IMP  2.2.1
The Integrative Modeling Platform
ProjectionMask.h
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1 /**
2  * \file IMP/em2d/ProjectionMask.h
3  * \brief projection masks
4  * Copyright 2007-2014 IMP Inventors. All rights reserved.
5 */
6 
7 #ifndef IMPEM2D_PROJECTION_MASK_H
8 #define IMPEM2D_PROJECTION_MASK_H
9 
10 #include "IMP/em2d/em2d_config.h"
12 #include "IMP/em2d/CenteredMat.h"
13 #include "IMP/atom/Mass.h"
14 #include "IMP/em/exp.h"
15 #include "IMP/algebra/Vector3D.h"
16 #include "IMP/algebra/Vector2D.h"
17 #include "IMP/algebra/Rotation3D.h"
20 #include "IMP/core/XYZR.h"
21 #include "IMP/Particle.h"
22 #include "IMP/base/exception.h"
23 #include <complex>
24 #include <boost/shared_ptr.hpp>
25 
26 IMPEM2D_BEGIN_NAMESPACE
27 
28 class ProjectionMask;
29 class MasksManager;
30 
31 typedef boost::shared_ptr<ProjectionMask> ProjectionMaskPtr;
32 typedef boost::shared_ptr<MasksManager> MasksManagerPtr;
33 
34 //! Mask that contains the projection of a given particles. This matrices
35 //! speed up projecting because the only have to be computed once for a model
36 class IMPEM2DEXPORT ProjectionMask {
37 #ifdef SWIG
38  ProjectionMask() {}
39 #endif
40  public:
41 #if !defined(DOXYGEN) && !defined(SWIG)
44  double voxelsize, double mass = 1.0);
45 
46  //! Generates the mask
47  /*!
48  \param[in] KP Kernel parameteres to employ. See the EM module
49  \param[in] params Kernel parameteres associated with radius to employ
50  \param[in] mass Mass to give to the mask
51  */
52  void create(const em::KernelParameters &KP,
54  double mass = 1.0);
55 #endif
56 
57  //! Adds the values of the mask to a matrix at the given pixel
58  /*!
59  \param[out] m matrix where the values of the mask are added.
60  \param[in] v pixel where to apply the values. Currently used as integer.
61  */
62  void apply(cv::Mat &m, const algebra::Vector2D &v);
63 
64  void show(std::ostream &out = std::cout) const;
65 
66  ~ProjectionMask();
67 
68  protected:
69  int dim_; // dimension of the mask
70  double sq_pixelsize_; // Used to save multiplications
71  cv::Mat data_; // actual matrix with the mask
72 };
73 
75 
76 // Place a matrix in another
77 // Very ugly but very fast projecting function
78 
79 /*!
80  \param[in] mask matrix to place in m
81  \param[in] m matrix
82  \param[in] v Pixel of the matrix dest where the center of m is put.
83 */
84 inline void do_place(cv::Mat &mask, cv::Mat &m, const algebra::Vector2D &v) {
85 
86  // v is the vector of coordinates respect to the center of the matrix m
87  int vi = algebra::get_rounded(v[0]);
88  int vj = algebra::get_rounded(v[1]);
89 
90  // Centers for the matrix
91  int center[2];
92  center[0] = static_cast<int>(0.5 * m.rows);
93  center[1] = static_cast<int>(0.5 * m.cols);
94 
95  int start[2], end[2];
96  start[0] = -center[0];
97  start[1] = -center[1];
98  end[0] = m.rows - 1 - center[0];
99  end[1] = m.cols - 1 - center[1];
100 
101  // Check range: If the vector is outside the matrix, don't do anything.
102  if (vi < start[0] || vi > end[0]) return;
103  if (vj < start[1] || vj > end[1]) return;
104 
105  // Centers for the mask
106  int mcenter[2];
107  mcenter[0] = static_cast<int>(0.5 * mask.rows);
108  mcenter[1] = static_cast<int>(0.5 * mask.cols);
109 
110  int mstart[2], mend[2];
111  mstart[0] = -mcenter[0];
112  mstart[1] = -mcenter[1];
113  mend[0] = mask.rows - 1 - mcenter[0];
114  mend[1] = mask.cols - 1 - mcenter[1];
115 
116  // Get the admisible range for the mask
117  int start_i = std::max(start[0] - vi, mstart[0]);
118  int start_j = std::max(start[1] - vj, mstart[1]);
119  int end_i = std::min(end[0] - vi, mend[0]);
120  int end_j = std::min(end[1] - vj, mend[1]);
121 
122  int row = vi + center[0];
123  int col = vj + center[1];
124 
125  for (int i = start_i; i <= end_i; ++i) {
126  int p = i + row;
127  for (int j = start_j; j <= end_j; ++j) {
128  m.at<double>(p, j + col) +=
129  mask.at<double>(i + mcenter[0], j + mcenter[1]);
130  }
131  }
132 }
133 
134 //! Manage of projection masks
135 class IMPEM2DEXPORT MasksManager {
136  public:
137  MasksManager() {
138  is_setup_ = false;
139  };
140 
141  MasksManager(double resolution, double pixelsize) {
142  setup_kernel(resolution, pixelsize);
143  }
144 
145  //! Initializes the kernel
146  inline void setup_kernel(double resolution, double pixelsize) {
147  kernel_params_ = em::KernelParameters((float)resolution);
148  pixelsize_ = pixelsize;
149  is_setup_ = true;
150  }
151 
152  //! Generates all the masks for a set of particles. This is the function
153  //! you typically want to use
154  void create_masks(const kernel::ParticlesTemp &ps);
155 
156  //! Creates the adequate mask for a particle of given radius
157  /*!
158  \param[in] radius of the particle
159  \param[in] mass of the particle
160  */
161  void create_mask(double radius, double mass);
162 
163  //! Returns the adequate mask for a particle of given radius
164  ProjectionMaskPtr find_mask(double radius);
165 
166  void show(std::ostream &out = std::cout) const;
167 
168  unsigned int get_number_of_masks() const { return radii2mask_.size(); }
169 
170  ~MasksManager();
171 
172  protected:
173  // A map to store the masks
174  std::map<double, ProjectionMaskPtr> radii2mask_;
175  // Kernel Params for the particles
176  em::KernelParameters kernel_params_;
177  // Pixel size for the masks
178  double pixelsize_;
179  bool is_setup_;
180 };
181 
183 
184 IMPEM2D_END_NAMESPACE
185 
186 #endif /* IMPEM2D_PROJECTION_MASK_H */
A decorator for particles with mass.
VectorD< 2 > Vector2D
Definition: VectorD.h:391
Calculates kernel parameters as a function of a specific radius.
void setup_kernel(double resolution, double pixelsize)
Initializes the kernel.
Simple 2D vector class.
#define IMP_VALUES(Name, PluralName)
Define the type for storing sets of values.
Calculates and stores gaussian kernel parameters.
inteface with OpenCV Copyright 2007-2014 IMP Inventors. All rights reserved.
An approximation of the exponential function.
int get_rounded(const T &x)
Rounds a number to next integer.
Stores and converts spherical coordinates.
Simple 3D rotation class.
Exception definitions and assertions.
Import IMP/kernel/Particle.h in the namespace.
void show(Hierarchy h, std::ostream &out=std::cout)
Print out a molecular hierarchy.
Simple 3D vector class.
void do_place(cv::Mat &mask, cv::Mat &m, const algebra::Vector2D &v)
Decorator for a sphere-like particle.
Manage of projection masks.
Decorator for OpenCV matrix to use relative coordinates Copyright 2007-2014 IMP Inventors. All rights reserved.