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35 /*! \libinternal \file
37 * Declares density similarity measures and their derivatives.
39 * \author Christian Blau <blau@kth.se>
41 * \ingroup module_math
43 #ifndef GMX_MATH_DENSITYFIT_H
44 #define GMX_MATH_DENSITYFIT_H
46 #include "gromacs/mdspan/extensions.h"
47 #include "gromacs/utility/classhelpers.h"
48 #include "gromacs/utility/enumerationhelpers.h"
49 #include "gromacs/utility/real.h"
54 * The methods that determine how two densities are compared to one another.
56 enum class DensitySimilarityMeasureMethod
58 /*! \brief Measure similarity between densities as normalized inner product of their
62 * \mathrm{Similarity}(\rho_{\mathrm{r}},\rho_{\mathrm{c}}) =
63 * \frac{1}{N_\mathrm{voxel}}/\sum_{v=1}^{N_\mathrm{voxel}} \rho^v_{\mathrm{r}}
69 /*! \brief Measure similarity between densities by negative relative entropy.
70 * \note Voxels with negative values are ignored.
73 * \mathrm{Similarity}(\rho_{\mathrm{r}},\rho_{\mathrm{c}}) =
74 * \sum_{v=1}^{N_\mathrm{voxel}}
75 * \rho^v_{\mathrm{r}} (\log(\rho^v_{\mathrm{c}}) - \log(\rho^v_{\mathrm{r}}))
80 /*! \brief Measure similarity between densities by cross correlation.
83 * \mathrm{Similarity}(\rho_{\mathrm{r}},\rho_{\mathrm{c}}) =
84 * \frac{\sum_{v}\left((\rho_{\mathrm{r}} - \bar{\rho}_{\mathrm{r}})(\rho_{\mathrm{c}} - \bar{\rho}_{\mathrm{c}})\right)}
85 * {\sqrt{\sum_v(\rho_{\mathrm{r}} - \bar{\rho}_{\mathrm{r}})^2 \sum_v (\rho_{\mathrm{c}} - \bar{\rho}_{\mathrm{c}})^2}}
92 //! Name the methods that may be used to evaluate similarity between densities
93 const EnumerationArray<DensitySimilarityMeasureMethod, const char* const> c_densitySimilarityMeasureMethodNames = {
94 { "inner-product", "relative-entropy", "cross-correlation" }
97 /* Forward declaration of implementation class outside class to allow
98 * choose implementation class during construction of the DensitySimilarityMeasure*/
99 class DensitySimilarityMeasureImpl;
101 /*! \libinternal \brief
102 * Measure similarity and gradient between densities.
104 class DensitySimilarityMeasure
107 //! a three-dimensional const view into density data
108 using density = basic_mdspan<const float, dynamicExtents3D>;
109 /*! \brief Chose comparison method and set reference density.
110 * \param[in] method defines how densities are compared to one another
111 * \param[in] referenceDensity
112 * \throws NotImplementedError if method is not known
114 DensitySimilarityMeasure(DensitySimilarityMeasureMethod method, density referenceDensity);
115 ~DensitySimilarityMeasure();
117 DensitySimilarityMeasure(const DensitySimilarityMeasure& other);
119 DensitySimilarityMeasure& operator=(const DensitySimilarityMeasure& other);
121 DensitySimilarityMeasure(DensitySimilarityMeasure&& other) noexcept;
123 DensitySimilarityMeasure& operator=(DensitySimilarityMeasure&& other) noexcept;
125 /*! \brief Derivative of the density similarity measure at all voxels.
126 * \param[in] comparedDensity the variable density
127 * \returns density similarity measure derivative
129 density gradient(density comparedDensity);
130 /*! \brief Similarity between reference and compared density.
131 * \param[in] comparedDensity the variable density
132 * \returns density similarity
134 real similarity(density comparedDensity);
137 std::unique_ptr<DensitySimilarityMeasureImpl> impl_;