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IMP Reference Guide  develop.8b7eb21230,2024/06/24
The Integrative Modeling Platform
CollisionCrossSection.h
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1 /**
2  * \file IMP/em2d/CollisionCrossSection.h
3  * \brief
4  *
5  * Copyright 2007-2022 IMP Inventors. All rights reserved.
6  *
7  */
8 
9 #ifndef IMPEM2D_COLLISION_CROSS_SECTION_H
10 #define IMPEM2D_COLLISION_CROSS_SECTION_H
11 
14 #include "IMP/em2d/project.h"
15 #include "IMP/macros.h"
16 #include "IMP/Particle.h"
17 
18 IMPEM2D_BEGIN_NAMESPACE
19 
20 //! Determine the collision cross section for some projections of particles
21 class IMPEM2DEXPORT CollisionCrossSection : public IMP::Object {
22  public:
23  /*!
24  \param[in] n_projections Number of projections to use for obtaining the CCS
25  \param[in] resolution "Resolution" to use to generate the projections.
26  \param[in] pixel_size size in A/pix to use when generating the projections
27  \param[in] projection_image_size The size of the projections to generate;
28  for this value you should request a size so that
29  pixel_size * projection_image_size >= Max distance between two
30  particles.
31  */
32  CollisionCrossSection(unsigned int n_projections, double resolution,
33  double pixel_size, double projection_image_size);
34 
35  /**
36  * Particles used to calculate their collision cross section
37  * @param ps The particles
38  */
39  void set_model_particles(const ParticlesTemp &ps);
40 
41  //! Returns the collision cross section.
42  /** Before using this function you need
43  to set the particles with set_model_particles()
44  @return The collision cross section
45  */
46  double get_ccs() const;
47 
48  //! Shows information about the class
49  /** @param out Stream used to show the information
50  */
51  void show(std::ostream &out) const {
52  out << "Collision Cross section." << std::endl;
53  }
55 
56  protected:
57  //! Gets the sum of the values in the pixels with value > 0
58  /** \param[in] m The projected area is computed for this matrix
59  \return Values of the area
60  */
61  double get_projected_area(const cv::Mat &m) const;
62 
63  unsigned int n_projections_;
64  double resolution_;
65  double pixel_size_;
66  unsigned int img_size_;
67  bool particles_set_;
69  cv::Mat average_projection_;
70  em2d::MasksManagerPtr masks_manager_;
71  double collision_cross_section_;
72 };
74 
75 IMPEM2D_END_NAMESPACE
76 
77 #endif /* IMPEM2D_COLLISION_CROSS_SECTION_H */
Generation of projections from models or density maps Copyright 2007-2022 IMP Inventors. All rights reserved.
projection masks Copyright 2007-2023 IMP Inventors. All rights reserved.
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
Definition: object_macros.h:25
void show(std::ostream &out) const
Shows information about the class.
Various general useful macros for IMP.
Common base class for heavy weight IMP objects.
Definition: Object.h:111
Classes to handle individual model particles. (Note that implementation of inline functions is in int...
#define IMP_OBJECTS(Name, PluralName)
Define the types for storing lists of object pointers.
Definition: object_macros.h:44
Determine the collision cross section for some projections of particles.
Registration results class Copyright 2007-2022 IMP Inventors. All rights reserved.