void	set_shelf (Hash_shelf *shelf)
	Sets the shelf that the particle is in. More...

float	distancesq_corrected (const particle_track *part_in) const
	Returns the displacement squared corrected for the net drift. More...

bool	has_track () const
	returns if the track is set More...

bool	has_next () const
	returns if a particle has a next More...

const utilities::Tuplef	get_corrected_pos () const
	returns the position with the cumulative displacement subtracted off More...

int	get_value (utilities::D_TYPE type, int &val) const

float	get_value (utilities::D_TYPE type, float &val) const

std::complex< float >	get_value (utilities::D_TYPE type, std::complex< float > &val) const

void	print () const
	Pring out a rasonable representation of the partile. More...

template<class T >
T	get_wrapper_value (utilities::D_TYPE type, T &val) const
	Returns the a value associated with the particle directly from the wrapper, by passing all logic in the particle object. More...

const utilities::Tuplef &	get_position () const
	returns a tuple of the particle's position More...

int	get_ind () const
	returns the index of the current particle More...

int	get_frame () const
	returns the frame of the current particle More...

float	distancesq (const particle_base *part_in) const
	Retruns the distance from this particle to part_in. More...

const utilities::Tuplef	get_disp (const particle_base *part_in) const
	Returns the uncorrected forward displacement. More...

float	get_r (const utilities::Tuplef &origin) const
	Returns the distance of the particle from the specified origin. More...

float	get_theta (const utilities::Tuplef &origin) const
	Returns the angle in the plane from the Y-axis. More...

void	sort_neighborhood ()
	Sorts the neighborhood vector in ascending order. More...

bool	no_neighborhood_repeats () const
	checks to make sure the neighborhood does not include any repeats, returns true if the neighborhood is repeat free. More...

bool	add_to_neighborhood (const particle *in)
	adds a particle to the neighborhood if it is close enough returns true if the particle is added, false otherwise More...

void	fill_phi_6 ()
	Fills the order parameter with $\Phi_6$ . More...

std::complex< float >	compute_phi_6 () const
	computes and returns the order parameter $\Phi_6$ . More...

std::complex< float >	get_scaler_order_pram () const
	returns the scaler order parameter More...

unsigned int	get_neighborhood_size () const
	returns the number of particles with in max_neighborhood_range_ of the particle (assuming that these have been initialized More...

const std::vector< const particle * >	get_neighborhood () const
	returns the neighborhood vector More...

Static Public Member Functions
static float	get_max_range ()
	returns the maximum neighborhood range More...

static void	intialize_wrapper_in (const utilities::Wrapper_in *in)
	Intialize the static input wrapper for all particles. More...

static void	clear_wrapper_in ()
	Cleans up the set wrapper_in. More...

static void	set_neighborhood_range (float in)
	Sets the maximum neighborhood range, there needs to be something to make sure that this doesn't get changed with out updating the. More...

static float	get_neighborhood_range ()
	returns the range of the neighborhood More...

Public Attributes
std::list< std::pair < particle_track , float > >	n_pos_link
	pointer to a list of particles to be used durring the tracking process More...

std::list< std::pair < particle_track , float > >	p_pos_link
	h pointer to a list of particles to be used durring the tracking process More...

Protected Attributes
int	ind_
	Identifier that comes from the wrapper. More...

utilities::Tuplef	position_
	New attempt at storing the position data, this has the problem of taking more memory, but it might help the time. More...

int	frame_
	The frame of the particle. More...

std::vector< const particle * >	neighborhood_
	Vector of the particles with in max_range_ in the Hash_shelf_ of the particle. More...

std::complex< float >	s_order_parameter_
	Scaler order parameter, ex phi_6 in 2D. More...

Static Protected Attributes
static const utilities::Wrapper_in *	wrapper_in_ = NULL
	object that takes care of all the underling data structures. More...

static float	max_neighborhood_range_ = 0
	Maximum distance to be part of the neighborhood. More...

Private Member Functions
bool	step_backwards (int n, particle_track *&next)
	Returns true if there is a particle n steps forward and passes a pointer to it out as a reference, if there is not a particle, returns false. More...

bool	step_forwards (int n, particle_track *&next)
	Returns true if there is a particle n steps forward and passes a pointer to it out as a reference, if there is not a particle, returns false. More...

void	set_track (Track_box *i_track)
	sets what track the particle belongs to. More...

particle_track *	reset_track (Track_box *i_track, int &count)
	sets the track pointer with out any sanity checks, used for track splitting. More...

void	clear_next ()
	cuts the track pointers More...

void	clear_prev ()
	cuts track pointers More...

void	set_next (particle_track *n_next)
	Sets the pointer to the next particle. More...

void	set_prev (particle_track *n_prev)
	Sets the pointer to the previous particle. More...

void	clear_track_data ()
	Clears all of the data associated with the tracking. More...

void	clear_data_forward ()
	Clears the track data form all particles after the current particle. More...

void	clear_data_backward ()
	Clears the track data from all particles before this particle. More...

Private Attributes
particle_track *	next_
	next particle in track More...

particle_track *	prev_
	prev particle in track More...

Track_box *	track_
	Pointer to which track the particle is in. More...

Hash_shelf *	shelf_
	Pointer to the shelf that the particle lives in. More...

Friends
class	Track_box
	Friends with Track_box to allow it to screw with the linked list directly with out having to go through the getter/setter functions to remove an uneeded level of indrection, still keep the sanity check on not nuking the list for most uses. More...

class	track_list

Detailed Description

Class for particles that are aware of tracking.

This class carries additional information about which track the particle is in and some members needed for tracking.

Constructor & Destructor Documentation

particle_track::particle_track	(	int	i_ind,
		int	frame
	)

particle_track::particle_track	(	int	i_ind,
		utilities::Tuplef	pos,
		unsigned int	frame
	)

constructor that does not require any calls to the wrapper to get set up.

particle_track::~particle_track ( )

Destructor.

References n_pos_link, and p_pos_link.

Member Function Documentation

bool particle_base::add_to_neighborhood ( const particle * in)

inherited

adds a particle to the neighborhood if it is close enough returns true if the particle is added, false otherwise

References tracking::particle_base::distancesq(), tracking::particle_base::frame_, tracking::particle_base::max_neighborhood_range_, and tracking::particle_base::neighborhood_.

Referenced by tracking::Hash_shelf::fill_in_neighborhood().

void particle_track::clear_data_backward ( )

private

Clears the track data from all particles before this particle.

This leave this particle as the head of the track, ie t_prev_ ==NULL

References clear_data_backward(), next_, prev_, and track_.

Referenced by clear_data_backward(), and tracking::Track_box::trim_track().

void particle_track::clear_data_forward ( )

private

Clears the track data form all particles after the current particle.

This leaves the current particle in the track as the last particle, ie t_next_ == NULL

References clear_data_forward(), next_, prev_, and track_.

Referenced by clear_data_forward(), and tracking::Track_box::trim_track().

void tracking::particle_track::clear_next ( )

inlineprivate

cuts the track pointers

References next_.

Referenced by tracking::Track_box::split_track().

void tracking::particle_track::clear_prev ( )

inlineprivate

cuts track pointers

References prev_.

Referenced by tracking::Track_box::split_track().

void particle_track::clear_track_data ( )

private

Clears all of the data associated with the tracking.

References next_, prev_, and track_.

void particle_base::clear_wrapper_in ( )

staticinherited

Cleans up the set wrapper_in.

References tracking::particle_base::wrapper_in_.

Referenced by tracking::hash_case::~hash_case(), and tracking::Master_box::~Master_box().

complex< float > particle_base::compute_phi_6 ( ) const

inherited

computes and returns the order parameter $\Phi_6$ .

Defined by

$\Phi_{6}(r_{m}) = \frac{1}{N_{b}}\sum_{n=1}^{N_{b}}e^{6 i\theta_{mn} }$

References tracking::particle_base::neighborhood_, and tracking::particle_base::position_.

Referenced by tracking::particle_base::fill_phi_6().

float particle_base::distancesq ( const particle_base * part_in) const

inherited

Retruns the distance from this particle to part_in.

References utilities::Tuple< T, length >::dist_sqr(), and tracking::particle_base::position_.

Referenced by tracking::particle_base::add_to_neighborhood(), tracking::Corr_gofr::compute(), tracking::Corr_pair_diffusion::compute(), tracking::hash_case::fill_pos_link_next(), tracking::particle_base::lthan(), tracking::Track_shelf::msd(), and tracking::Corr_goftheta::trim_nhood().

float particle_track::distancesq_corrected ( const particle_track * part_in) const

Returns the displacement squared corrected for the net drift.

References tracking::Hash_shelf::get_cum_forward_disp(), tracking::particle_base::position_, and shelf_.

Referenced by tracking::Accum_chi4_self::add_particle(), tracking::Track_shelf::disp_sq_hist(), and tracking::Track_shelf::msd_corrected().

void particle_base::fill_phi_6 ( )

inherited

Fills the order parameter with $\Phi_6$ .

See compute_phi_6()

References tracking::particle_base::compute_phi_6(), tracking::particle_base::print(), and tracking::particle_base::s_order_parameter_.

const utilities::Tuplef particle_track::get_corrected_disp ( const particle_track * part_in) const

Returns the corrected forward displacement.

The assumption is that this particle is the initial position and part_in is the final position.

Parameters

[in] part_in the final position of the particle

Returns: the vector from this to part_in

References tracking::Hash_shelf::get_cum_forward_disp(), tracking::particle_base::position_, and shelf_.

Referenced by tracking::Corr_pair_diffusion::compute(), tracking::Track_shelf::compute_corrected_TA(), tracking::Track_shelf::compute_corrected_TA_ncuts(), and tracking::Track_box::extract_corrected_disp().

const utilities::Tuplef particle_track::get_corrected_pos ( ) const

returns the position with the cumulative displacement subtracted off

References tracking::Hash_shelf::get_cum_forward_disp(), tracking::particle_base::position_, and shelf_.

Referenced by tracking::Track_box::extract_corrected_pos().

const utilities::Tuplef particle_base::get_disp ( const particle_base * part_in) const

inherited

Returns the uncorrected forward displacement.

References tracking::particle_base::position_.

Referenced by tracking::Corr_theta_2pt::compute(), tracking::Hash_shelf::compute_mean_forward_disp(), and tracking::Track_box::extract_raw_disp().

int tracking::particle_base::get_frame ( ) const

inlineinherited

returns the frame of the current particle

References tracking::particle_base::frame_.

Referenced by tracking::Track_box::output_to_wrapper(), and tracking::Track_shelf::output_to_wrapper().

int tracking::particle_base::get_ind ( ) const

inlineinherited

returns the index of the current particle

References tracking::particle_base::ind_.

Referenced by get_value(), tracking::Track_shelf::output_to_wrapper(), and tracking::Hash_shelf::push().

static float tracking::particle_base::get_max_range ( )

inlinestaticinherited

returns the maximum neighborhood range

References tracking::particle_base::max_neighborhood_range_.

Referenced by tracking::Hash_shelf::fill_in_neighborhood().

const std::vector<const particle*> tracking::particle_base::get_neighborhood ( ) const

inlineinherited

returns the neighborhood vector

References tracking::particle_base::neighborhood_.

static float tracking::particle_base::get_neighborhood_range ( )

inlinestaticinherited

returns the range of the neighborhood

References tracking::particle_base::max_neighborhood_range_.

Referenced by tracking::hash_box::compute_corr().

unsigned int tracking::particle_base::get_neighborhood_size ( ) const

inlineinherited

returns the number of particles with in max_neighborhood_range_ of the particle (assuming that these have been initialized

References tracking::particle_base::neighborhood_.

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

const particle_track* tracking::particle_track::get_next ( ) const

inline

Returns a pointer to the next particle in the track.

If this is the last particle in the track than NULL will be returned.

References next_.

Referenced by tracking::Accum_chi4_self::add_particle(), tracking::track_list::clean_lists(), tracking::Hash_shelf::compute_mean_forward_disp(), tracking::Track_box::extract_corrected_disp(), tracking::Track_box::extract_corrected_pos(), tracking::Track_box::extract_raw_disp(), tracking::Track_box::extract_raw_pos(), tracking::Track_box::output_to_wrapper(), tracking::Track_box::split_to_parts(), and tracking::Track_box::~Track_box().

particle_track* tracking::particle_track::get_next ( )

inline

Returns a pointer to the next particle in the track.

If this is the last particle in the track than NULL will be returned that is not const protected

References next_.

const utilities::Tuplef& tracking::particle_base::get_position ( ) const

inlineinherited

returns a tuple of the particle's position

References tracking::particle_base::position_.

Referenced by tracking::Accum_sofq_ND::add_particle(), tracking::Accum_sofq::add_particle(), tracking::Corr_goftheta::compute(), tracking::Corr_pair_diffusion::compute(), tracking::Track_box::extract_raw_pos(), and tracking::Hash_shelf::hash_function().

const particle_track* tracking::particle_track::get_prev ( ) const

inline

Returns a pointer to the previous particle in the track.

If this is the first particle in the track than NULL will be returned.

References prev_.

Referenced by tracking::track_list::clean_lists(), and tracking::Track_box::split_track().

particle_track* tracking::particle_track::get_prev ( )

inline

Returns a pointer to the previous particle in the track.

If this is the first particle in the track than NULL will be returned.

References prev_.

float particle_base::get_r ( const utilities::Tuplef & origin) const

inherited

Returns the distance of the particle from the specified origin.

Parameters

origin the cordinates of the new origin

References tracking::particle_base::position_.

std::complex<float> tracking::particle_base::get_scaler_order_pram ( ) const

inlineinherited

returns the scaler order parameter

References tracking::particle_base::s_order_parameter_.

const Hash_shelf* tracking::particle_track::get_shelf ( ) const

inline

Returns pointer to the shelf the particle resides in.

References shelf_.

float particle_base::get_theta ( const utilities::Tuplef & origin) const

inherited

Returns the angle in the plane from the Y-axis.

Parameters

origin the cordinates of the new origin

References tracking::particle_base::position_.

Track_box * particle_track::get_track ( ) const

get what track the particle belongs to.

Each particle can only belong to one track.

References track_.

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

int particle_track::get_track_id ( ) const

Retruns the identifer of the Track_box the particle is in.

References tracking::Track_box::get_id(), and track_.

int particle_track::get_value	(	utilities::D_TYPE	type,
		int &	val
	)		const

References utilities::D_NEXT_INDX, utilities::D_PREV_INDX, utilities::D_TRACKID, tracking::Track_box::get_id(), tracking::particle_base::get_ind(), tracking::particle_base::get_value(), next_, prev_, track_, utilities::V_INT, and utilities::v_type().

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

float particle_track::get_value	(	utilities::D_TYPE	type,
		float &	val
	)		const

References tracking::particle_base::get_value().

std::complex< float > particle_track::get_value	(	utilities::D_TYPE	type,
		std::complex< float > &	val
	)		const

References tracking::particle_base::get_value().

template<class T >

template int particle_base::get_wrapper_value	(	utilities::D_TYPE	type,
		T &	val
	)		const

inherited

Returns the a value associated with the particle directly from the wrapper, by passing all logic in the particle object.

References tracking::particle_base::frame_, utilities::Wrapper_in::get_value(), tracking::particle_base::ind_, and tracking::particle_base::wrapper_in_.

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

bool particle_track::has_next ( ) const

returns if a particle has a next

References next_.

bool particle_track::has_track ( ) const

returns if the track is set

References track_.

void particle_base::intialize_wrapper_in ( const utilities::Wrapper_in * in)

staticinherited

Intialize the static input wrapper for all particles.

References tracking::particle_base::wrapper_in_.

Referenced by tracking::hash_case::init(), and tracking::Master_box::priv_init().

bool particle_base::no_neighborhood_repeats ( ) const

inherited

checks to make sure the neighborhood does not include any repeats, returns true if the neighborhood is repeat free.

Mostly for debugging

References tracking::particle_base::neighborhood_.

void particle_base::print ( ) const

inherited

Pring out a rasonable representation of the partile.

References tracking::particle_base::frame_, tracking::particle_base::ind_, and tracking::particle_base::position_.

Referenced by tracking::particle_base::fill_phi_6(), print_t(), and tracking::Hash_shelf::push().

void particle_track::print_t ( int more) const

recursive print function for printing out the sequence of a track.

Parameters

more	how many more particles to descend

References next_, tracking::particle_base::print(), and print_t().

Referenced by tracking::Track_box::print(), and print_t().

particle_track * particle_track::reset_track	(	Track_box *	i_track,
		int &	count
	)

private

sets the track pointer with out any sanity checks, used for track splitting.

Walks down the list to reset all particles.

References next_, reset_track(), and track_.

Referenced by tracking::Track_box::push_back(), reset_track(), and tracking::Track_box::Track_box().

static void tracking::particle_base::set_neighborhood_range ( float in)

inlinestaticinherited

Sets the maximum neighborhood range, there needs to be something to make sure that this doesn't get changed with out updating the.

References tracking::particle_base::max_neighborhood_range_.

void particle_track::set_next ( particle_track * n_next)

private

Sets the pointer to the next particle.

If next isn't NULL before being set, then this function thows the error "nuking the list" to prevent accidental destruction of the track.

Parameters

[in] n_next pointer to the particle to be set as next

References next_.

Referenced by tracking::Track_box::push_back().

void particle_track::set_prev ( particle_track * n_prev)

private

Sets the pointer to the previous particle.

If prev isn't NULL before being set, then this function thows the error "nuking the list" to prevent accidental destruction of the track.

Parameters

n_prev pointer to the particle to be set as prev

References prev_.

Referenced by tracking::Track_box::push_back().

void particle_track::set_shelf ( Hash_shelf * shelf)

Sets the shelf that the particle is in.

References shelf_.

Referenced by tracking::hash_case::init().

void particle_track::set_track ( Track_box * i_track)

private

sets what track the particle belongs to.

Each particle can only belong to one track. This code will do sanity checks to make sure that tracks are not accidentally moved from track to track. If track is already non-NULL then the error "moving between lists!" is thrown.

Parameters

i_track pointer to the Track_box that represents the track this particle is to be a part of

References track_.

void particle_base::sort_neighborhood ( )

inherited

Sorts the neighborhood vector in ascending order.

References tracking::particle_base::neighborhood_.

Referenced by tracking::Hash_shelf::fill_in_neighborhood().

bool particle_track::step_backwards	(	int	n,
		const particle_track *&	next
	)		const

Returns true if there is a particle n steps backwards and passes a pointer to it out as a reference, if there is not a particle, returns false.

Todo:: fix naming sematics

Parameters

n	[in] number of steps to take
next	[out] pointer to the nth particle

Returns: true if the nth particle exists

References next_, prev_, and step_backwards().

Referenced by tracking::Track_box::at(), and step_backwards().

bool particle_track::step_backwards	(	int	n,
		particle_track *&	next
	)

private

Returns true if there is a particle n steps forward and passes a pointer to it out as a reference, if there is not a particle, returns false.

Private, non-const version

Parameters

n	[in] number of steps to take
next	[out] pointer to the nth particle

Returns: true if the nth particle exists

References prev_, and step_backwards().

bool particle_track::step_forwards	(	int	n,
		const particle_track *&	next
	)		const

Returns true if there is a particle n steps forward and passes a pointer to it out as a reference, if there is not a particle, returns false.

Parameters

n	[in] number of steps to take
next	[out] pointer to the nth particle

Returns: true if the nth particle exists

References next_, and step_forwards().

Referenced by tracking::Track_box::at(), tracking::Corr_pair_diffusion::compute(), tracking::Track_shelf::compute_corrected_TA(), tracking::Track_shelf::compute_corrected_TA_ncuts(), tracking::Track_shelf::disp_sq_hist(), tracking::Track_shelf::msd(), tracking::Track_shelf::msd_corrected(), step_forwards(), and tracking::Track_box::trim_track().

bool particle_track::step_forwards	(	int	n,
		particle_track *&	next
	)

private

Returns true if there is a particle n steps forward and passes a pointer to it out as a reference, if there is not a particle, returns false.

Private, non-const version

Parameters

n	[in] number of steps to take
next	[out] pointer to the nth particle

Returns: true if the nth particle exists

References next_, and step_forwards().

Friends And Related Function Documentation

friend class Track_box

friend

Friends with Track_box to allow it to screw with the linked list directly with out having to go through the getter/setter functions to remove an uneeded level of indrection, still keep the sanity check on not nuking the list for most uses.

friend class track_list

friend