Class to perform registration of model projections to images. More...

#include <IMP/em2d/ProjectionFinder.h>

Inheritance diagram for IMP::em2d::ProjectionFinder:

Detailed Description

Class to perform registration of model projections to images.

Definition at line 76 of file ProjectionFinder.h.

Public Member Functions
void	get_coarse_registration ()

double	get_coarse_registration_time () const
	Time employed for the coarse registration part. More...

void	get_complete_registration ()

double	get_fine_registration_time () const
	Time employed for the fine registration part. More...

double	get_global_score () const

unsigned int	get_number_of_projections () const

unsigned int	get_number_of_subjects () const

double	get_preprocessing_time () const
	Time employed for preprocessing. More...

RegistrationResults	get_registration_results () const

bool	get_save_match_images () const

virtual std::string	get_type_name () const

virtual ::IMP::base::VersionInfo	get_version_info () const
	Get information about the module and version of the object. More...

void	set_fast_mode (unsigned int n)

void	set_model_particles (const kernel::ParticlesTemp &ps)
	Set the particles where the em2D restraint is applied. More...

void	set_number_of_class_averages_members (Ints n_members)

void	set_projections (const em2d::Images &projections)
	Set the projections of the model to use for initial coarse correlation. More...

void	set_save_match_images (bool x)

void	set_subjects (const em2d::Images &subjects)
	Set EM images to use as restraints. More...

void	set_variance_images (const em2d::Images &variances)
	Set the projections of the model to use for initial coarse correlation. More...

void	setup (ScoreFunction *score_function, const Em2DRestraintParameters &params)
	Initializes the parameters to generate and match projections. More...

void	show (std::ostream &out) const

Public Member Functions inherited from IMP::base::Object
virtual void	clear_caches ()

CheckLevel	get_check_level () const

LogLevel	get_log_level () const

void	set_check_level (CheckLevel l)

void	set_log_level (LogLevel l)
	Set the logging level used in this object. More...

void	set_was_used (bool tf) const

void	show (std::ostream &out=std::cout) const

const std::string &	get_name () const

void	set_name (std::string name)

Protected Member Functions
void	do_preprocess_for_fast_coarse_registration (const cv::Mat &m, algebra::Vector2D &center, cv::Mat &POLAR_AUTOC)

void	do_preprocess_projection (unsigned int j)

void	do_preprocess_subject (unsigned int i)

void	get_coarse_registrations_for_subject (unsigned int i, RegistrationResults &coarse_RRs)
	Coarse registration for one subject. More...

Protected Member Functions inherited from IMP::base::Object
	Object (std::string name)
	Construct an object with the given name. More...

virtual void	do_destroy ()

Protected Attributes
double	coarse_registration_time_

bool	fast_optimization_mode_

double	fine_registration_time_

MasksManagerPtr	masks_manager_

kernel::ParticlesTemp	model_particles_

Ints	n_members_

unsigned int	number_of_optimized_projections_

bool	parameters_setup_

Em2DRestraintParameters	params_

bool	particles_set_

PolarResamplingParameters	polar_params_

double	preprocessing_time_

em2d::Images	projections_

algebra::Vector2Ds	projections_cog_

std::vector< cv::Mat >	PROJECTIONS_POLAR_AUTOC_

bool	registration_done_

RegistrationResults	registration_results_

base::Pointer< ScoreFunction >	score_function_

em2d::Images	subjects_
	Main parameters. More...

std::vector< cv::Mat >	SUBJECTS_

algebra::Vector2Ds	subjects_cog_

std::vector< cv::Mat >	SUBJECTS_POLAR_AUTOC_

em2d::Images	variances_

Member Function Documentation

void IMP::em2d::ProjectionFinder::do_preprocess_for_fast_coarse_registration	(	const cv::Mat &	m,
		algebra::Vector2D &	center,
		cv::Mat &	POLAR_AUTOC
	)

protected

Computes the weighted centroid and the FFT of the polar-resampled autocorrelation.

void IMP::em2d::ProjectionFinder::get_coarse_registration ( )

Coarse registration of all the images using the projections Based in 2D alignments of the images

Note: Given that this registration is based on 2D alignment maximizing the cross correlation, the a better score is the best correlation

double IMP::em2d::ProjectionFinder::get_coarse_registration_time ( ) const

Time employed for the coarse registration part.

void IMP::em2d::ProjectionFinder::get_coarse_registrations_for_subject	(	unsigned int	i,
		RegistrationResults &	coarse_RRs
	)

protected

Coarse registration for one subject.

void IMP::em2d::ProjectionFinder::get_complete_registration ( )

Performs complete registration of projections against the images. This means the coarse registration followed by simplex optimization

double IMP::em2d::ProjectionFinder::get_fine_registration_time ( ) const

Time employed for the fine registration part.

double IMP::em2d::ProjectionFinder::get_global_score ( ) const

Get the em2d score for a model after the registration performed: coarse or complete.

double IMP::em2d::ProjectionFinder::get_preprocessing_time ( ) const

Time employed for preprocessing.

RegistrationResults IMP::em2d::ProjectionFinder::get_registration_results ( ) const

Recover the registration results. Only works if a registration has been done previously

virtual ::IMP::base::VersionInfo IMP::em2d::ProjectionFinder::get_version_info ( ) const

virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 166 of file ProjectionFinder.h.

void IMP::em2d::ProjectionFinder::set_fast_mode ( unsigned int n )

With this fast mode, only the first number n of best scoring projections during the coarse search are refined. Saves vast times of computation time with some loss of accuracy. Try starting with 1 (risky) or 2, and increase it to get more chances of finding the best projection

void IMP::em2d::ProjectionFinder::set_model_particles ( const kernel::ParticlesTemp & ps )

Set the particles where the em2D restraint is applied.

void IMP::em2d::ProjectionFinder::set_projections ( const em2d::Images & projections )

Set the projections of the model to use for initial coarse correlation.

void IMP::em2d::ProjectionFinder::set_save_match_images ( bool x )

The projections of the model that best match the subject EM images are saved.

Their name will be: coarse-match-i.spi for coarse registration and fine_match-i.spi for full registration.

Definition at line 117 of file ProjectionFinder.h.

void IMP::em2d::ProjectionFinder::set_subjects ( const em2d::Images & subjects )

Set EM images to use as restraints.

void IMP::em2d::ProjectionFinder::set_variance_images ( const em2d::Images & variances )

Set the projections of the model to use for initial coarse correlation.

void IMP::em2d::ProjectionFinder::setup	(	ScoreFunction *	score_function,
		const Em2DRestraintParameters &	params
	)

Initializes the parameters to generate and match projections.

Definition at line 84 of file ProjectionFinder.h.

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Member Data Documentation

MasksManagerPtr IMP::em2d::ProjectionFinder::masks_manager_

protected

MasksManager masks_manager_;

Definition at line 209 of file ProjectionFinder.h.

em2d::Images IMP::em2d::ProjectionFinder::subjects_

protected

Main parameters.

Definition at line 184 of file ProjectionFinder.h.

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

ProjectionFinder.h

Detailed Description

Public Member Functions

Protected Member Functions

Protected Attributes

Member Function Documentation

Member Data Documentation