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SampledDensityMap.h

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/**
 *  \file SampledDensityMap.h
 *  \brief Sampled density map.
 *
 *  Copyright 2007-2010 IMP Inventors. All rights reserved.
 *
 */

#ifndef IMPEM_SAMPLED_DENSITY_MAP_H
#define IMPEM_SAMPLED_DENSITY_MAP_H

#include "em_config.h"
#include "exp.h"
#include "DensityMap.h"
#include "DensityHeader.h"
#include "def.h"
#include "KernelParameters.h"
#include <vector>
#include "IMP/base_types.h"
#include "IMP/core/XYZR.h"
#include "IMP/atom/Mass.h"
IMPEM_BEGIN_NAMESPACE

// an advantage of using const double over define is that it limits the use
// of pointers to affect the data:
//#define PI 3.141592653589793238462643383
//define could be manipulated with a const *int ptr declaration.


//! Class for sampling a density map from particles
class IMPEMEXPORT SampledDensityMap: public DensityMap
{

public:


  //! Creates a new density map for sampled map.
  /** The header of the map is not determined and no data is being allocated
   */
  SampledDensityMap() {
  }

  //! The size of the map is determined by the header and the data is allocated.
  SampledDensityMap(const DensityHeader &header);

  //! Generatea a sampled density map from the particles.
  /** /param[in] ps     particles with XYZ, radius and weight attributes
      /param[in] resolution   half width the Gaussian
      /param[in] voxel_size
      /param[in] sig_cutoff   Choose what should be the sigma cutoff for
                 accurate sampling. It is used in two functions;
                 (i)  to determine the size of the grid dimensions
                 (ii) to determine the voxels around the coords participating
                      in the sampling procedure.
   */
  SampledDensityMap(const Particles &ps, emreal resolution,
   emreal voxel_size,
   IMP::FloatKey radius_key=IMP::core::XYZR::get_default_radius_key(),
   IMP::FloatKey mass_key=IMP::atom::Mass::get_mass_key(),
   int sig_cuttoff=3);

  //! Resampling beads on an EM grid
  /**
  \note The density of a particle p centered at pl at position gl is:
  \f$\frac{{Z}e^{\frac{{-0.5}({p_l}-{g_l})}{\sigma}}}{\sqrt{{2}{\pi}\sigma}}\f$
    , such that \f${Z}\f$ is the weight of the particle and \f${\sigma}\f$
      is defined to be \f${0.425}\f$ times the resolution,
      to follow the 'full width at half maxima'
      criterion. For more details please refer to Topf et al, Structure, 2008.
   */
  virtual void resample();

  //!setting particles in case they were not set by the constructor
  void set_particles(IMP::Particles &ps,
     IMP::FloatKey radius_key = IMP::core::XYZR::get_default_radius_key(),
     IMP::FloatKey mass_key = IMP::atom::Mass::get_mass_key());
  void calc_sampling_bounding_box(const emreal &x,const emreal &y,
                                  const emreal &z,
                                  const emreal &kdist,
                                  int &iminx,int &iminy, int &iminz,
                                  int &imaxx,int &imaxy, int &imaxz) const;

  KernelParameters *get_kernel_params()  { return &kernel_params_;}


  inline const core::XYZRs & get_xyzr_particles() const {return xyzr_;}
 // would go away on§ce we have a XYZRW decorator and the next function as well
  inline const Particles & get_sampled_particles() const {return ps_;}
  inline FloatKey  get_weight_key() const {return weight_key_;}
  inline FloatKey  get_radius_key() const {return radius_key_;}


  IMP_REF_COUNTED_DESTRUCTOR(SampledDensityMap);
protected:
  //! Calculate the parameters of the particles bounding box
  /** \param[in] ps particles with XYZ, radius and weight attributes
      \return the particles bounding box
   */
  IMP::algebra::BoundingBoxD<3>
     calculate_particles_bounding_box(const Particles &ps);
  void set_header(const algebra::VectorD<3> &lower_bound,
                  const algebra::VectorD<3> &upper_bound,
                  emreal maxradius, emreal resolution, emreal voxel_size,
                  int sig_offset);

  //bookkeeping functions
  int lower_voxel_shift(const emreal &loc, const emreal &kdist,
                        const emreal &orig, int ndim) const {
    int imin;
    imin = static_cast<int>(std::floor((loc-kdist-orig)
                                        / header_.get_spacing()));
    //bookkeeping
    if (imin < 0)
      imin = 0;
    if (imin > ndim-1)
      imin = ndim-1;
    return imin;
  }


  int upper_voxel_shift(const emreal &loc, const emreal &kdist,
                        const emreal &orig, int ndim) const {
    int imax;
    imax = static_cast<int>(std::floor((loc+kdist-orig)
                                        / header_.get_spacing()));
    //bookkeeping
    if (imax < 0) imax = 0;
    if (imax > ndim-1) imax = ndim-1;
    return imax;
  }
protected:
  //! kernel handling
  KernelParameters kernel_params_;
  Particles ps_;
  core::XYZRs xyzr_; //each voxel decorator would contain X,Y,Z,R
  // std::vector<atom::Mass> weight_;
  FloatKey weight_key_;
  FloatKey radius_key_;
  FloatKey x_key_,y_key_,z_key_;
};

IMPEM_END_NAMESPACE

#endif  /* IMPEM_SAMPLED_DENSITY_MAP_H */

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