DecayCurve.h

Go to the documentation of this file.

 
#ifndef IMPBFF_DECAYCURVE_H
#define IMPBFF_DECAYCURVE_H
#include <IMP/bff/bff_config.h>
#include <cmath>
#include <vector>
#include <numeric>
#include <algorithm>
#include <iostream> /* std::cerr */
#include <string>
#include <cstring> /* strcmp */
#include <limits> /* std::numeric_limits */
#include <IMP/bff/internal/MovingAverage.h>
#include <IMP/bff/internal/json.h>
#include <IMP/bff/DecayRoutines.h>
 
IMPBFF_BEGIN_NAMESPACE
 
enum NoiseModelTypes{
    NOISE_NA,
    NOISE_POISSON
};
 
class IMPBFFEXPORT DecayCurve {
    friend class DecayConvolution;
    friend class DecayPileup;
    friend class DecayLinearization;
    friend class DecayScale;
    friend class DecayScore;
    friend class DecayPattern;
 
private:
 
    int noise_model = NOISE_NA; 
    double current_shift = 0.0; 
    double acquisition_time = std::numeric_limits<double>::max(); 
    std::vector<double> dx = {1.0}; 
    std::vector<double> x = std::vector<double>(); 
    std::vector<double> _y; 
    std::vector<double> y = std::vector<double>(); 
    std::vector<double> ey = std::vector<double>(); 
    void compute_noise(int noise_model = NOISE_POISSON);
 
public:
 
    static std::vector<double> shift_array(
            double *input, int n_input,
            double shift
    );
    
    size_t size() const;
    
    bool empty();
    
    std::vector<double> get_dx();
    
    void resize(size_t n, double v=0.0, double dx=1.0);
    
    double get_average_dx();
    
    std::vector<double>& get_x();
 
    void set_x(const std::vector<double>& v);
 
    void set_x(double* input, int n_input);
 
    std::vector<double>& get_y();
 
    void set_y(std::vector<double>& v);
 
    void set_y(double* input, int n_input);
 
    std::vector<double>& get_ey();
 
    void set_ey(std::vector<double>& v);
 
    void set_ey(double* input, int n_input);
 
    void set_acquisition_time(double v);
 
    double get_acquisition_time() const;
 
    void set_shift(double v);
 
    double get_shift();
 
    std::string get_json() const;
 
    int read_json(std::string json_string);
 
    DecayCurve(
            std::vector<double> x = std::vector<double>(),
            std::vector<double> y  = std::vector<double>(),
            std::vector<double> ey  = std::vector<double>(),
            double acquisition_time = std::numeric_limits<double>::max(),
            int noise_model = NOISE_POISSON,
            int size = -1
    );
 
    double sum(int start=0, int stop=-1);
 
    void apply_simple_moving_average(int start, int stop, int n_window=5, bool normalize=false);
 
    DecayCurve& operator+(double v) const;
 
    DecayCurve& operator-(double v) const;
 
    DecayCurve& operator*(double v) const;
 
    DecayCurve& operator/(double v) const;
 
    DecayCurve& operator+=(double v);
 
    DecayCurve& operator-=(double v);
 
    DecayCurve& operator*=(double v);
 
    DecayCurve& operator/=(double v);
 
    DecayCurve& operator+(const DecayCurve& other) const;
 
    DecayCurve& operator-(const DecayCurve& other) const;
 
    DecayCurve& operator*(const DecayCurve& other) const;
 
    DecayCurve& operator/(const DecayCurve& other) const;
 
    DecayCurve& operator=(const DecayCurve& other);
 
    DecayCurve& operator<<(double v);
 
};
 
IMPBFF_END_NAMESPACE
 
 
#endif //IMPBFF_DECAYCURVE_H