GaussianShapeAlignment.hpp

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/* 
 * GaussianShapeAlignment.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_GAUSSIANSHAPEALIGNMENT_HPP
#define CDPL_SHAPE_GAUSSIANSHAPEALIGNMENT_HPP
 
#include <vector>
#include <cstddef>
#include <utility>
#include <unordered_map>
#include <memory>
#include <functional>
 
#include <boost/functional/hash.hpp>
#include <boost/iterator/transform_iterator.hpp>
 
#include "CDPL/Shape/APIPrefix.hpp"
#include "CDPL/Shape/GaussianShapeFunctionAlignment.hpp"
#include "CDPL/Shape/GaussianShapeFunction.hpp"
#include "CDPL/Shape/GaussianShapeSet.hpp"
#include "CDPL/Shape/AlignmentResult.hpp"
#include "CDPL/Shape/AlignmentResultSelectionMode.hpp"
#include "CDPL/Math/Matrix.hpp"
#include "CDPL/Util/ObjectStack.hpp"
 
 
namespace CDPL
{
 
    namespace Shape
    {
 
        class CDPL_SHAPE_API GaussianShapeAlignment
        {
 
            typedef std::vector<AlignmentResult>        ResultList;
            typedef std::vector<GaussianShapeFunction*> ShapeFunctionList;
 
            typedef const GaussianShape& (*GetShapeFunction)(const GaussianShapeFunction*);
 
          public:
            static constexpr double DEF_OPTIMIZATION_STOP_GRADIENT       = 1.0;
            static constexpr std::size_t DEF_MAX_OPTIMIZATION_ITERATIONS = 20;
            static constexpr std::size_t  DEF_MAX_PRODUCT_ORDER          = 1;
            static constexpr unsigned int DEF_RESULT_SELECTION_MODE      = AlignmentResultSelectionMode::BEST_PER_REFERENCE_SET;
            static constexpr double       DEF_DISTANCE_CUTOFF            = 0.0;
 
            typedef std::shared_ptr<GaussianShapeAlignment> SharedPointer;
 
            typedef ResultList::const_iterator                                                     ConstResultIterator;
            typedef ResultList::iterator                                                           ResultIterator;
            typedef boost::transform_iterator<GetShapeFunction, ShapeFunctionList::const_iterator> ConstShapeIterator;
 
            typedef GaussianShapeFunctionAlignment::ColorFilterFunction                 ColorFilterFunction;
            typedef GaussianShapeFunctionAlignment::ColorMatchFunction                  ColorMatchFunction;
            typedef std::function<double(const AlignmentResult&)>                       ScoringFunction;
            typedef std::function<bool(const AlignmentResult&, const AlignmentResult&)> ResultCompareFunction;
 
            GaussianShapeAlignment();
 
            GaussianShapeAlignment(const GaussianShape& ref_shape);
 
            GaussianShapeAlignment(const GaussianShapeSet& ref_shapes);
 
            ~GaussianShapeAlignment();
 
            void setOverlapFunction(GaussianShapeOverlapFunction& func);
 
            GaussianShapeOverlapFunction& getOverlapFunction() const;
 
            const FastGaussianShapeOverlapFunction& getDefaultOverlapFunction() const;
 
            FastGaussianShapeOverlapFunction& getDefaultOverlapFunction();
 
            void setStartGenerator(GaussianShapeAlignmentStartGenerator& gen);
 
            GaussianShapeAlignmentStartGenerator& getStartGenerator() const;
 
            const PrincipalAxesAlignmentStartGenerator& getDefaultStartGenerator() const;
 
            PrincipalAxesAlignmentStartGenerator& getDefaultStartGenerator();
 
            void setColorMatchFunction(const ColorMatchFunction& func);
 
            const ColorMatchFunction& getColorMatchFunction() const;
 
            void setColorFilterFunction(const ColorFilterFunction& func);
 
            const ColorFilterFunction& getColorFilterFunction() const;
 
            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 calcSelfOverlaps(bool calc);
 
            bool calcSelfOverlaps() const;
 
            void calcColorSelfOverlaps(bool calc);
 
            bool calcColorSelfOverlaps() const;
 
            void calcColorOverlaps(bool calc);
 
            bool calcColorOverlaps() 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 setMaxOrder(std::size_t max_order);
 
            std::size_t getMaxOrder() const;
 
            void setDistanceCutoff(double cutoff);
 
            double getDistanceCutoff() 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;
 
            const GaussianShape& getReferenceShape(std::size_t idx) const;
 
            ConstShapeIterator getReferenceShapesBegin() const;
 
            ConstShapeIterator getReferenceShapesEnd() const;
 
            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();
 
          private:
            typedef GaussianShape::SharedPointer GaussianShapePtr;
 
            struct ShapeMetaData
            {
 
                std::size_t      setIndex;
                std::size_t      index;
                unsigned int     symClass;
                Math::Matrix4D   transform;
                double           selfOverlap;
                double           colSelfOverlap;
                GaussianShapePtr shape;
            };
 
            typedef std::pair<std::size_t, std::size_t> ResultID;
 
            GaussianShapeAlignment(const GaussianShapeAlignment& alignment);
 
            GaussianShapeAlignment& operator=(const GaussianShapeAlignment& alignment);
 
            void prepareForAlignment(GaussianShapeFunction& func, ShapeMetaData& data, bool ref);
 
            void processResults(std::size_t ref_idx, std::size_t al_idx);
 
            bool getResultIndex(const ResultID& res_id, std::size_t& res_idx);
 
            GaussianShapeFunction* allocShapeFunction(const GaussianShape& shape);
 
            typedef Util::ObjectStack<GaussianShapeFunction>                          ShapeFunctionCache;
            typedef std::vector<ShapeMetaData>                                        ShapeMetaDataArray;
            typedef std::unordered_map<ResultID, std::size_t, boost::hash<ResultID> > ResultIndexMap;
 
            ShapeFunctionCache             shapeFuncCache;
            bool                           calcSlfOverlaps;
            bool                           calcColSlfOverlaps;
            unsigned int                   resultSelMode;
            ResultCompareFunction          resultCmpFunc;
            ScoringFunction                scoringFunc;
            GaussianShapeFunctionAlignment shapeFuncAlmnt;
            ShapeFunctionList              refShapeFuncs;
            ShapeMetaDataArray             refShapeMetaData;
            GaussianShapeFunction          algdShapeFunc;
            ShapeMetaData                  algdShapeMetaData;
            ResultIndexMap                 resIndexMap;
            ResultList                     results;
            std::size_t                    currSetIndex;
            std::size_t                    currShapeIndex;
        };
    } // namespace Shape
} // namespace CDPL
 
#endif // CDPL_SHAPE_GAUSSIANSHAPEALIGNMENT_HPP