SqrtMower.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2020.
//
// 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: Mathias Walzer $
// $Authors: $
// --------------------------------------------------------------------------
//
#pragma once
 
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSExperiment.h>
 
#include <cmath>
 
namespace OpenMS
{
  class OPENMS_DLLAPI SqrtMower :
    public DefaultParamHandler
  {
public:
 
    // @name Constructors and Destructors
    // @{
    SqrtMower();
    ~SqrtMower() override;
 
    SqrtMower(const SqrtMower & source);
    SqrtMower & operator=(const SqrtMower & source);
    // @}
 
    template <typename SpectrumType>
    void filterSpectrum(SpectrumType & spectrum)
    {
      bool warning = false;
      for (typename SpectrumType::Iterator it = spectrum.begin(); it != spectrum.end(); ++it)
      {
        double intens = it->getIntensity();
        if (intens < 0)
        {
          intens = 0;
          warning = true;
        }
        it->setIntensity(std::sqrt(intens));
      }
      if (warning)
      {
        std::cerr << "Warning negative intensities were set to zero" << std::endl;
      }
      return;
    }
 
    void filterPeakSpectrum(PeakSpectrum & spectrum);
 
    void filterPeakMap(PeakMap & exp);
 
    //TODO reimplement DefaultParamHandler::updateMembers_()
 
    // @}
 
  };
 
}