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class to perform registration of model projections to images images
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 ¶ms) |
| Initializes the parameters to generate and match projections. | |
| void | show (std::ostream &out) const |
| Public Member Functions inherited from IMP::base::Object | |
| std::size_t | __hash__ () const |
| virtual std::string | get_type_name () const =0 |
| Return a string identifying the type of the object. | |
| 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. | |
| void | set_was_used (bool tf) const |
| const std::string & | get_name () const |
| void | set_name (std::string name) |
Static Public Member Functions | |
| static ProjectionFinder * | get_from (IMP::base::Object *o) |
Protected Member Functions | |
| void | do_preprocess_for_fast_coarse_registration (const cv::Mat &m, algebra::Vector2D ¢er, 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) | |
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_ |
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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
| double IMP::em2d::ProjectionFinder::get_coarse_registration_time | ( | ) | const |
Time employed for the coarse registration part.
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protected |
Coarse registration for one subject.
| 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_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
| 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_model_particles | ( | const 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.
| 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.
| [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 |
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protected |
MasksManager masks_manager_;
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protected |
Main parameters.
