ProjectionMask.h

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/**
 *  \file IMP/em2d/ProjectionMask.h
 *  \brief projection masks
 *  Copyright 2007-2026 IMP Inventors. All rights reserved.
*/

#ifndef IMPEM2D_PROJECTION_MASK_H
#define IMPEM2D_PROJECTION_MASK_H

#include <IMP/em2d/em2d_config.h>
#include "IMP/em2d/Matrix.h"
#include "IMP/atom/Mass.h"
#include "IMP/em/exp.h"
#include "IMP/algebra/Vector3D.h"
#include "IMP/algebra/Vector2D.h"
#include "IMP/algebra/Rotation3D.h"
#include "IMP/algebra/SphericalVector3D.h"
#include "IMP/em/KernelParameters.h"
#include "IMP/core/XYZR.h"
#include "IMP/Particle.h"
#include "IMP/exception.h"
#include <complex>
#include <memory>
#include <cereal/access.hpp>

IMPEM2D_BEGIN_NAMESPACE

class ProjectionMask;
class MasksManager;

typedef std::shared_ptr<ProjectionMask> ProjectionMaskPtr;
typedef std::shared_ptr<MasksManager> MasksManagerPtr;

//! Mask that contains the projection of a given particles. This matrices
//! speed up projecting because the only have to be computed once for a model
class IMPEM2DEXPORT ProjectionMask {
 public:
  ProjectionMask() {}
#if !defined(DOXYGEN) && !defined(SWIG)
  ProjectionMask(const em::KernelParameters& kparams,
                 double voxelsize, double mass = 1.0);

  //! Generates the mask
  /*!
    \param[in] kparams Kernel parameters to employ. See the EM module
    \param[in] mass Mass to give to the mask
  */
  void create(const em::KernelParameters& kparams,
              double mass = 1.0);
#endif

  //! Adds the values of the mask to a matrix at the given pixel
  /*!
    \param[out] m matrix where the values of the mask are added.
    \param[in] v pixel where to apply the values. Currently used as integer.
  */
  void apply(DoubleMatrix &m, const algebra::Vector2D &v);

  void show(std::ostream &out = std::cout) const;

  ~ProjectionMask();

 protected:
  int dim_;              // dimension of the mask
  double sq_pixelsize_;  // Used to save multiplications
  DoubleMatrix data_;         // actual matrix with the mask
private:
  friend class cereal::access;

  template<class Archive> void serialize(Archive &ar) {
    ar(dim_, sq_pixelsize_, data_);
  }
};

IMP_VALUES(ProjectionMask, ProjectionMasks);

IMPEM2D_END_NAMESPACE

namespace cereal {
  template<class Archive> inline void save(
       Archive &ar, const std::map<double,
                               IMP::em2d::ProjectionMaskPtr> &m) {
    size_t sz = m.size();
    ar(sz);
    for (const auto &p : m) {
      ar(p.first);
      ar(*(p.second));
    }
  }

  template<class Archive> inline void load(
       Archive &ar, std::map<double, IMP::em2d::ProjectionMaskPtr> &m) {
    m.clear();
    size_t sz;
    ar(sz);
    for (size_t i = 0; i < sz; ++i) {
      double mass;
      IMP::em2d::ProjectionMaskPtr ptr(new IMP::em2d::ProjectionMask());
      ar(mass);
      ar(*ptr);
      m[mass] = ptr;
    }
  }
}

IMPEM2D_BEGIN_NAMESPACE

// Place a matrix in another
// Very ugly but very fast projecting function

/*!
  \param[in] mask matrix to place in m
  \param[in] m matrix
  \param[in] v Pixel of the matrix dest where the center of m is put.
*/
inline void do_place(DoubleMatrix &mask, DoubleMatrix &m,
                     const algebra::Vector2D &v) {

  // v is the vector of coordinates respect to the center of the matrix m
  int vi = algebra::get_rounded(v[0]);
  int vj = algebra::get_rounded(v[1]);

  // Centers for the matrix
  int center[2];
  center[0] = static_cast<int>(0.5 * m.rows());
  center[1] = static_cast<int>(0.5 * m.cols());

  int start[2], end[2];
  start[0] = -center[0];
  start[1] = -center[1];
  end[0] = m.rows() - 1 - center[0];
  end[1] = m.cols() - 1 - center[1];

  // Check range: If the vector is outside the matrix, don't do anything.
  if (vi < start[0] || vi > end[0]) return;
  if (vj < start[1] || vj > end[1]) return;

  // Centers for the mask
  int mcenter[2];
  mcenter[0] = static_cast<int>(0.5 * mask.rows());
  mcenter[1] = static_cast<int>(0.5 * mask.cols());

  int mstart[2], mend[2];
  mstart[0] = -mcenter[0];
  mstart[1] = -mcenter[1];
  mend[0] = mask.rows() - 1 - mcenter[0];
  mend[1] = mask.cols() - 1 - mcenter[1];

  // Get the admissible range for the mask
  int start_i = std::max(start[0] - vi, mstart[0]);
  int start_j = std::max(start[1] - vj, mstart[1]);
  int end_i = std::min(end[0] - vi, mend[0]);
  int end_j = std::min(end[1] - vj, mend[1]);

  int row = vi + center[0];
  int col = vj + center[1];

  if (end_i < start_i || end_j < start_j) return;
  int n_rows = end_i - start_i + 1, n_cols = end_j - start_j + 1;
  m.block(start_i + row, start_j + col, n_rows, n_cols) +=
      mask.block(start_i + mcenter[0], start_j + mcenter[1], n_rows, n_cols);
}

//! Management of projection masks
class IMPEM2DEXPORT MasksManager {
 public:
  MasksManager() {
    is_setup_ = false;
  };

  MasksManager(double resolution, double pixelsize) {
    setup_kernel(resolution, pixelsize);
  }

  //! Initializes the kernel
  inline void setup_kernel(double resolution, double pixelsize) {
    kernel_params_ = em::KernelParameters((float)resolution);
    pixelsize_ = pixelsize;
    is_setup_ = true;
  }

  //! Generates all the masks for a set of particles. This is the function
  //! you typically want to use
  void create_masks(const ParticlesTemp &ps);

  //! Creates the adequate mask for a particle of given mass
  /*!
    \param[in] mass of the particle
  */
  void create_mask(double mass);

  //! Returns the adequate mask for a particle of given mass
  ProjectionMaskPtr find_mask(double mass);

  void show(std::ostream &out = std::cout) const;

  unsigned int get_number_of_masks() const { return mass2mask_.size(); }

  ~MasksManager();

 protected:
  // A map to store the masks
  std::map<double, ProjectionMaskPtr> mass2mask_;
  // Kernel Params for the particles
  em::KernelParameters kernel_params_;
  // Pixel size for the masks
  double pixelsize_;
  bool is_setup_;

private:
  friend class cereal::access;

  template<class Archive> void serialize(Archive &ar) {
    ar(mass2mask_, kernel_params_, pixelsize_, is_setup_);
  }

};

IMP_VALUES(MasksManager, MasksManagers);

IMPEM2D_END_NAMESPACE

#endif /* IMPEM2D_PROJECTION_MASK_H */