/usr/include/relion-1.3/src/backprojector.h is in librelion-dev-common 1.3+dfsg-2.
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*
* Author: "Sjors H.W. Scheres"
* MRC Laboratory of Molecular Biology
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* This complete copyright notice must be included in any revised version of the
* source code. Additional authorship citations may be added, but existing
* author citations must be preserved.
***************************************************************************/
/*
* backprojector.h
*
* Created on: 24 Aug 2010
* Author: scheres
*/
#ifndef BACKPROJECTOR_H_
#define BACKPROJECTOR_H_
#include "src/projector.h"
#include "src/mask.h"
#include "src/tabfuncs.h"
#include "src/symmetries.h"
class BackProjector: public Projector
{
public:
// For backward projection: sum of weights
MultidimArray<double> weight;
// Tabulated blob values
TabFtBlob tab_ftblob;
// Symmetry object
SymList SL;
public:
/** Empty constructor
*
* A BackProjector is created.
*
* @code
* BackProjector BPref(orisize, 3, "d2");
* @endcode
*/
BackProjector(int _ori_size, int _ref_dim, FileName fn_sym,
int _interpolator = TRILINEAR, int _padding_factor_3d = 2, int _r_min_nn = 10,
int _blob_order = 0, double _blob_radius = 1.9, double _blob_alpha = 15)
{
// Store original dimension
ori_size = _ori_size;
// Set dimensionality of the references
ref_dim = _ref_dim;
// Set the symmetry object
SL.read_sym_file(fn_sym);
// Padding factor for the map
padding_factor = _padding_factor_3d;
// Interpolation scheme
interpolator = _interpolator;
// Minimum radius for NN interpolation
r_min_nn = _r_min_nn;
// Precalculate tabulated ftblob values
tab_ftblob.initialise(_blob_radius * padding_factor, _blob_alpha, _blob_order, 10000);
}
/** Copy constructor
*
* The created BackProjector is a perfect copy of the input array but with a
* different memory assignment.
*
* @code
* BackProjector V2(V1);
* @endcode
*/
BackProjector(const BackProjector& op)
{
clear();
*this = op;
}
/** Assignment.
*
* You can build as complex assignment expressions as you like. Multiple
* assignment is allowed.
*/
BackProjector& operator=(const BackProjector& op)
{
if (&op != this)
{
// Projector stuff (is this necessary in C++?)
data = op.data;
ori_size = op.ori_size;
pad_size = op.pad_size;
r_max = op.r_max;
r_min_nn = op.r_min_nn;
interpolator = op.interpolator;
padding_factor = op.padding_factor;
ref_dim = op.ref_dim;
// BackProjector stuff
weight = op.weight;
tab_ftblob = op.tab_ftblob;
SL = op.SL;
}
return *this;
}
/** Destructor
*
* Clears everything
*
* @code
* FourierInterpolator fourint;
* @endcode
*/
~BackProjector()
{
clear();
}
void clear()
{
weight.clear();
Projector::clear();
}
// Initialise data and weight arrays to the given size and set all values to zero
void initialiseDataAndWeight(int current_size = -1);
// Initialise data and weight arrays to the given size and set all values to zero
void initZeros(int current_size = -1);
/*
* Set a 2D Fourier Transform back into the 2D or 3D data array
* Depending on the dimension of the map, this will be a backprojection or a rotation operation
*/
void set2DFourierTransform(const MultidimArray<Complex > &img_in,
const Matrix2D<double> &A, bool inv,
const MultidimArray<double> *Mweight = NULL)
{
// Back-rotation of a 3D Fourier Transform
switch (ref_dim)
{
case 2:
backrotate2D(img_in, A, inv, Mweight);
break;
case 3:
backproject(img_in, A, inv, Mweight);
break;
default:
REPORT_ERROR("Backprojector::set2DSlice%%ERROR: Dimension of the data array should be 2 or 3");
}
}
/*
* Set an in-plane rotated version of the 2D map into the data array (mere interpolation)
* If a exp_Mweight is given, rather than adding 1 to all relevant pixels in the weight array, we use exp_Mweight
*/
void backrotate2D(const MultidimArray<Complex > &img_in,
const Matrix2D<double> &A, bool inv,
const MultidimArray<double> *Mweight = NULL);
/*
* Set a 2D slice in the 3D map (backward projection)
* If a exp_Mweight is given, rather than adding 1 to all relevant pixels in the weight array, we use exp_Mweight
*/
void backproject(const MultidimArray<Complex > &img_in,
const Matrix2D<double> &A, bool inv,
const MultidimArray<double> *Mweight = NULL);
/*
* Get only the lowest resolution components from the data and weight array
* (to be joined together for two independent halves in order to force convergence in the same orientation)
*/
void getLowResDataAndWeight(MultidimArray<Complex > &lowres_data, MultidimArray<double> &lowres_weight,
int lowres_r_max);
/*
* Set only the lowest resolution components from the data and weight array
* (to be joined together for two independent halves in order to force convergence in the same orientation)
*/
void setLowResDataAndWeight(MultidimArray<Complex > &lowres_data, MultidimArray<double> &lowres_weight,
int lowres_r_max);
/*
* Get complex array at the original size as the straightforward average
* padding_factor*padding_factor*padding_factor voxels
* This will then be used for FSC calculation between two random halves
*/
void getDownsampledAverage(MultidimArray<Complex > &avg);
/*
* From two of the straightforward downsampled averages, calculate an FSC curve
*/
void calculateDownSampledFourierShellCorrelation(MultidimArray<Complex > &avg1,
MultidimArray<Complex > &avg2,
MultidimArray<double> &fsc);
/* Get the 3D reconstruction
* If do_map is true, 1 will be added to all weights
* alpha will contain the noise-reduction spectrum
*/
void reconstruct(MultidimArray<double> &vol_out,
int max_iter_preweight,
bool do_map,
double tau2_fudge,
MultidimArray<double> &tau2,
MultidimArray<double> &sigma2,
MultidimArray<double> &evidence_vs_prior,
MultidimArray<double> fsc,
double normalise = 1.,
bool update_tau2_with_fsc = false,
bool is_whole_instead_of_half = false,
int nr_threads = 1,
int minres_map = -1);
/* Enforce hermitian symmetry on data and on weight (all points in the x==0 plane)
* Because the interpolations are numerical, hermitian symmetry may be broken.
* Repairing it here gives like a 2-fold averaging correction for interpolation errors...
*/
void enforceHermitianSymmetry(MultidimArray<Complex > &mydata,
MultidimArray<double> &myweight);
/* Applies the symmetry from the SymList object to the weight and the data array
*/
void symmetrise(MultidimArray<Complex > &mydata,
MultidimArray<double> &myweight, int my_rmax2);
/* Convolute in Fourier-space with the blob by multiplication in real-space
* Note the convlution is done on the complex array inside the transformer object!!
*/
void convoluteBlobRealSpace(FourierTransformer &transformer, bool do_mask = false);
/* Calculate the inverse FFT of Fin and windows the result to ori_size
* Also pass the transformer, to prevent making and clearing a new one before clearing the one in reconstruct()
*/
void windowToOridimRealSpace(FourierTransformer &transformer, MultidimArray<Complex > &Fin, MultidimArray<double> &Mout, int nr_threads = 1);
/*
* Go from the Projector-centered fourier transform back to FFTW-uncentered one
*/
template <typename T>
void decenter(MultidimArray<T> &Min, MultidimArray<T> &Mout, int my_rmax2)
{
// Mout should already have the right size
// Initialize to zero
Mout.initZeros();
FOR_ALL_ELEMENTS_IN_FFTW_TRANSFORM(Mout)
{
if (kp*kp + ip*ip + jp*jp <= my_rmax2)
DIRECT_A3D_ELEM(Mout, k, i, j) = A3D_ELEM(Min, kp, ip, jp);
}
}
};
#endif /* BACKPROJECTOR_H_ */
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