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CoarseCC.h
Go to the documentation of this file.
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/**
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* \file IMP/em/CoarseCC.h
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* \brief Perform coarse fitting between two density objects.
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*
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* Copyright 2007-2013 IMP Inventors. All rights reserved.
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*
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*/
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#ifndef IMPEM_COARSE_CC_H
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#define IMPEM_COARSE_CC_H
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#include <IMP/em/em_config.h>
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#include "
exp.h
"
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#include "
DensityMap.h
"
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#include "
SampledDensityMap.h
"
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#include "
SurfaceShellDensityMap.h
"
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#include "
def.h
"
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#include <vector>
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#include <
IMP/core/rigid_bodies.h
>
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#include <
IMP/Refiner.h
>
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#include "
masking.h
"
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IMPEM_BEGIN_NAMESPACE
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//! Responsible for performing coarse fitting between two density objects.
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/** The pixels involved are derived from the positions of N particles.
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*/
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class
IMPEMEXPORT
CoarseCC
:
public
IMP::base::Object
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{
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public
:
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CoarseCC
():
Object
(
"CoarseCC%1%"
){}
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//! Calculates the value of the EM fitting term.
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/** \note The function returns scalefac*(1-ccc)
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to support minimization optimization. The ccc value (cross
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correlation coefficient) is calculate by the
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cross_correlation_coefficient function.
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\param[in] data DensityMap class containing the EM map. note:
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correct RMSD and mean MUST be in the header!
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\param[in] model_map SampledDensityMap class prepared to contain the
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simulated EM map for the model.
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\param[in] scalefactor scale factor to apply to the value of the cross
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correlation term
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\param[in] recalc_rms determines wheather the RMS of both maps
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should be recalcualted prior to the correlation calculation.
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False is faster, but potentially innacurate
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\param[in] resample if true, the model density map is resampled
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\param[in] norm_factors if set these precalcualted terms are used
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for normalization
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\return the value of the cross correlation term: scalefac*(1-ccc)
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\relatesalso cross_correlation_coefficient
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*/
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static
float
calc_score(
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DensityMap
*data,
SampledDensityMap
*model_map,
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float
scalefactor,
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bool
recalc_rms=
true
,
bool
resample=
true
,
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FloatPair
norm_factors=
FloatPair
(0.,0.));
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#if !defined(IMP_DOXYGEN) && !defined(SWIG)
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/**
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Computes the derivatives of the cross correlation term scalefac*(1-ccc) at each
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voxel of the map.
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\param[in] em_map the target density map.
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\param[in] model_map the density map of the model
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\param[in] model_ps the particles sampled in model_map
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\param[in] mass_key the key of the mass attribute of the particles
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\param[in] scalefac scale factor to apply to the value of the cross
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correlation term
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\return a vector of derivatives
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\note: The function assumes that correct RMS are calculated for the densities
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*/
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static
algebra::Vector3Ds
calc_derivatives(
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const
DensityMap
*em_map,
const
DensityMap
*model_map,
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const
Particles &model_ps,
const
FloatKey
&mass_key,
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KernelParameters
*kernel_params,
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const
float
&scalefac,
const
algebra::Vector3Ds
&dv);
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#endif
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//!Calculates the cross correlation coefficient between two maps
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/** Cross correlation coefficient between the em density and the density of a
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model. The function applied is:
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\f$\frac{\sum_{i=1}^{N}{{td}_i}{{md}_i}-{N}
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{{mean}_{td}}
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{{mean}_{md}}}
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{N\sigma_{{td}}\sigma_{{md}}}\f$, such that \f$N\f$ is the number of
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voxels, \f${td}\f$ is the target density,
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\f${tm}\f$ is the model density,
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\param[in] grid1 The first 3D grid
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\param[in] grid2 The second 3D grid
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\param[in] grid2_voxel_data_threshold voxels with value lower
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than threshold
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in grid2 are not summed (avoid calculating correlation on
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voxels below the threshold
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\param[in] allow_padding determines wheather the two maps should be padded
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to have the same size before the calcualtion is performed.
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If set to false and the grids are not of the same size,
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the function will throw an exception.
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\param[in] norm_factors if set these precacluated terms are used
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for normalization
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\return the cross correlation coefficient value between two density maps
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\note This is not the local CC function
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\todo check that the mean is always subtracted from the em-density.
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The problem is that we divide by nvox*d1_mean*d2_mean, but if we
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use voxel_data_threshold that does not consist of the entire map
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this would be wrong. Fix it.
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*/
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static
double
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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//! Local cross correlation function
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static
float
local_cross_correlation_coefficient(
const
DensityMap
*em_map,
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DensityMap
*model_map,
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float
voxel_data_threshold);
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IMP_OBJECT_METHODS
(
CoarseCC
);
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};
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IMPEM_END_NAMESPACE
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#endif
/* IMPEM_COARSE_CC_H */