/**
 * \file EnvelopeScore.h
 * \brief class for envelope based scoring using MapDistanceTransform
 *
 * Copyright 2007-2013 IMP Inventors. All rights reserved.
 *
 */

#ifndef IMPEM_ENVELOPE_SCORE_H
#define IMPEM_ENVELOPE_SCORE_H

#include <IMP/em/em_config.h>
#include <IMP/em/MapDistanceTransform.h>
#include <IMP/base/Object.h>

#include <vector>

IMPEM_BEGIN_NAMESPACE

//! class for envelope based scoring using MapDistanceTransform
class IMPEMEXPORT EnvelopeScore : public IMP::base::Object {
public:
  // init with MapDistanceTransform
  EnvelopeScore(const MapDistanceTransform* mdt);

  /** check for penetration with respect to the envelope as defined
      by the distance transform
      \param [in] points - check this set of points for penetration
      \param [in] penetration_thr - threshold that defines penetration
      use penetration_thr=0 to require for all points inside the envelope
      to allow some penetration set the threshold to the -distance of
      the allowed penetration distance. Recommended value is map
      resolution.
  */
  bool is_penetrating(const std::vector<IMP::algebra::Vector3D>& points,
                      float penetration_thr) const;

  /** same as above
      \param [in] trans - apply this transformation on points before
      checking for penetrations
  */
  bool is_penetrating(const std::vector<IMP::algebra::Vector3D>& points,
                      const IMP::algebra::Transformation3D& trans,
                      float penetration_thr) const;

  /**
      score points with respect to the distance transform
      the score awards points that fall into the envelope
      and penalizes for points outside the envelope
  */
  double score(const std::vector<IMP::algebra::Vector3D>& points) const;

  /** same as above
      \param [in] trans - apply this transformation on points before scoring
  */
  double score(const std::vector<IMP::algebra::Vector3D>& points,
            const IMP::algebra::Transformation3D& trans) const;

  // methods required by Object
  IMP::base::VersionInfo get_version_info() const {
    return IMP::base::VersionInfo(get_module_name(), get_module_version());
  }

  ~EnvelopeScore() {}

 private:
  unsigned int find_range(float distance) const {
    for(unsigned int i=0; i< ranges_.size(); i++)
      if(distance <= ranges_[i]) return i;
    return ranges_.size();
  }

 private:
  const MapDistanceTransform* mdt_;
  std::vector<float> ranges_;
  std::vector<int> weights_;
  std::vector<long> inner_voxels_;
  std::vector<long> neighbors_;
};

IMPEM_END_NAMESPACE

#endif /* IMPEM_ENVELOPE_SCORE_H */