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IMP Reference Guide  develop.3e83b1f578,2019/10/15
The Integrative Modeling Platform
IMP::em::CoarseCC Class Reference

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

#include <IMP/em/CoarseCC.h>

+ Inheritance diagram for IMP::em::CoarseCC:

Detailed Description

Responsible for performing coarse fitting between two density objects.

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

Definition at line 28 of file CoarseCC.h.

Public Member Functions

virtual std::string get_type_name () const
 
virtual ::IMP::VersionInfo get_version_info () const
 Get information about the module and version of the object. More...
 
- Public Member Functions inherited from IMP::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)
 

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. More...
 

Additional Inherited Members

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

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

Calculates the value of the EM fitting term.

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]dataDensityMap class containing the EM map. note: correct RMSD and mean MUST be in the header!
[in]model_mapSampledDensityMap class prepared to contain the simulated EM map for the model.
[in]scalefactorscale factor to apply to the value of the cross correlation term
[in]recalc_rmsdetermines whether the RMS of both maps should be recalculated prior to the correlation calculation. False is faster, but potentially inaccurate
[in]resampleif true, the model density map is resampled
[in]norm_factorsif set these precalculated terms are used for normalization
Returns
the value of the cross correlation term: scalefac*(1-ccc)
See Also
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

Calculates the cross correlation coefficient between two maps.

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]grid1The first 3D grid
[in]grid2The second 3D grid
[in]grid2_voxel_data_thresholdvoxels with value lower than threshold in grid2 are not summed (avoid calculating correlation on voxels below the threshold
[in]allow_paddingdetermines whether the two maps should be padded to have the same size before the calculation is performed. If set to false and the grids are not of the same size, the function will throw an exception.
[in]norm_factorsif set these precalculated terms are used for normalization
Returns
the cross correlation coefficient value between two density maps
Note
This is not the local CC function
virtual ::IMP::VersionInfo IMP::em::CoarseCC::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Reimplemented in IMP::em::CoarseCCatIntervals.

Definition at line 120 of file CoarseCC.h.

static float IMP::em::CoarseCC::local_cross_correlation_coefficient ( const DensityMap em_map,
DensityMap model_map,
float  voxel_data_threshold 
)
static

Local cross correlation function.


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