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//
// $Id$
//
//
// Original author: Witold Wolski <wewolski@gmail.com>
//
// Copyright : ETH Zurich
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
//
#ifndef CONVERT2DENSE_H
#define CONVERT2DENSE_H
#include <vector>
#include <iostream>
#include <numeric>
#include <boost/assert.hpp>
#include <boost/cstdint.hpp>
#include "pwiz/utility/findmf/base/resample/masscomparefunctors.hpp"
#include "pwiz/utility/findmf/base/resample/breakspec.hpp"
#include "pwiz/utility/findmf/base/resample/bin1d.hpp"
namespace ralab
{
namespace base
{
namespace resample
{
typedef boost::int32_t int32_t;
struct Convert2Dense
{
ralab::base::resample::Bin1D bin_;
std::vector<int32_t> idx_;//small workder vecs
std::vector<double> weight_;
double am_; //parameter describing the sampling width
Convert2Dense(double am = 0.1):bin_(),idx_(),weight_(),am_(){
}
/// computes split points of an map.
std::size_t defBreak(std::pair<double, double> & mzrange, double ppm ){
ralab::base::resample::PPMCompFunctor<double> ppmf(ppm);
ralab::base::resample::breaks( mzrange.first - 1. , mzrange.second + 1. , ppmf , bin_.breaks_ );
bin_.reset();
return bin_.breaks_.size();
}
/// Converts a sparse spec to a dense spec
template<typename Tmass, typename Tintens, typename Tout >
void convert2dense(Tmass beginMass, Tmass endMass, Tintens intens,
Tout ass
)
{
for( ; beginMass != (endMass -1) ; ++beginMass, ++intens ){
double mass1 = *beginMass;
double mass2 = *(beginMass+1);
double predmass2 = mass1 + (am_* sqrt(mass1))*1.01;
if(mass2 > predmass2){
mass2 = predmass2;
}
double deltamass = mass2-mass1;
double deltamasshalf;
if(true){
deltamasshalf= deltamass/2.;
}
else{
deltamasshalf = deltamass;
}
bin_(mass1-deltamasshalf,mass2-deltamasshalf,idx_,weight_);
double intensd = static_cast<double>(*intens);
double sum = std::accumulate(weight_.begin(),weight_.end(),0.);
BOOST_ASSERT(fabs(deltamass- sum) < 1e-11);
double check = 0.;
for(std::size_t i = 0 ; i < idx_.size();++i){
if((idx_[i]>=0) &(idx_[i] < static_cast<int32_t>(bin_.breaks_.size() - 1)))
{
double bb= intensd * weight_[i]/deltamass;
*(ass + idx_[i]) += bb;
check += bb;
}
}
BOOST_ASSERT( fabs(check - intensd) < 1e-3 );
}
}//convert2dense
void getMids(std::vector<double> & mids)
{
ralab::base::resample::getMids(bin_.breaks_, mids );
}
/// Converts a sparse spec to a dense spec
template<typename Tmass, typename Tintens >
void convert2dense(Tmass beginMass, Tmass endMass, Tintens intens,
std::vector<typename std::iterator_traits<Tintens>::value_type > & gg
){
gg.resize(bin_.breaks_.size() - 1);
convert2dense(beginMass,endMass, intens, gg.begin());
}
};
}
}
}
#endif // CONVERT2DENSE_H
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