Responsible for performing coarse fitting between two density objects.
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#include <IMP/em/CoarseCC.h>
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| 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...
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| 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...
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static float | local_cross_correlation_coefficient (const DensityMap *em_map, DensityMap *model_map, float voxel_data_threshold) |
| | Local cross correlation function.
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| | Object (std::string name) |
| | Construct an object with the given name. More...
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The pixels involved are derived from the positions of N particles.
Definition at line 28 of file CoarseCC.h.
- 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) See cross_correlation_coefficient
| static double IMP::em::CoarseCC::cross_correlation_coefficient |
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const DensityMap * |
grid1, |
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const DensityMap * |
grid2, |
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float |
grid2_voxel_data_threshold, |
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bool |
allow_padding = false, |
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FloatPair |
norm_factors = FloatPair(0., 0.) |
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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
The documentation for this class was generated from the following file:
Inheritance diagram for IMP::em::CoarseCC: