FastGaussianShapeAlignment.hpp

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/* 
 * FastGaussianShapeAlignment.hpp 
 *
 * This file is part of the Chemical Data Processing Toolkit
 *
 * Copyright (C) 2003 Thomas Seidel <thomas.seidel@univie.ac.at>
 *
 * This library is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 2 of the License, or (at your option) any later version.
 *
 * This library 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
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this library; see the file COPYING. If not, write to
 * the Free Software Foundation, Inc., 59 Temple Place - Suite 330,
 * Boston, MA 02111-1307, USA.
 */
 
#ifndef CDPL_SHAPE_FASTGAUSSIANSHAPEALIGNMENT_HPP
#define CDPL_SHAPE_FASTGAUSSIANSHAPEALIGNMENT_HPP
 
#include <vector>
#include <cstddef>
#include <utility>
#include <unordered_map>
#include <memory>
#include <functional>
 
#include <boost/functional/hash.hpp>
#include <boost/random/mersenne_twister.hpp>
 
#include "CDPL/Shape/APIPrefix.hpp"
#include "CDPL/Shape/GaussianShapeSet.hpp"
#include "CDPL/Shape/AlignmentResult.hpp"
#include "CDPL/Shape/AlignmentResultSelectionMode.hpp"
#include "CDPL/Shape/QuaternionTransformation.hpp"
#include "CDPL/Math/Matrix.hpp"
#include "CDPL/Math/VectorArray.hpp"
#include "CDPL/Math/QuaternionExpression.hpp"
#include "CDPL/Math/BFGSMinimizer.hpp"
 
 
namespace CDPL
{
 
    namespace Shape
    {
 
        class CDPL_SHAPE_API FastGaussianShapeAlignment
        {
 
            typedef std::vector<AlignmentResult> ResultList;
 
          public:
            static constexpr double DEF_OPTIMIZATION_STOP_GRADIENT        = 1.0;
            static constexpr std::size_t  DEF_MAX_OPTIMIZATION_ITERATIONS = 20;
            static constexpr unsigned int DEF_RESULT_SELECTION_MODE       = AlignmentResultSelectionMode::BEST_PER_REFERENCE_SET;
            static constexpr double       DEF_SYMMETRY_THRESHOLD          = 0.15;
            static constexpr std::size_t DEF_NUM_RANDOM_STARTS            = 4;
            static constexpr double      DEF_MAX_RANDOM_TRANSLATION       = 2.0;
 
            typedef std::shared_ptr<FastGaussianShapeAlignment> SharedPointer;
 
            typedef ResultList::const_iterator ConstResultIterator;
            typedef ResultList::iterator       ResultIterator;
 
            typedef std::function<double(const AlignmentResult&)>                       ScoringFunction;
            typedef std::function<bool(const AlignmentResult&, const AlignmentResult&)> ResultCompareFunction;
 
            FastGaussianShapeAlignment();
 
            FastGaussianShapeAlignment(const GaussianShape& ref_shape);
 
            FastGaussianShapeAlignment(const GaussianShapeSet& ref_shapes);
 
            ~FastGaussianShapeAlignment();
 
            void setResultCompareFunction(const ResultCompareFunction& func);
 
            const ResultCompareFunction& getResultCompareFunction() const;
 
            void setScoringFunction(const ScoringFunction& func);
 
            const ScoringFunction& getScoringFunction() const;
 
            void setResultSelectionMode(unsigned int mode);
 
            unsigned int getResultSelectionMode() const;
 
            void performAlignment(bool perf_align);
 
            bool performAlignment() const;
 
            void optimizeOverlap(bool optimize);
 
            bool optimizeOverlap() const;
 
            void greedyOptimization(bool greedy);
 
            bool greedyOptimization() const;
 
            void setMaxNumOptimizationIterations(std::size_t max_iter);
 
            std::size_t getMaxNumOptimizationIterations() const;
 
            void setOptimizationStopGradient(double grad_norm);
 
            double getOptimizationStopGradient() const;
 
            void clearReferenceShapes();
 
            void addReferenceShape(const GaussianShape& shape, bool new_set = true);
 
            void addReferenceShapes(const GaussianShapeSet& shapes, bool new_set = true);
 
            std::size_t getNumReferenceShapes() const;
 
            void genShapeCenterStarts(bool generate);
 
            bool genShapeCenterStarts() const;
 
            void genColorCenterStarts(bool generate);
 
            bool genColorCenterStarts() const;
 
            void genNonColorCenterStarts(bool generate);
 
            bool genNonColorCenterStarts() const;
 
            void genRandomStarts(bool generate);
 
            bool genRandomStarts() const;
 
            void genForAlignedShapeCenters(bool generate);
 
            bool genForAlignedShapeCenters() const;
 
            void genForReferenceShapeCenters(bool generate);
 
            bool genForReferenceShapeCenters() const;
 
            void genForLargerShapeCenters(bool generate);
 
            bool genForLargerShapeCenters() const;
 
            void setSymmetryThreshold(double thresh);
 
            double getSymmetryThreshold();
 
            void setMaxRandomTranslation(double max_trans);
 
            double getMaxRandomTranslation() const;
 
            void setNumRandomStarts(std::size_t num_starts);
 
            std::size_t getNumRandomStarts() const;
 
            void setRandomSeed(unsigned int seed);
 
            bool align(const GaussianShape& shape);
 
            bool align(const GaussianShapeSet& shapes);
 
            std::size_t getNumResults() const;
 
            const AlignmentResult& getResult(std::size_t idx) const;
 
            AlignmentResult& getResult(std::size_t idx);
 
            ConstResultIterator getResultsBegin() const;
 
            ConstResultIterator getResultsEnd() const;
 
            ResultIterator getResultsBegin();
 
            ResultIterator getResultsEnd();
 
            ConstResultIterator begin() const;
 
            ConstResultIterator end() const;
 
            ResultIterator begin();
 
            ResultIterator end();
 
          private:
            struct ShapeData
            {
 
                struct Element
                {
 
                    std::size_t    color;
                    Math::Vector3D center;
                    double         radius;
                    double         delta;
                    double         weightFactor;
                    double         volume;
                };
 
                typedef std::vector<Element> ElementArray;
 
                ElementArray   elements;
                std::size_t    colElemOffs;
                std::size_t    setIndex;
                std::size_t    index;
                unsigned int   symClass;
                Math::Matrix4D transform;
                double         selfOverlap;
                double         colSelfOverlap;
                bool           equalNonColDelta;
            };
 
            typedef std::pair<std::size_t, std::size_t> ResultID;
 
            FastGaussianShapeAlignment(const FastGaussianShapeAlignment& alignment);
 
            FastGaussianShapeAlignment& operator=(const FastGaussianShapeAlignment& alignment);
 
            void alignAndProcessResults(std::size_t ref_idx, std::size_t al_idx);
            void processResult(AlignmentResult& res, std::size_t ref_idx, std::size_t al_idx);
 
            void setupShapeData(const GaussianShape& shape, ShapeData& data, bool ref);
            void setupShapeDataElement(const GaussianShape::Element& gs_elem, ShapeData::Element& sd_elem) const;
 
            void prepareForAlignment();
 
            bool generateStartTransforms(const ShapeData& ref_data);
 
            void generateTransformsForElementCenters(const ShapeData& data, unsigned int axes_swap_flags, bool ref_shape);
            void generateTransforms(const Math::Vector3D& ctr_trans, unsigned int axes_swap_flags);
 
            template <typename QE>
            void addStartTransform(Math::Vector3D::ConstPointer ctr_trans_data, const Math::QuaternionExpression<QE>& rot_quat);
 
            void transformAlignedShape();
 
            double calcAlignmentFunctionValue(const QuaternionTransformation& xform_quat);
            double calcAlignmentFunctionGradient(const QuaternionTransformation& xform_quat, QuaternionTransformation& xform_grad);
 
            double calcOverlap(const ShapeData& ref_data, const ShapeData& ovl_data, bool color) const;
            double calcOverlapGradient(const ShapeData& ref_data, Math::Vector3DArray& grad) const;
 
            bool getResultIndex(const ResultID& res_id, std::size_t& res_idx);
 
            typedef std::vector<ShapeData>                                            ShapeDataArray;
            typedef std::unordered_map<ResultID, std::size_t, boost::hash<ResultID> > ResultIndexMap;
            typedef std::vector<QuaternionTransformation>                             StartTransformList;
            typedef boost::random::mt11213b                                           RandomEngine;
            typedef Math::BFGSMinimizer<QuaternionTransformation>                     BFGSMinimizer;
 
            bool                     perfAlignment;
            bool                     optOverlap;
            bool                     greedyOpt;
            std::size_t              maxNumOptIters;
            double                   optStopGrad;
            unsigned int             resultSelMode;
            ResultCompareFunction    resultCmpFunc;
            ScoringFunction          scoringFunc;
            ShapeDataArray           refShapeData;
            ShapeData                algdShapeData;
            ResultIndexMap           resIndexMap;
            ResultList               results;
            std::size_t              currSetIndex;
            std::size_t              currShapeIndex;
            bool                     shapeCtrStarts;
            bool                     colCtrStarts;
            bool                     nonColCtrStarts;
            bool                     randomStarts;
            bool                     genForAlgdShape;
            bool                     genForRefShape;
            bool                     genForLargerShape;
            double                   symThreshold;
            double                   maxRandomTrans;
            std::size_t              numRandomStarts;
            std::size_t              numSubTransforms;
            RandomEngine             randomEngine;
            StartTransformList       startTransforms;
            Math::Vector3DArray      startPoseCoords;
            Math::Vector3DArray      optPoseCoordsGrad;
            BFGSMinimizer            minimizer;
            Math::Matrix4D           xformMatrix;
            QuaternionTransformation normXformQuat;
            std::size_t              currRefShapeIdx;
        };
    } // namespace Shape
} // namespace CDPL
 
#endif // CDPL_SHAPE_FASTGAUSSIANSHAPEALIGNMENT_HPP