/usr/include/mia-2.4/mia/core/ica_template.hh is in libmia-2.4-dev 2.4.3-5.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 | /* -*- mia-c++ -*-
*
* This file is part of MIA - a toolbox for medical image analysis
* Copyright (c) Leipzig, Madrid 1999-2016 Gert Wollny
*
* MIA is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with MIA; if not, see <http://www.gnu.org/licenses/>.
*
*/
#ifndef mia_core_ica_template_hh
#define mia_core_ica_template_hh
#include <mia/core/icaanalysisbase.hh>
#include <vector>
#ifndef EXPORT_TDataSeriesICA
#ifdef WIN32
# define EXPORT_TDataSeriesICA __declspec(dllimport)
#else
# ifdef __GNUC__
# define EXPORT_TDataSeriesICA __attribute__((visibility("default")))
# else
# define EXPORT_TDataSeriesICA
# endif
#endif
#endif
NS_MIA_BEGIN
/**
\ingroup perf
\brief Templated representation of a ICA series analyis
This class provides a generic implementation for the ICA analysis
of data series.
\tparam Data some kind of data set ofwhich series are analyzed
The class \a Data must somehow provide:
- a typedef \a Pointer for a pointer like representation of itself
or on of its base classes (preferable based on boost::shared_ptr)
- a typedef \a dimsize_type for its the size seperated into dimensions
- a method \a get_size() that returns \a dimsize_type
- a method \a size() that returns the number of elements hold by itself
- STL comaptible const and non-const iterators returned by
functions named \a begin() and \a end()
*/
template <class Data>
class EXPORT_TDataSeriesICA TDataSeriesICA {
public:
/** a set of indices used for addressing a subset of the independend componsts
*/
typedef CICAAnalysis::IndexSet IndexSet;
/** a (shared) pointer to itself */
typedef typename Data::Pointer PData;
/**
\brief ICA initialization
The contructor for an ICA
\param icatool tool used for the ICA analysis
\param initializer data set containing all the time steps of input data
\param strip_mean strip the mean from the series before processing
*/
TDataSeriesICA(const CICAAnalysisFactory& icatool, const std::vector<Data>& initializer, bool strip_mean);
/** Runs the ICA
\param ncomponents retained components
\param strip_mean strip the mean from the input
\param ica_normalize normalize the ICA after processing
\param guess provide an initial guess (leave empty, if not wanted)
*/
bool run(size_t ncomponents, bool strip_mean, bool ica_normalize,
std::vector<std::vector<float> > guess = std::vector<std::vector<float> >());
/** Normalizes the ICs to the range of [-1,1] and correct the mixing matrix accordingly.
This operation does not change the output of a mix.
*/
void normalize();
/// Normalizes the Mixing Matrix columns to have zero mean.
void normalize_Mix();
/**
\returns the mixed signal at index \a idx
*/
Data get_mix(size_t idx) const;
/// \returns the mean of the input data
const Data& get_mean_image() const;
/**
Evaluate a partial mix of the ICs
\param idx time indes
\param skip set of components to skip when mixing
\returns the mixed data
*/
Data get_incomplete_mix(size_t idx, const IndexSet& skip) const;
/**
Evaluate a partial mix of the ICs by using the given indes set
\param idx time indes
\param comps set of components to use when mixing
\returns the mixed data
*/
Data get_partial_mix(size_t idx, const IndexSet& comps) const;
/// \returns the mixing curves as vector of vectors
CSlopeColumns get_mixing_curves() const;
/**
Obtain a specific mixing curve
\param idx: index of requested curve, throws invalid_argument if index is out of bounds
\returns a mixing curve
*/
std::vector<float> get_mixing_curve(unsigned idx) const;
/// \returns the feature data relating to component \a idx
PData get_feature_image(size_t idx) const;
/**
Evaluate a mix as sum and difference of ICs
\param plus add these ICs
\param minus subtract these ICs
\returns the combined signal
*/
PData get_delta_feature(const IndexSet& plus, const IndexSet& minus)const;
/**
replace a mixing series by a new set
\param index component number of the mixing curve to be replaced
\param series new mixing data
*/
void set_mixing_series(size_t index, const std::vector<float>& series);
/**
sets the number of iterations in the ICA
\param n
*/
void set_max_iterations(int n);
/**
Set the ICA approach to either FICA_APPROACH_DEFL(default) or FICA_APPROACH_SYMM.
\param approach
*/
void set_approach(CICAAnalysis::EApproach approach);
~TDataSeriesICA();
private:
PICAAnalysis m_analysis;
typedef typename Data::dimsize_type dimsize_type;
dimsize_type m_size;
Data m_mean;
};
NS_MIA_END
#endif
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