normalization.hpp

Go to the documentation of this file.

#ifndef GENESIS_UTILS_COLOR_NORMALIZATION_H_
#define GENESIS_UTILS_COLOR_NORMALIZATION_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 <cassert>
#include <cmath>
#include <limits>
#include <map>
#include <stdexcept>
#include <string>
#include <vector>
 
namespace genesis {
namespace utils {
 
// =================================================================================================
//     Color Normalization
// =================================================================================================
 
class ColorNormalization
{
public:
 
    // -------------------------------------------------------------------------
    //     Constructors and Rule of Five
    // -------------------------------------------------------------------------
 
    ColorNormalization() = default;
    virtual ~ColorNormalization() = default;
 
    ColorNormalization(ColorNormalization const&) = default;
    ColorNormalization(ColorNormalization&&)      = default;
 
    ColorNormalization& operator= (ColorNormalization const&) = default;
    ColorNormalization& operator= (ColorNormalization&&)      = default;
 
    // -------------------------------------------------------------------------
    //     Accessors
    // -------------------------------------------------------------------------
 
    double mask_value() const
    {
        return mask_value_;
    }
 
    bool is_valid() const
    {
        return is_valid_();
    }
 
    // -------------------------------------------------------------------------
    //     Modificators
    // -------------------------------------------------------------------------
 
    ColorNormalization& mask_value( double value )
    {
        mask_value_ = value;
        return *this;
    }
 
    // -------------------------------------------------------------------------
    //     Normalize
    // -------------------------------------------------------------------------
 
    double operator()( double value ) const
    {
        if( ! std::isfinite( value ) || value == mask_value_ ) {
            return std::numeric_limits<double>::quiet_NaN();
        }
        return normalize_( value );
    }
 
    std::vector<double> operator() ( std::vector<double> const& values ) const
    {
        using it_type = std::vector<double>::const_iterator;
        return operator()<it_type>( values.begin(), values.end() );
    }
 
    template <class ForwardIterator>
    std::vector<double> operator()( ForwardIterator first, ForwardIterator last ) const
    {
        std::vector<double> result;
        while( first != last ) {
            result.push_back( operator()( *first ) );
            ++first;
        }
        return result;
    }
 
    // -------------------------------------------------------------------------
    //     (Pure) Virtual Functions
    // -------------------------------------------------------------------------
 
protected:
 
    virtual double normalize_( double value ) const = 0;
 
    virtual bool is_valid_() const = 0;
 
    // -------------------------------------------------------------------------
    //     Data Members
    // -------------------------------------------------------------------------
 
private:
 
    double mask_value_ = std::numeric_limits<double>::quiet_NaN();
 
};
 
} // namespace utils
} // namespace genesis
 
#endif // include guard