BayesEM3D.h File Reference

Compute a Bayesian formalism score and its derivatives to assess degree of match between a tested model and a density object. More...

#include <IMP/Refiner.h>
#include <IMP/core/rigid_bodies.h>
#include <IMP/em/KernelParameters.h>
#include <IMP/em/MRCReaderWriter.h>
#include <IMP/em/em_config.h>
#include <vector>
#include "DensityMap.h"
#include "def.h"

Include dependency graph for BayesEM3D.h:

This graph shows which files directly or indirectly include this file:

Go to the source code of this file.

Namespaces
	IMP
	Base functionality and abstract base classes for representation, scoring and sampling.
	IMP::em
	Basic utilities for handling cryo-electron microscopy 3D density maps.

Functions
double	IMP::em::bayesem3d_get_cross_correlation_coefficient (const DensityMap *em1, const DensityMap *em2)
	Compute a normalized cross-correlation coefficient. More...
Floats	IMP::em::bayesem3d_get_cumulative_sum (DensityMap *em)
	Compute the cumulative sum of the histogram computed from EM map. More...
std::map< double, double >	IMP::em::bayesem3d_get_cumulative_sum_with_reference (DensityMap *em)
	Compute the cumulative sum of the histogram given a reference. More...
DensityMap *	IMP::em::bayesem3d_get_density_from_particle (DensityMap *em, const IMP::ParticlesTemp &ps, double resolution, const double window_size=1.0)
std::map< double, int >	IMP::em::bayesem3d_get_distinct_and_counts (DensityMap *em)
	Get histogram of density in EM map. More...
FloatPair	IMP::em::bayesem3d_get_em_density_squared (DensityMap *em, long number_of_voxels)
	Compute the sum of the density and the sum of the squares of the density. More...
FloatPair	IMP::em::bayesem3d_get_logabssumexp (double x, double y, double sx, double sy)
	Numerically stable logabssumexp. More...
FloatPair	IMP::em::bayesem3d_get_logabssumprodexp (double x, double y, double wx, double wy)
	Numerically stable logabssumprodexp. More...
double	IMP::em::bayesem3d_get_logsumexp (double x, double y)
	Numerically stable logsumexp. More...
double	IMP::em::bayesem3d_get_logsumprodexp (double x, double y, double wx, double wy)
	Numerically stable logsumexpprod. More...
void	IMP::em::bayesem3d_get_normalized_intensities (DensityMap *em, const IMP::ParticlesTemp &ps, double resolution)
std::pair< double, algebra::Vector3Ds >	IMP::em::bayesem3d_get_score_and_derivative (DensityMap *em, const IMP::ParticlesTemp &ps, double resolution, double sigma, const double window_size=1.0)
	The function returns the negative log of the Normal distributed difference between a normalized EM density map and a tested model. To support sampling and optimization, the derivative of the score is also returned. More...
std::vector< double >	IMP::em::bayesem3d_get_value (Particle *p, const algebra::Vector3D &pt, double mass_ii, const IMP::em::KernelParameters &kps)
	Compute the score and derivatives for a particle at a given voxel. More...
std::vector< double >	IMP::em::bayesem3d_get_value_no_deriv (Particle *p, const algebra::Vector3D &pt, double mass_ii, const IMP::em::KernelParameters &kps)
	Compute the score without its derivative. More...
double	IMP::em::bayesem3d_linear_interpolate (const Floats &x_data, const Floats &y_data, double x, bool extrapolate)
	Basic linear interpolation given vectors of values. More...

Detailed Description

Compute a Bayesian formalism score and its derivatives to assess degree of match between a tested model and a density object.

Copyright 2007-2020 IMP Inventors. All rights reserved.

Definition in file BayesEM3D.h.