IMP::em2d::ProjectionFinder Class Reference

class to perform registration of model projections to images images

#include <IMP/em2d/ProjectionFinder.h>

Inheritance diagram for IMP::em2d::ProjectionFinder:

Public Member Functions
void	get_coarse_registration ()
double	get_coarse_registration_time () const
	Time employed for the coarse registration part.
void	get_complete_registration ()
double	get_fine_registration_time () const
	Time employed for the fine registration part.
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.
RegistrationResults	get_registration_results () const
bool	get_save_match_images () const
void	set_fast_mode (unsigned int n)
void	set_model_particles (const ParticlesTemp &ps)
	Set the particles where the em2D restraint is applied.
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.
void	set_save_match_images (bool x)
void	set_subjects (const em2d::Images &subjects)
	Set EM images to use as restraints.
void	set_variance_images (const em2d::Images &variances)
	Set the projections of the model to use for initial coarse correlation.
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 ()
virtual IMP::base::VersionInfo	get_version_info () const =0
	Get information about the module and version of the object.
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.
Protected Member Functions inherited from IMP::base::Object
	Object (std::string name)
	Construct an object with the given name. More...

Protected Attributes
double	coarse_registration_time_
bool	fast_optimization_mode_
double	fine_registration_time_
MasksManagerPtr	masks_manager_
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_
Pointer< ScoreFunction >	score_function_
em2d::Images	subjects_
	Main parameters.
std::vector< cv::Mat >	SUBJECTS_
algebra::Vector2Ds	subjects_cog_
std::vector< cv::Mat >	SUBJECTS_POLAR_AUTOC_
em2d::Images	variances_

Related Functions
(Note that these are not member functions.)
typedef IMP::base::Vector < IMP::base::WeakPointer < ProjectionFinder > >	ProjectionFindersTemp
Related Functions inherited from IMP::base::Object
typedef IMP::base::Vector < IMP::base::WeakPointer < Object > >	ObjectsTemp

Detailed Description

Definition at line 78 of file ProjectionFinder.h.

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

void IMP::em2d::ProjectionFinder::get_complete_registration

(

)

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

double IMP::em2d::ProjectionFinder::get_global_score

(

)

const

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

RegistrationResults IMP::em2d::ProjectionFinder::get_registration_results

(

)

const

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

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 increased it for get more chances of finding the best projection

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 137 of file ProjectionFinder.h.

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

Parameters

[in]	resolution	to employ to generate projections for matching with the EM images. Default is the maximum possible, 1.
[in]	coarse_registration_method	Method for 1st step of projection finding, the 2D alignment: 0 => FFT alignment no preprocessing. 1 => FFT alignment with preprocessing (Default and recommended). 2 => FFT alginment and centers of gravity (fast, but only works for low noise) during testing.
[in]	optimization	steps to use by the simplex optimizer. The default value is the one found during the benchmark to perform well
[in]	simplex_initial_length	Initial value to start the simplex search The default value is based on the benchmark results
[in]	Value	of the simplex length stop the search. The smaller, the more accurate the finder, but slower

Definition at line 102 of file ProjectionFinder.h.

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Friends And Related Function Documentation

typedef IMP::base::Vector<IMP::base::WeakPointer< ProjectionFinder > > ProjectionFindersTemp

related

Pass a set of objects.

Definition at line 243 of file ProjectionFinder.h.

Member Data Documentation

MasksManagerPtr IMP::em2d::ProjectionFinder::masks_manager_

protected

MasksManager masks_manager_;

Definition at line 240 of file ProjectionFinder.h.

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

• ProjectionFinder.h