IMP  2.1.1
The Integrative Modeling Platform
DensityDataPoints.h
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1 /**
2  * \file IMP/multifit/DensityDataPoints.h
3  * \brief Handling of data for anchor points segmentation
4  *
5  * Copyright 2007-2013 IMP Inventors. All rights reserved.
6  *
7  */
8 
9 #ifndef IMPMULTIFIT_DENSITY_DATA_POINTS_H
10 #define IMPMULTIFIT_DENSITY_DATA_POINTS_H
11 
12 #include <IMP/base_types.h>
13 #include <IMP/kernel/Particle.h>
14 #include <IMP/algebra/standard_grids.h>
15 #include <IMP/statistics/internal/random_generator.h>
16 #include <IMP/statistics/internal/DataPoints.h>
17 #include <IMP/em/converters.h>
18 #include <IMP/em/DensityMap.h>
19 #include <IMP/algebra/Vector3D.h>
20 #include <IMP/algebra/internal/tnt_array2d.h>
21 #include <IMP/algebra/internal/tnt_array2d_utils.h>
22 #include <IMP/atom/Hierarchy.h>
23 #include <boost/scoped_ptr.hpp>
24 #include <IMP/multifit/multifit_config.h>
25 #include <map>
26 
27 IMPMULTIFIT_BEGIN_NAMESPACE
28 typedef IMP::algebra::DenseGrid3D<double> DensGrid;
29 
30 IMPMULTIFITEXPORT
31 em::DensityMap *grid2map(const DensGrid &dg,float spacing);
32 
33 
34 //! Stores density voxels as a vector of Array1D.
35 /**
36 \note This manipulation is needed for matrix operations.
37  */
38 class IMPMULTIFITEXPORT DensityDataPoints
39  : public IMP::statistics::internal::XYZDataPoints
40 {
41  public:
42  DensityDataPoints(em::DensityMap *dens,
43  float density_threshold);
44  DensityDataPoints(const DensGrid &dens,
45  float density_threshold);
46  IMP::statistics::internal::Array1DD sample() const;
47 
48  // em::DensityMap* get_density_map() const {return dens_;}
49 
50  IMP_OBJECT_METHODS(DensityDataPoints);
51  protected:
52  void populate_data();
53  void set_max_min_density_values();
54  void set_density(em::DensityMap *d);
55  void set_density(const DensGrid &dens);
56  //TODO - change back once DensityMap will be Grid3D
57  //Pointer<DensGrid> dens_; /// TODO - make the class an object
58  boost::scoped_ptr<DensGrid> dens_;
59  // em::DensityMap *dens_;
60  double max_value_,min_value_;
61  double threshold_;
62 };
63 IMP_OBJECTS(DensityDataPoints, DensityDataPointsList);
64 
65 IMPMULTIFIT_END_NAMESPACE
66 
67 #endif /* IMPMULTIFIT_DENSITY_DATA_POINTS_H */
base_types.h
Import IMP/kernel/base_types.h in the namespace.
converters.h
Converters of density values.
DensityMap.h
Class for handling density maps.
Hierarchy.h
Decorator for helping deal with a hierarchy of molecules.
IMP::em::DensityMap
Class for handling density maps.
Definition: DensityMap.h:98
IMP_OBJECT_METHODS
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
Definition: base/object_macros.h:25
IMP::multifit::DensityDataPoints
Stores density voxels as a vector of Array1D.
Definition: DensityDataPoints.h:38
Particle.h
Classes to handle individual model particles.
IMP_OBJECTS
#define IMP_OBJECTS(Name, PluralName)
Define the types for storing sets of objects.
Definition: base/object_macros.h:77
Vector3D.h
Simple 3D vector class.
standard_grids.h
A class to represent a voxel grid.