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IMP Reference Guide  2.20.2
The Integrative Modeling Platform
KernelParameters.h
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1 /**
2  * \file IMP/em/KernelParameters.h
3  * \brief Calculates and stores Gaussian kernel parameters.
4  *
5  * Copyright 2007-2022 IMP Inventors. All rights reserved.
6  *
7  */
8 
9 #ifndef IMPEM_KERNEL_PARAMETERS_H
10 #define IMPEM_KERNEL_PARAMETERS_H
11 #include "def.h"
12 #include <IMP/base_types.h>
13 #include <boost/scoped_array.hpp>
14 #include <IMP/exception.h>
15 #include <IMP/log.h>
16 #include <map>
17 #include <cmath>
18 #include <algorithm>
19 #include <iostream>
20 #include <iomanip>
21 #include <vector>
22 #include <limits>
23 #include <IMP/em/internal/RadiusDependentKernelParameters.h>
24 #include <cereal/access.hpp>
25 
26 IMPEM_BEGIN_NAMESPACE
27 
28 //! Calculates and stores Gaussian kernel parameters
29 class IMPEMEXPORT KernelParameters {
30  public:
31  KernelParameters() { initialized_ = false; }
32 
33  KernelParameters(float resolution) {
34  init(resolution);
35  initialized_ = true;
36  }
37 
39 
40  //! Get sigma as a function of the resolution according to the
41  //! full width at half maximum criterion
42  inline float get_rsig() const { return rsig_; }
43 
44  //! Get squared sigma as a function of the resolution according to the
45  //! full width at half maximum criterion
46  inline float get_rsigsq() const { return rsigsq_; }
47 
48  //! Get the inverse of sigma squared
49  inline float get_inv_rsigsq() const { return inv_rsigsq_; }
50 
51  //! Gets the number of sigma used.
52  /**
53  \note We use 3, which means that 99% of the density is considered
54  */
55  inline float get_timessig() const { return timessig_; }
56 
57  //! Get the non-sigma portion of the Gaussian normalization factor
58  inline float get_sq2pi3() const { return sq2pi3_; }
59 
60  //! Get the Gaussian normalization factor
61  inline float get_rnormfac() const { return rnormfac_; }
62 
63  //! Get the length of the Gaussian (sigma*number_of_sigmas_used)
64  inline float get_rkdist() const { return rkdist_; }
65 
66  //! Get the squared length of the Gaussian (sigma*number_of_sigmas_used)
67  inline float get_rkdistsq() const { return rkdistsq_; }
68 
69  //! Gets the value of lim parameter
70  inline float get_lim() const { return lim_; }
71 
72 #if !defined(SWIG) && !defined(IMP_DOXYGEN)
73  //! Get radius dependent kernel parameters
74  /**
75  \param[in] radius searching for parameters of this radius
76  \param[in] eps tolerance around radius to search for
77  \note cached values are used if available for radius +/- eps
78  */
79  const internal::RadiusDependentKernelParameters& get_params(float radius,
80  float eps = 0.001);
81 #endif
82 
83  IMP_SHOWABLE_INLINE(KernelParameters, out << "rsig: " << rsig_ << std::endl;);
84 
85  protected:
86  float resolution_;
87  float timessig_; // 3.0 is used by default
88  float rsig_, rsigsq_, inv_rsigsq_; // resolution dependent sigma
89  float sq2pi3_, rnormfac_;
90  float rkdist_, rkdistsq_, lim_;
91  bool initialized_;
92  typedef std::map<float, const internal::RadiusDependentKernelParameters *>
93  KernelMap;
94  KernelMap radii2params_;
95 
96  void init(float resolution);
97 
98  friend class cereal::access;
99 
100  template<class Archive> void save(Archive &ar) const {
101  ar(resolution_);
102  }
103 
104  template<class Archive> void load(Archive &ar) {
105  float resolution;
106  ar(resolution);
107  init(resolution);
108  initialized_ = true;
109  }
110 
111 };
112 
114 
115 #if !defined(IMP_DOXYGEN) && !defined(SWIG)
116 class IMPEMEXPORT Kernel3D {
117  public:
118  Kernel3D() {}
119  Kernel3D(const Kernel3D& other) {
120  size_ = other.size_;
121  dim_ext_ = other.dim_ext_;
122  data_.reset(new double[size_]);
123  std::copy(other.data_.get(), other.data_.get() + size_, data_.get());
124  }
125  Kernel3D(int size, int ext) {
126  size_ = size;
127  dim_ext_ = ext;
128  data_.reset(new double[size_]);
129  IMP_INTERNAL_CHECK(data_, "Can not allocate vector\n");
130  for (int i = 0; i < size_; i++) data_[i] = 0.;
131  }
132  double* get_data() const { return data_.get(); }
133  int get_size() const { return size_; }
134  int get_extent() const { return dim_ext_; }
135 
136  protected:
137  boost::scoped_array<double> data_;
138  int size_;
139  int dim_ext_;
140 };
141 IMPEMEXPORT
142 Kernel3D create_3d_gaussian(double sigma, double sigma_factor);
143 IMPEMEXPORT
144 Kernel3D create_3d_laplacian();
145 //! Truncate a kernel according to an input sigma
146 IMPEMEXPORT
147 Kernel3D get_truncated(double* data, int extent, double sigmap,
148  double sigma_fac);
149 #endif
150 IMPEM_END_NAMESPACE
151 
152 #endif /* IMPEM_KERNEL_PARAMETERS_H */
Basic types used by IMP.
#define IMP_SHOWABLE_INLINE(Name, how_to_show)
Declare the methods needed by an object that can be printed.
float get_rnormfac() const
Get the Gaussian normalization factor.
Definitions for EMBED.
Calculates and stores Gaussian kernel parameters.
Exception definitions and assertions.
A more IMP-like version of the std::vector.
Definition: Vector.h:42
#define IMP_INTERNAL_CHECK(expr, message)
An assertion to check for internal errors in IMP. An IMP::ErrorException will be thrown.
Definition: check_macros.h:139
#define IMP_VALUES(Name, PluralName)
Define the type for storing sets of values.
Definition: value_macros.h:23
float get_rkdist() const
Get the length of the Gaussian (sigma*number_of_sigmas_used)
float get_lim() const
Gets the value of lim parameter.
float get_rkdistsq() const
Get the squared length of the Gaussian (sigma*number_of_sigmas_used)
float get_sq2pi3() const
Get the non-sigma portion of the Gaussian normalization factor.
float get_inv_rsigsq() const
Get the inverse of sigma squared.
float get_timessig() const
Gets the number of sigma used.
Logging and error reporting support.