norm_boundary.hpp

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#ifndef GENESIS_UTILS_COLOR_NORM_BOUNDARY_H_
#define GENESIS_UTILS_COLOR_NORM_BOUNDARY_H_
 
/*
    Genesis - A toolkit for working with phylogenetic data.
    Copyright (C) 2014-2023 Lucas Czech
 
    This program 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 this program.  If not, see <http://www.gnu.org/licenses/>.
 
    Contact:
    Lucas Czech <lczech@carnegiescience.edu>
    Department of Plant Biology, Carnegie Institution For Science
    260 Panama Street, Stanford, CA 94305, USA
*/
 
#include "genesis/utils/text/string.hpp"
#include "genesis/utils/color/color.hpp"
#include "genesis/utils/color/map.hpp"
#include "genesis/utils/color/normalization.hpp"
#include "genesis/utils/tools/tickmarks.hpp"
 
#include <algorithm>
#include <cassert>
#include <cmath>
#include <limits>
#include <map>
#include <stdexcept>
#include <string>
#include <vector>
 
namespace genesis {
namespace utils {
 
// =================================================================================================
//     Color Normalization Boundary
// =================================================================================================
 
class ColorNormalizationBoundary
    : public ColorNormalization
{
public:
 
    // -------------------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------------------
 
    ColorNormalizationBoundary() = default;
 
    explicit ColorNormalizationBoundary( std::vector<double> const& boundaries )
        : boundaries_( boundaries )
    {
        ColorNormalizationBoundary::is_valid_or_throw_();
    }
 
    ColorNormalizationBoundary( double min, double max, size_t intervals )
    {
        scale( min, max, intervals );
    }
 
    virtual ~ColorNormalizationBoundary() override = default;
 
    ColorNormalizationBoundary(ColorNormalizationBoundary const&) = default;
    ColorNormalizationBoundary(ColorNormalizationBoundary&&)      = default;
 
    ColorNormalizationBoundary& operator= (ColorNormalizationBoundary const&) = default;
    ColorNormalizationBoundary& operator= (ColorNormalizationBoundary&&)      = default;
 
    // -------------------------------------------------------------------------
    //     Accessors
    // -------------------------------------------------------------------------
 
    std::vector<double> const& boundaries() const
    {
        return boundaries_;
    }
 
    long interval( double value ) const
    {
        // Make sure that the norm is set up correctly.
        // This is now done while setting, so no need to do this here.
        // is_valid_or_throw_();
 
        // Extreme cases: value is not within the boundaries.
        // For the upper limit, we return size-1, as this is the first interval index
        // that is not reachable with valid (within-boundary) values.
        assert( boundaries_.size() >= 3 );
        if( value < boundaries_.front() ) {
            return -1;
        }
        if( value > boundaries_.back() ) {
            return boundaries_.size() - 1;
        }
 
        // Get an iterator to the boundary, and turn it into an interval index upon return.
        // The index calculation has a special case if the value hits exaclty the highest
        // boundary value. In that case, the iterator points to the end of the boundary vector.
        // In all other cases, the iterator points to the end of interval boundary,
        // so we subtract one to get the interval index.
        // The first assertion checks this special case.
        // The second assertion holds because we already checked that the value is not less than
        // the first boundary.
        auto const it = std::upper_bound( boundaries_.begin(), boundaries_.end(), value );
        assert(( it != boundaries_.end() ) xor ( value == boundaries_.back() ));
        assert( it != boundaries_.begin() );
 
        if( it == boundaries_.end() ) {
            return boundaries_.size() - 2;
        } else {
            return std::distance( boundaries_.begin(), it ) - 1;
        }
    }
 
    // -------------------------------------------------------------------------
    //     Modificators
    // -------------------------------------------------------------------------
 
    ColorNormalizationBoundary& boundaries( std::vector<double> const& values )
    {
        boundaries_ = values;
        is_valid_or_throw_();
        return *this;
    }
 
    ColorNormalizationBoundary& scale( double min, double max, size_t intervals )
    {
        // Make evenly distributed boundary intervals between min and max.
        // We add max separately to increase precision.
        boundaries_.clear();
        double const interv = ( max - min ) / static_cast<double>( intervals );
        for( size_t i = 0; i < intervals; ++i ) {
            boundaries_.push_back( min + static_cast<double>(i) * interv );
        }
        boundaries_.push_back( max );
        ColorNormalizationBoundary::is_valid_or_throw_();
 
        return *this;
    }
 
    ColorNormalizationBoundary& autoscale( std::vector<double> const& values, size_t intervals )
    {
        return autoscale( values.begin(), values.end(), intervals );
    }
 
    template <class ForwardIterator>
    ColorNormalizationBoundary& autoscale(
        ForwardIterator first, ForwardIterator last, size_t intervals
    ) {
        // New values, so that we first do not override the current ones.
        auto min = std::numeric_limits<double>::max();
        auto max = std::numeric_limits<double>::lowest();
 
        size_t cnt = 0;
        while( first != last ) {
            if( ! std::isfinite( *first ) || *first == mask_value() ) {
                ++first;
                continue;
            }
            if( *first < min ) {
                min = *first;
            }
            if( *first > max ) {
                max = *first;
            }
 
            ++cnt;
            ++first;
        }
 
        // Only update if we found values.
        if( cnt == 0 ) {
            return *this;
        }
 
        scale( min, max, intervals );
        return *this;
    }
 
    // -------------------------------------------------------------------------
    //     (Pure) Virtual Functions
    // -------------------------------------------------------------------------
 
protected:
 
    virtual bool is_valid_() const override
    {
        return boundaries_.size() >= 3 && std::is_sorted( boundaries_.begin(), boundaries_.end() );
    }
 
    virtual void is_valid_or_throw_() const
    {
        if( boundaries_.size() < 3 ) {
            throw std::runtime_error( "Invalid Color Normalization with less than three boundaries." );
        }
        if( ! std::is_sorted( boundaries_.begin(), boundaries_.end() ) ) {
            throw std::runtime_error( "Invalid Color Normalization with unsorted boundaries." );
        }
    }
 
    virtual double normalize_( double value ) const override
    {
        auto const idx = interval( value );
 
        // Special cases: the value is outside of the boundaries.
        if( idx < 0 ) {
            return -1.0;
        }
        if( idx >= static_cast<long>( boundaries_.size() - 1 )) {
            return 2.0;
        }
 
        // If we are inside the boundaries, calculate a fixed position depending on the interval.
        // As the index returned for too large values is size-1, we need to use size-2 here
        // to normalize properly so that the max value corresponds to a normalized value of 1.0.
        assert( boundaries_.size() >= 3 );
        return static_cast<double>( idx ) / static_cast<double>( boundaries_.size() - 2 );
    }
 
    // -------------------------------------------------------------------------
    //     Data Members
    // -------------------------------------------------------------------------
 
private:
 
    std::vector<double> boundaries_;
 
};
 
} // namespace utils
} // namespace genesis
 
#endif // include guardmask_value_