libopenms-dev 1.11.1-5 / usr / include / OpenMS / TRANSFORMATIONS / FEATUREFINDER / TraceFitter.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Stephan Aiche$
// $Authors: Stephan Aiche, Marc Sturm $
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#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_TRACEFITTER_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_TRACEFITTER_H

#include <OpenMS/CONCEPT/LogStream.h>

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmPickedHelperStructs.h>

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>

#include <gsl/gsl_rng.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_multifit_nlin.h>
#include <gsl/gsl_blas.h>

namespace OpenMS
{

  /**
   * @brief Abstract fitter for RT profile fitting
   *
   * This class provides the basic interface and some functionality to fit multiple mass traces to
   * a given RT shape model using the Levenberg-Marquardt algorithm.
   *
   * @todo docu needs update
   *
   */
  template <class PeakType>
  class TraceFitter :
    public DefaultParamHandler
  {

public:
    /// default constructor.
    TraceFitter() :
      DefaultParamHandler("TraceFitter")
    {
      this->defaults_.setValue("max_iteration", 500, "Maximum number of iterations using by Levenberg-Marquardt algorithm.", StringList::create("advanced"));
      this->defaults_.setValue("epsilon_abs", 0.0001, "Absolute error used by the Levenberg-Marquardt algorithm.", StringList::create("advanced"));
      this->defaults_.setValue("epsilon_rel", 0.0001, "Relative error used by the Levenberg-Marquardt algorithm.", StringList::create("advanced"));
    }

    /// copy constructor
    TraceFitter(const TraceFitter & source) :
      DefaultParamHandler(source),
      epsilon_abs_(source.epsilon_abs_),
      epsilon_rel_(source.epsilon_rel_),
      max_iterations_(source.max_iterations_)
    {
    }

    /// assignment operator
    virtual TraceFitter & operator=(const TraceFitter & source)
    {
      DefaultParamHandler::operator=(source);
      max_iterations_ = source.max_iterations_;
      epsilon_abs_  = source.epsilon_abs_;
      epsilon_rel_ = source.epsilon_rel_;
      updateMembers_();

      return *this;
    }

    /// destructor
    virtual ~TraceFitter()
    {
    }

    /**
     * Main method of the TraceFitter which triggers the actual fitting.
     */
    virtual void fit(FeatureFinderAlgorithmPickedHelperStructs::MassTraces<PeakType> & traces) = 0;

    /**
     * Returns the lower bound of the fitted RT model
     */
    virtual DoubleReal getLowerRTBound() const = 0;

    /**
     * Returns the upper bound of the fitted RT model
     */
    virtual DoubleReal getUpperRTBound() const = 0;

    /**
     * Returns the height of the fitted model
     */
    virtual DoubleReal getHeight() const = 0;

    /**
     * Returns the center position of the fitted model
     */
    virtual DoubleReal getCenter() const = 0;

    /**
     * Returns the mass trace width at half max (FWHM)
     */
    virtual DoubleReal getFWHM() const = 0;

    /**
     * Returns the theoretical value of the fitted model at position k in the passed Mass Trace
     *
     * @param trace the mass trace for which the value should be computed
     * @param k  use the position of the k-th peak to compute the value
     */
    virtual DoubleReal computeTheoretical(const FeatureFinderAlgorithmPickedHelperStructs::MassTrace<PeakType> & trace, Size k) = 0;

    /**
     * Checks if the fitted model fills out at least 'min_rt_span' of the RT span
     *
     * @param rt_bounds RT boundaries of the fitted model
     * @param min_rt_span Minimum RT span in relation to extended area that has to remain after model fitting
     */
    virtual bool checkMinimalRTSpan(const std::pair<DoubleReal, DoubleReal> & rt_bounds, const DoubleReal min_rt_span) = 0;

    /**
     * Checks if the fitted model is not to big
     *
     * @param max_rt_span Maximum RT span in relation to extended area that the model is allowed to have
     */
    virtual bool checkMaximalRTSpan(const DoubleReal max_rt_span) = 0;

    /**
     * ???
     * @todo docu needs update
     */
    virtual DoubleReal getFeatureIntensityContribution() = 0;

    /**
     * Returns a textual representation of the fitted model function, that can be plotted using Gnuplot
     *
     * @param trace The MassTrace that should be plotted
     * @param function_name The name of the function (e.g. f(x) -> function_name = f)
     * @param baseline The intensity of the baseline
     * @param rt_shift A shift value, that allows to plot all RT profiles side by side, even if they would overlap in reality.
     *                 This should be 0 for the first mass trace and increase by a fixed value for each mass trace.
     */
    virtual String getGnuplotFormula(FeatureFinderAlgorithmPickedHelperStructs::MassTrace<PeakType> const & trace, const char function_name, const DoubleReal baseline, const DoubleReal rt_shift) = 0;

protected:

    /**
     * Prints the state of the current iteration (e.g., values of the parameters)
     *
     * @param iter Number of current iteration.
     * @param s The solver that also contains all the parameters.
     */
    virtual void printState_(SignedSize iter, gsl_multifit_fdfsolver * s) = 0;

    virtual void updateMembers_()
    {
      max_iterations_ = this->param_.getValue("max_iteration");
      epsilon_abs_ = this->param_.getValue("epsilon_abs");
      epsilon_rel_ = this->param_.getValue("epsilon_rel");
    }

    /**
     * Updates all member variables to the fitted values stored in the solver.
     *
     * @param s The solver containing the fitted parameter values.
     */
    virtual void getOptimizedParameters_(gsl_multifit_fdfsolver * s) = 0;

    /**
     * Optimize the given parameters using the Levenberg-Marquardt algorithm.
     */
    void optimize_(FeatureFinderAlgorithmPickedHelperStructs::MassTraces<PeakType> & traces, const Size num_params, double x_init[],
                   Int (* residual)(const gsl_vector * x, void * params, gsl_vector * f),
                   Int (* jacobian)(const gsl_vector * x, void * params, gsl_matrix * J),
                   Int (* evaluate)(const gsl_vector * x, void * params, gsl_vector * f, gsl_matrix * J))
    {
      const gsl_multifit_fdfsolver_type * T;
      gsl_multifit_fdfsolver * s;

      const size_t data_count = traces.getPeakCount();

      // gsl always expects N>=p or default gsl error handler invoked,
      // cause Jacobian be rectangular M x N with M>=N
      if (data_count < num_params) throw Exception::UnableToFit(__FILE__, __LINE__, __PRETTY_FUNCTION__, "UnableToFit-FinalSet", "Skipping feature, gsl always expects N>=p");

      gsl_multifit_function_fdf func;
      gsl_vector_view x = gsl_vector_view_array(x_init, num_params);
      gsl_rng_env_setup();
      func.f = (residual);
      func.df = (jacobian);
      func.fdf = (evaluate);
      func.n = data_count;
      func.p = num_params;
      func.params = &traces;
      T = gsl_multifit_fdfsolver_lmsder;
      s = gsl_multifit_fdfsolver_alloc(T, data_count, num_params);
      gsl_multifit_fdfsolver_set(s, &func, &x.vector);
      SignedSize iter = 0;
      Int gsl_status_;
      do
      {
        iter++;
        gsl_status_ = gsl_multifit_fdfsolver_iterate(s);
        printState_(iter, s);
        if (gsl_status_) break;
        gsl_status_ = gsl_multifit_test_delta(s->dx, s->x, epsilon_abs_, epsilon_rel_);
      }
      while (gsl_status_ == GSL_CONTINUE && iter < max_iterations_);

      // get the parameters out of the fdfsolver
      getOptimizedParameters_(s);

      gsl_multifit_fdfsolver_free(s);
    }

    /** Test for the convergence of the sequence by comparing the last iteration step dx with the absolute error epsabs and relative error epsrel to the current position x */
    /// Absolute error
    DoubleReal epsilon_abs_;
    /// Relative error
    DoubleReal epsilon_rel_;
    /// Maximum number of iterations
    SignedSize max_iterations_;

  };

}

#endif // #ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_FEATUREFINDERALGORITHMPICKED_RTFITTING_H