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// --------------------------------------------------------------------------
// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Andreas Bertsch $
// $Authors: Andreas Bertsch $
// --------------------------------------------------------------------------
//
#include <OpenMS/MATH/STATISTICS/GaussFitter.h>
#include <sstream>
using namespace std;
#define GAUSS_FITTER_VERBOSE
#undef GAUSS_FITTER_VERBOSE
#include <iostream>
namespace OpenMS
{
namespace Math
{
GaussFitter::GaussFitter()
{
init_param_.A = 0.06;
init_param_.x0 = 3.0;
init_param_.sigma = 0.5;
}
GaussFitter::~GaussFitter()
{
}
void GaussFitter::setInitialParameters(const GaussFitResult & param)
{
init_param_.A = param.A;
init_param_.x0 = param.x0;
init_param_.sigma = param.sigma;
}
const String & GaussFitter::getGnuplotFormula() const
{
return gnuplot_formula_;
}
int GaussFitter::gaussFitterf_(const gsl_vector * x, void * params, gsl_vector * f)
{
vector<DPosition<2> > * data = static_cast<vector<DPosition<2> > *>(params);
double A = gsl_vector_get(x, 0);
double x0 = gsl_vector_get(x, 1);
double sig = gsl_vector_get(x, 2);
UInt i = 0;
for (vector<DPosition<2> >::iterator it = data->begin(); it != data->end(); ++it)
{
gsl_vector_set(f, i++, A * exp(-1.0 * pow(it->getX() - x0, 2) / (2 * pow(sig, 2))) - it->getY());
}
return GSL_SUCCESS;
}
int GaussFitter::gaussFitterdf_(const gsl_vector * x, void * params, gsl_matrix * J)
{
vector<DPosition<2> > * data = static_cast<vector<DPosition<2> > *>(params);
double A = gsl_vector_get(x, 0);
double x0 = gsl_vector_get(x, 1);
double sig = gsl_vector_get(x, 2);
UInt i = 0;
for (vector<DPosition<2> >::iterator it = data->begin(); it != data->end(); ++it)
{
gsl_matrix_set(J, i, 0, exp(-1.0 * pow(it->getX() - x0, 2) / (2 * pow(sig, 2))));
gsl_matrix_set(J, i, 1, (A * exp(-1.0 * pow(it->getX() - x0, 2) / (2 * pow(sig, 2))) * (-1 * (-2 * it->getX() + 2.0 * x0) / (2 * pow(sig, 2)))));
gsl_matrix_set(J, i++, 2, (A * exp(-1.0 * pow(it->getX() - x0, 2) / (2 * pow(sig, 2))) * (pow(it->getX() - x0, 2) / (4 * pow(sig, 3)))));
}
return GSL_SUCCESS;
}
int GaussFitter::gaussFitterfdf_(const gsl_vector * x, void * params, gsl_vector * f, gsl_matrix * J)
{
gaussFitterf_(x, params, f);
gaussFitterdf_(x, params, J);
return GSL_SUCCESS;
}
#ifdef GAUSS_FITTER_VERBOSE
void GaussFitter::printState_(size_t iter, gsl_multifit_fdfsolver * s)
{
printf("iter: %3u x = % 15.8f % 15.8f % 15.8f "
"|f(x)| = %g\n",
iter,
gsl_vector_get(s->x, 0),
gsl_vector_get(s->x, 1),
gsl_vector_get(s->x, 2),
/*gsl_blas_dnrm2(s->f)*/ 0);
}
#endif
GaussFitter::GaussFitResult GaussFitter::fit(vector<DPosition<2> > & input)
{
const gsl_multifit_fdfsolver_type * T = NULL;
gsl_multifit_fdfsolver * s = NULL;
int status(0);
size_t iter = 0;
const size_t p = 3;
//gsl_matrix *covar = gsl_matrix_alloc (p, p);
gsl_multifit_function_fdf f;
double x_init[3] = { init_param_.A, init_param_.x0, init_param_.sigma };
gsl_vector_view x = gsl_vector_view_array(x_init, p);
const gsl_rng_type * type = NULL;
gsl_rng * r = NULL;
gsl_rng_env_setup();
type = gsl_rng_default;
r = gsl_rng_alloc(type);
f.f = &gaussFitterf_;
f.df = &gaussFitterdf_;
f.fdf = &gaussFitterfdf_;
f.n = input.size();
f.p = p;
f.params = &input;
T = gsl_multifit_fdfsolver_lmsder;
s = gsl_multifit_fdfsolver_alloc(T, input.size(), p);
gsl_multifit_fdfsolver_set(s, &f, &x.vector);
#ifdef GAUSS_FITTER_VERBOSE
printState_(iter, s);
#endif
do
{
iter++;
status = gsl_multifit_fdfsolver_iterate(s);
#ifdef GAUSS_FITTER_VERBOSE
printf("status = %s\n", gsl_strerror(status));
printState_(iter, s);
cerr << "f(x)=" << gsl_vector_get(s->x, 0) << " * exp(-(x - " << gsl_vector_get(s->x, 1) << ") ** 2 / 2 / (" << gsl_vector_get(s->x, 2) << ") ** 2)";
#endif
if (status)
{
break;
}
status = gsl_multifit_test_delta(s->dx, s->x,
1e-4, 1e-4);
}
while (status == GSL_CONTINUE && iter < 500);
if (status != GSL_SUCCESS)
{
gsl_rng_free(r);
gsl_multifit_fdfsolver_free(s);
throw Exception::UnableToFit(__FILE__, __LINE__, __PRETTY_FUNCTION__, "UnableToFit-GaussFitter", "Could not fit the gaussian to the data");
}
// write the result in a GaussFitResult struct
GaussFitResult result;
result.A = gsl_vector_get(s->x, 0);
result.x0 = gsl_vector_get(s->x, 1);
result.sigma = gsl_vector_get(s->x, 2);
// build a formula with the fitted parameters for gnuplot
stringstream formula;
formula << "f(x)=" << result.A << " * exp(-(x - " << result.x0 << ") ** 2 / 2 / (" << result.sigma << ") ** 2)";
gnuplot_formula_ = formula.str();
#ifdef GAUSS_FITTER_VERBOSE
cout << gnuplot_formula_ << endl;
#endif
gsl_rng_free(r);
gsl_multifit_fdfsolver_free(s);
return result;
}
} //namespace Math
} // namespace OpenMS
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