grid_embeddings.h

Go to the documentation of this file.

/**
 *  \file IMP/algebra/grid_embeddings.h
 *  \brief A class to represent a voxel grid.
 *
 *  Copyright 2007-2022 IMP Inventors. All rights reserved.
 *
 */

#ifndef IMPALGEBRA_GRID_EMBEDDINGS_H
#define IMPALGEBRA_GRID_EMBEDDINGS_H

#include <IMP/algebra/algebra_config.h>

#include <IMP/types.h>
#include "grid_indexes.h"
#include "Vector3D.h"
#include "BoundingBoxD.h"
#include <boost/iterator/transform_iterator.hpp>
#include <cereal/access.hpp>
#include <IMP/Vector.h>
#include <IMP/check_macros.h>
#include <IMP/exception.h>

#include <limits>

IMPALGEBRA_BEGIN_NAMESPACE

//! Embed a grid as an evenly spaced axis aligned grid.
template <int D>
class DefaultEmbeddingD {
  VectorD<D> origin_;
  VectorD<D> unit_cell_;
  // inverse
  VectorD<D> inverse_unit_cell_;

  friend class cereal::access;

  template<class Archive> void save(Archive &ar) const {
    ar(origin_, unit_cell_);
  }

  template<class Archive> void load(Archive &ar) {
    ar(origin_, unit_cell_);
    set_unit_cell(unit_cell_);  // sets inverse
  }

  template <class O>
  VectorD<D> get_elementwise_product(VectorD<D> v0, const O &v1) const {
    for (unsigned int i = 0; i < get_dimension(); ++i) {
      v0[i] *= v1[i];
    }
    return v0;
  }
  template <class O>
  VectorD<D> get_uniform_offset(const O &v0, double o) const {
    Floats ret(get_dimension());
    for (unsigned int i = 0; i < get_dimension(); ++i) {
      ret[i] = v0[i] + o;
    }
    return VectorD<D>(ret.begin(), ret.end());
  }
  void initialize_from_box(Ints ns, const BoundingBoxD<D> &bb) {
    Floats nuc(bb.get_dimension());
    for (unsigned int i = 0; i < bb.get_dimension(); ++i) {
      double side = bb.get_corner(1)[i] - bb.get_corner(0)[i];
      IMP_USAGE_CHECK(side > 0, "Can't have flat grid");
      nuc[i] = side / ns[i];
    }
    set_unit_cell(VectorD<D>(nuc.begin(), nuc.end()));
    set_origin(bb.get_corner(0));
  }

 public:
  DefaultEmbeddingD(const VectorD<D> &origin, const VectorD<D> &cell) {
    set_origin(origin);
    set_unit_cell(cell);
  }
  DefaultEmbeddingD() {}
  void set_origin(const VectorD<D> &o) { origin_ = o; }
  const VectorD<D> get_origin() const { return origin_; }
  unsigned int get_dimension() const { return get_origin().get_dimension(); }
  void set_unit_cell(const VectorD<D> &o) {
    unit_cell_ = o;
    Floats iuc(o.get_dimension());
    for (unsigned int i = 0; i < get_dimension(); ++i) {
      iuc[i] = 1.0 / unit_cell_[i];
    }
    inverse_unit_cell_ = VectorD<D>(iuc.begin(), iuc.end());
  }
#ifndef IMP_DOXYGEN
  //! Return the vector (1/u[0], 1/u[1], 1/u[2])
  const VectorD<D> &get_inverse_unit_cell() const { return inverse_unit_cell_; }
#endif
  //! Return the unit cell, relative to the origin.
  /** That is, the unit cell is
      \code
      BoundingBoxD<D>(get_zeros_vector_d<D>(),get_unit_cell());
      \endcode
  */
  const VectorD<D> &get_unit_cell() const { return unit_cell_; }
  //! Return the index that would contain the voxel if the grid extended there
  /** For example vectors below the "lower left" corner of the grid have
      indexes with all negative components. This operation will always
      succeed.
  */
  ExtendedGridIndexD<D> get_extended_index(const VectorD<D> &o) const {
    ExtendedGridIndexD<D> ret(typename ExtendedGridIndexD<D>::Uninitialized(),
                              origin_.get_dimension());
    for (unsigned int i = 0; i < get_dimension(); ++i) {
      double d = o[i] - origin_[i];
      double fi = d * inverse_unit_cell_[i];
      ret.access_data().get_data()[i] = static_cast<int>(std::floor(fi));
    }
    return ret;
  }
  GridIndexD<D> get_index(const VectorD<D> &o) const {
    GridIndexD<D> ret(typename GridIndexD<D>::Uninitialized(),
                      origin_.get_dimension());
    for (unsigned int i = 0; i < get_dimension(); ++i) {
      double d = o[i] - origin_[i];
      double fi = d * inverse_unit_cell_[i];
      ret.access_data().get_data()[i] = static_cast<int>(std::floor(fi));
    }
    return ret;
  }
  /** \name Center
      Return the coordinates of the center of the voxel.
      @{
  */
  VectorD<D> get_center(const ExtendedGridIndexD<D> &ei) const {
    return origin_ +
           get_elementwise_product(get_unit_cell(), get_uniform_offset(ei, .5));
  }
  VectorD<D> get_center(const GridIndexD<D> &ei) const {
    return origin_ +
           get_elementwise_product(get_unit_cell(), get_uniform_offset(ei, .5));
  }
  /** @} */

  /** \name Bounding box
      Return the bounding box of the voxel.
      @{
  */
  BoundingBoxD<D> get_bounding_box(const ExtendedGridIndexD<D> &ei) const {
    return BoundingBoxD<D>(
        origin_ + get_elementwise_product(unit_cell_, ei),
        origin_ +
            get_elementwise_product(unit_cell_, get_uniform_offset(ei, 1)));
  }
  BoundingBoxD<D> get_bounding_box(const GridIndexD<D> &ei) const {
    return BoundingBoxD<D>(
        origin_ + get_elementwise_product(unit_cell_, ei),
        origin_ +
            get_elementwise_product(unit_cell_, get_uniform_offset(ei, 1)));
  }
  /** @} */
  IMP_SHOWABLE_INLINE(DefaultEmbeddingD, out << "origin: " << origin_
                                             << "  unit cell: " << unit_cell_);
};

#if !defined(IMP_DOXYGEN)
typedef DefaultEmbeddingD<1> DefaultEmbedding1D;
typedef Vector<DefaultEmbedding1D> DefaultEmbedding1Ds;

typedef DefaultEmbeddingD<2> DefaultEmbedding2D;
typedef Vector<DefaultEmbedding2D> DefaultEmbedding2Ds;

typedef DefaultEmbeddingD<3> DefaultEmbedding3D;
typedef Vector<DefaultEmbedding3D> DefaultEmbedding3Ds;

typedef DefaultEmbeddingD<4> DefaultEmbedding4D;
typedef Vector<DefaultEmbedding4D> DefaultEmbedding4Ds;

typedef DefaultEmbeddingD<5> DefaultEmbedding5D;
typedef Vector<DefaultEmbedding5D> DefaultEmbedding5Ds;

typedef DefaultEmbeddingD<6> DefaultEmbedding6D;
typedef Vector<DefaultEmbedding6D> DefaultEmbedding6Ds;

typedef DefaultEmbeddingD<-1> DefaultEmbeddingKD;
typedef Vector<DefaultEmbeddingKD> DefaultEmbeddingKDs;
#endif

/** Embedding of a grid as log-evenly spaced axis aligned grid.*/
template <int D>
class LogEmbeddingD {
  VectorD<D> origin_;
  VectorD<D> unit_cell_;
  VectorD<D> base_;

  friend class cereal::access;

  template<class Archive> void serialize(Archive &ar) {
    ar(origin_, unit_cell_, base_);
  }

  template <class O>
  VectorD<D> get_coordinates(const O &index) const {
    VectorD<D> ret = origin_;
    for (unsigned int i = 0; i < unit_cell_.get_dimension(); ++i) {
      IMP_USAGE_CHECK(index[i] >= 0, "Out of range index in log graph.'");
      if (base_[i] != 1) {
        IMP_USAGE_CHECK(index[i] >= 0,
                        "Log grid axis must have positive index.");
        ret[i] += unit_cell_[i] * (1.0 - std::pow(base_[i], index[i])) /
                  (1.0 - base_[i]);
      } else {
        ret[i] += unit_cell_[i] * index[i];
      }
    }
    return ret;
  }
  template <class O>
  VectorD<D> get_uniform_offset(const O &v0, double o) const {
    Floats ret(get_dimension());
    for (unsigned int i = 0; i < get_dimension(); ++i) {
      ret[i] = v0[i] + o;
    }
    return VectorD<D>(ret.begin(), ret.end());
  }
  void initialize_from_box(Ints ns, const BoundingBoxD<D> &bb) {
    Floats nuc(bb.get_dimension());
    for (unsigned int i = 0; i < bb.get_dimension(); ++i) {
      double side = bb.get_corner(1)[i] - bb.get_corner(0)[i];
      IMP_USAGE_CHECK(side > 0, "Can't have flat grid");
      nuc[i] = side / ns[i];
    }
    set_unit_cell(VectorD<D>(nuc.begin(), nuc.end()));
    set_origin(bb.get_corner(0));
  }

 public:
  LogEmbeddingD(const VectorD<D> &origin, const VectorD<D> &cell,
                const VectorD<D> &base) {
    set_origin(origin);
    set_unit_cell(cell, base);
  }
  /** Embedding of a grid as a log-evenly distributed axis-aligned grid
      over the bounding box bb.

      @param bb the bounding box in which the grid is embedded
      @param bases bases[i] is a positive log base used for the grid
                   spacing in dimension i. Set base[i] to 1 in order
                   to create a standard evenly spaced grid along
                   dimension i.
      @param counts counts[i] is the number of discrete points in dimension i
      @param bound_centers if true, then the bounding box tightly bounds
             the centers of the voxels, not their extents.
  */
  LogEmbeddingD(const BoundingBoxD<D> &bb, const VectorD<D> &bases,
                const Ints &counts, bool bound_centers = false) {
    set_origin(bb.get_corner(0));
    VectorD<D> cell = bb.get_corner(0);
    for (unsigned int i = 0; i < bases.get_dimension(); ++i) {
      IMP_ALWAYS_CHECK(bases[i] > 0,
                       "LogEmbedding base #" << i << " cannot be negative",
                       IMP::ValueException);
      // cell[i](1-base[i]^counts[i])/(1-base[i])=width[i]
      if (bases[i] != 1) {
        cell[i] = (bb.get_corner(1)[i] - bb.get_corner(0)[i]) * (bases[i] - 1) /
                  (std::pow(bases[i], counts[i]) - 1.0);
      } else {
        cell[i] = (bb.get_corner(1)[i] - bb.get_corner(0)[i]) / counts[i];
      }
      IMP_INTERNAL_CHECK(
          .9 * cell[i] < bb.get_corner(1)[i] - bb.get_corner(0)[i],
          "Too large a cell side");
      IMP_INTERNAL_CHECK(cell[i] > 0, "Non-positive cell side");
    }
    set_unit_cell(cell, bases);
    if (bound_centers) {
      VectorD<D> lower_corner = get_center(GridIndexD<D>(
          typename GridIndexD<D>::Filled(), bases.get_dimension(), 0));
      VectorD<D> upper_corner = get_coordinates(
          get_uniform_offset(GridIndexD<D>(counts.begin(), counts.end()), -.5));
      VectorD<D> extents = upper_corner - lower_corner;
      VectorD<D> uc = cell;
      VectorD<D> orig = uc;
      for (unsigned int i = 0; i < uc.get_dimension(); ++i) {
        uc[i] =
            (bb.get_corner(1)[i] - bb.get_corner(0)[i]) / extents[i] * uc[i];
        if (base_[i] == 1) {
          orig[i] = bb.get_corner(0)[i] - .5 * uc[i];
        } else {
          /*orig[i]+ uc[i]*(1.0-std::pow(base_[i], index[i]))
            /(1.0-base_[i])==bb[i]*/
          orig[i] = bb.get_corner(0)[i] -
                    uc[i] * (1.0 - std::pow(bases[i], .5)) / (1.0 - bases[i]);
        }
      }
      set_origin(orig);
      set_unit_cell(uc, bases);
    }
  }
  LogEmbeddingD(const VectorD<D> &, const VectorD<D> &) {
    IMP_FAILURE("not supported");
  }
  LogEmbeddingD() {}
  void set_origin(const VectorD<D> &o) { origin_ = o; }
  const VectorD<D> get_origin() const { return origin_; }
  unsigned int get_dimension() const { return get_origin().get_dimension(); }
  void set_unit_cell(const VectorD<D> &o, const VectorD<D> &base) {
    unit_cell_ = o;
    base_ = base;
  }
  void set_unit_cell(const VectorD<D> &o) { unit_cell_ = o; }
  //! Return the unit cell, relative to the origin.
  /** That is, the unit cell is
      \code
      BoundingBoxD<D>(get_zeros_vector_d<D>(),get_unit_cell());
      \endcode
  */
  const VectorD<D> &get_unit_cell() const { return unit_cell_; }
  //! Return the index that would contain the voxel if the grid extended there
  /** For example vectors below the "lower left" corner of the grid have
      indexes with all negative components. This operation will always
      succeed.
  */
  ExtendedGridIndexD<D> get_extended_index(const VectorD<D> &o) const {
    ExtendedGridIndexD<D> ret(typename ExtendedGridIndexD<D>::Uninitialized(),
                              origin_.get_dimension());
    for (unsigned int i = 0; i < get_dimension(); ++i) {
      double d = o[i] - origin_[i];
      // cache everything
      double fi = d / unit_cell_[i];
      double li = std::log(fi) / std::log(base_[i]);
      ret.access_data().get_data()[i] = static_cast<int>(std::floor(li));
    }
    return ret;
  }
  GridIndexD<D> get_index(const VectorD<D> &o) const {
    ExtendedGridIndexD<D> ei = get_extended_index(o);
    return GridIndexD<D>(ei.begin(), ei.end());
  }
  /** \name Center
      Return the coordinates of the center of the voxel.
      @{
  */
  VectorD<D> get_center(const ExtendedGridIndexD<D> &ei) const {
    return get_coordinates(get_uniform_offset(ei, .5));
  }
  VectorD<D> get_center(const GridIndexD<D> &ei) const {
    return get_coordinates(get_uniform_offset(ei, .5));
  }
  /** @} */

  /** \name Bounding box
      Return the bounding box of the voxel.
      @{
  */
  BoundingBoxD<D> get_bounding_box(const ExtendedGridIndexD<D> &ei) const {
    return BoundingBoxD<D>(get_coordinates(ei),
                           get_coordinates(get_uniform_offset(ei, 1)));
  }
  BoundingBoxD<D> get_bounding_box(const GridIndexD<D> &ei) const {
    return get_bounding_box(ExtendedGridIndexD<D>(ei.begin(), ei.end()));
  }
  /** @} */
  IMP_SHOWABLE_INLINE(LogEmbeddingD, out << "origin: " << origin_
                                         << " base: " << base_);
};

#if !defined(IMP_DOXYGEN)
typedef LogEmbeddingD<1> LogEmbedding1D;
typedef Vector<LogEmbedding1D> LogEmbedding1Ds;

typedef LogEmbeddingD<2> LogEmbedding2D;
typedef Vector<LogEmbedding2D> LogEmbedding2Ds;

typedef LogEmbeddingD<3> LogEmbedding3D;
typedef Vector<LogEmbedding3D> LogEmbedding3Ds;

typedef LogEmbeddingD<4> LogEmbedding4D;
typedef Vector<LogEmbedding4D> LogEmbedding4Ds;

typedef LogEmbeddingD<5> LogEmbedding5D;
typedef Vector<LogEmbedding5D> LogEmbedding5Ds;

typedef LogEmbeddingD<6> LogEmbedding6D;
typedef Vector<LogEmbedding6D> LogEmbedding6Ds;

typedef LogEmbeddingD<-1> LogEmbeddingKD;
typedef Vector<LogEmbeddingKD> LogEmbeddingKDs;
#endif

IMPALGEBRA_END_NAMESPACE

#endif /* IMPALGEBRA_GRID_EMBEDDINGS_H */