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IMP Reference Guide  2.13.0
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 2007-2020 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 
25 IMPEM_BEGIN_NAMESPACE
26 
27 //! Calculates and stores Gaussian kernel parameters
28 class IMPEMEXPORT KernelParameters {
29  public:
30  KernelParameters() { initialized_ = false; }
31 
32  KernelParameters(float resolution) {
33  init(resolution);
34  initialized_ = true;
35  }
36 
38 
39  //! Get sigma as a function of the resolution according to the
40  //! full width at half maximum criterion
41  inline float get_rsig() const { return rsig_; }
42 
43  //! Get squared sigma as a function of the resolution according to the
44  //! full width at half maximum criterion
45  inline float get_rsigsq() const { return rsigsq_; }
46 
47  //! Get the inverse of sigma squared
48  inline float get_inv_rsigsq() const { return inv_rsigsq_; }
49 
50  //! Gets the number of sigma used.
51  /**
52  \note We use 3, which means that 99% of the density is considered
53  */
54  inline float get_timessig() const { return timessig_; }
55 
56  //! Get the non-sigma portion of the Gaussian normalization factor
57  inline float get_sq2pi3() const { return sq2pi3_; }
58 
59  //! Get the Gaussian normalization factor
60  inline float get_rnormfac() const { return rnormfac_; }
61 
62  //! Get the length of the Gaussian (sigma*number_of_sigmas_used)
63  inline float get_rkdist() const { return rkdist_; }
64 
65  //! Get the squared length of the Gaussian (sigma*number_of_sigmas_used)
66  inline float get_rkdistsq() const { return rkdistsq_; }
67 
68  //! Gets the value of lim parameter
69  inline float get_lim() const { return lim_; }
70 
71 #if !defined(SWIG) && !defined(IMP_DOXYGEN)
72  //! Get radius dependent kernel parameters
73  /**
74  \param[in] radius searching for parameters of this radius
75  \param[in] eps tolerance around radius to search for
76  \note cached values are used if available for radius +/- eps
77  */
78  const internal::RadiusDependentKernelParameters& get_params(float radius,
79  float eps = 0.001);
80 #endif
81 
82  IMP_SHOWABLE_INLINE(KernelParameters, out << "rsig: " << rsig_ << std::endl;);
83 
84  protected:
85  float timessig_; // 3.0 is used by default
86  float rsig_, rsigsq_, inv_rsigsq_; // resolution dependent sigma
87  float sq2pi3_, rnormfac_;
88  float rkdist_, rkdistsq_, lim_;
89  bool initialized_;
90  typedef std::map<float, const internal::RadiusDependentKernelParameters *>
91  KernelMap;
92  KernelMap radii2params_;
93 
94  void init(float resolution);
95 };
96 
98 
99 #if !defined(IMP_DOXYGEN) && !defined(SWIG)
100 class IMPEMEXPORT Kernel3D {
101  public:
102  Kernel3D() {}
103  Kernel3D(const Kernel3D& other) {
104  size_ = other.size_;
105  dim_ext_ = other.dim_ext_;
106  data_.reset(new double[size_]);
107  std::copy(other.data_.get(), other.data_.get() + size_, data_.get());
108  }
109  Kernel3D(int size, int ext) {
110  size_ = size;
111  dim_ext_ = ext;
112  data_.reset(new double[size_]);
113  IMP_INTERNAL_CHECK(data_, "Can not allocate vector\n");
114  for (int i = 0; i < size_; i++) data_[i] = 0.;
115  }
116  double* get_data() const { return data_.get(); }
117  int get_size() const { return size_; }
118  int get_extent() const { return dim_ext_; }
119 
120  protected:
121  boost::scoped_array<double> data_;
122  int size_;
123  int dim_ext_;
124 };
125 IMPEMEXPORT
126 Kernel3D create_3d_gaussian(double sigma, double sigma_factor);
127 IMPEMEXPORT
128 Kernel3D create_3d_laplacian();
129 //! Truncate a kernel according to an input sigma
130 IMPEMEXPORT
131 Kernel3D get_truncated(double* data, int extent, double sigmap,
132  double sigma_fac);
133 #endif
134 IMPEM_END_NAMESPACE
135 
136 #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:39
#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.