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:Static Public Member Functions | |
| 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. | |
Related Functions | |
(Note that these are not 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... | |
| Related Functions inherited from IMP::base::Object | |
| typedef IMP::base::Vector < IMP::base::WeakPointer < Object > > | ObjectsTemp |
Additional Inherited Members | |
| 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 inherited from IMP::base::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
Detailed Description
The pixels involved are derived from the positions of N particles.
Definition at line 28 of file CoarseCC.h.
Member Function Documentation
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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
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[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
Friends And Related Function Documentation
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related |
- 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
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[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)
The documentation for this class was generated from the following file: