Responsible for performing coarse fitting between two density objects. More...

#include <IMP/em/CoarseCC.h>

Inheritance diagram for IMP::em::CoarseCC:

Public Member Functions
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.

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

virtual void	do_destroy ()

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)

Static Public Member Functions
static float	calc_score (DensityMap data, SampledDensityMap model_map, float scalefactor, bool recalc_rms=true, bool resample=true, FloatPair norm_factors=FloatPair(0., 0.))
	Calculates the value of the EM fitting term. More...

static double	cross_correlation_coefficient (const DensityMap grid1, const DensityMap grid2, float grid2_voxel_data_threshold, bool allow_padding=false, FloatPair norm_factors=FloatPair(0., 0.))
	Calculates the cross correlation coefficient between two maps. More...

static float	local_cross_correlation_coefficient (const DensityMap em_map, DensityMap model_map, float voxel_data_threshold)
	Local cross correlation function.

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

	Object ()

Detailed Description

The pixels involved are derived from the positions of N particles.

Definition at line 28 of file CoarseCC.h.

Member Function Documentation

static float IMP::em::CoarseCC::calc_score	(	DensityMap *	data,
		SampledDensityMap *	model_map,
		float	scalefactor,
		bool	recalc_rms = `true`,
		bool	resample = `true`,
		FloatPair	norm_factors = `FloatPair(0., 0.)`
	)

static

Note: The function returns scalefac*(1-ccc) to support minimization optimization. The ccc value (cross correlation coefficient) is calculate by the cross_correlation_coefficient function.

Parameters

[in]	data	DensityMap class containing the EM map. note: correct RMSD and mean MUST be in the header!
[in]	model_map	SampledDensityMap class prepared to contain the simulated EM map for the model.
[in]	scalefactor	scale factor to apply to the value of the cross correlation term
[in]	recalc_rms	determines wheather the RMS of both maps should be recalcualted prior to the correlation calculation. False is faster, but potentially innacurate
[in]	resample	if true, the model density map is resampled
[in]	norm_factors	if set these precalcualted terms are used for normalization

Returns: the value of the cross correlation term: scalefac*(1-ccc) See cross_correlation_coefficient

static double IMP::em::CoarseCC::cross_correlation_coefficient	(	const DensityMap *	grid1,
		const DensityMap *	grid2,
		float	grid2_voxel_data_threshold,
		bool	allow_padding = `false`,
		FloatPair	norm_factors = `FloatPair(0., 0.)`
	)

static

Cross correlation coefficient between the em density and the density of a model. The function applied is: \(\frac{\sum_{i=1}^{N}{{td}_i}{{md}_i}-{N} {{mean}_{td}} {{mean}_{md}}} {N\sigma_{{td}}\sigma_{{md}}}\), such that \(N\) is the number of voxels, \({td}\) is the target density, \({tm}\) is the model density,

Parameters

[in]	grid1	The first 3D grid
[in]	grid2	The second 3D grid
[in]	grid2_voxel_data_threshold	voxels with value lower than threshold in grid2 are not summed (avoid calculating correlation on voxels below the threshold
[in]	allow_padding	determines wheather the two maps should be padded to have the same size before the calcualtion is performed. If set to false and the grids are not of the same size, the function will throw an exception.
[in]	norm_factors	if set these precacluated terms are used for normalization

Returns: the cross correlation coefficient value between two density maps

Note: This is not the local CC function

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

CoarseCC.h

Public Member Functions

Static Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation