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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: Alexandra Zerck $
// $Authors: $
// --------------------------------------------------------------------------
#include <OpenMS/CONCEPT/ClassTest.h>
///////////////////////////
#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/TwoDOptimization.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/FORMAT/ParamXMLFile.h>
///////////////////////////
using namespace OpenMS;
using namespace std;
START_TEST(TwoDOptimization, "$Id: TwoDOptimization_test.C 11338 2013-06-05 20:48:48Z hroest $")
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
TwoDOptimization* ptr = 0;
TwoDOptimization* nullPointer = 0;
START_SECTION((TwoDOptimization ( )))
ptr = new TwoDOptimization();
TEST_NOT_EQUAL(ptr, nullPointer)
END_SECTION
START_SECTION((~TwoDOptimization()))
delete ptr;
END_SECTION
START_SECTION((TwoDOptimization& operator=(const TwoDOptimization& opt)))
TwoDOptimization opt_2d;
struct OptimizationFunctions::PenaltyFactorsIntensity penalties;
penalties.pos = 2;
penalties.height = 3;
penalties.lWidth = 4;
penalties.rWidth = 5;
opt_2d.setPenalties(penalties);
opt_2d.setMaxIterations(10);
opt_2d.setMaxAbsError(0.01);
opt_2d.setMaxRelError(0.001);
TwoDOptimization opt_2d_copy;
opt_2d_copy = opt_2d;
struct OptimizationFunctions::PenaltyFactorsIntensity penalties_copy = opt_2d_copy.getPenalties();
unsigned int number = opt_2d_copy.getMaxIterations();
DoubleReal abs_err = opt_2d_copy.getMaxAbsError();
DoubleReal rel_err = opt_2d_copy.getMaxRelError();
TEST_REAL_SIMILAR(penalties.pos,penalties_copy.pos)
TEST_REAL_SIMILAR(penalties.lWidth,penalties_copy.lWidth)
TEST_REAL_SIMILAR(penalties.rWidth,penalties_copy.rWidth)
TEST_REAL_SIMILAR(penalties.height,penalties_copy.height)
TEST_EQUAL(number == 10, true)
TEST_REAL_SIMILAR(abs_err, 0.01)
TEST_REAL_SIMILAR(rel_err, 0.001)
END_SECTION
START_SECTION((TwoDOptimization(const TwoDOptimization& opt)))
TOLERANCE_ABSOLUTE(0.001)
TwoDOptimization opt_2d;
struct OptimizationFunctions::PenaltyFactorsIntensity penalties;
opt_2d.setPenalties(penalties);
opt_2d.setMaxIterations(10);
opt_2d.setMaxAbsError(0.01);
opt_2d.setMaxRelError(0.001);
TwoDOptimization opt_2d_copy(opt_2d);
struct OptimizationFunctions::PenaltyFactorsIntensity penalties_copy = opt_2d_copy.getPenalties();
unsigned int number = opt_2d_copy.getMaxIterations();
DoubleReal abs_err = opt_2d_copy.getMaxAbsError();
DoubleReal rel_err = opt_2d_copy.getMaxRelError();
TEST_REAL_SIMILAR(penalties.pos,penalties_copy.pos)
TEST_REAL_SIMILAR(penalties.lWidth,penalties_copy.lWidth)
TEST_REAL_SIMILAR(penalties.rWidth,penalties_copy.rWidth)
TEST_REAL_SIMILAR(penalties.height,penalties_copy.height)
TEST_EQUAL(number == 10, true)
TEST_REAL_SIMILAR(abs_err, 0.01)
TEST_REAL_SIMILAR(rel_err, 0.001)
END_SECTION
START_SECTION(( template <typename InputSpectrumIterator,typename OutputPeakType> void optimize(InputSpectrumIterator first,InputSpectrumIterator last,MSExperiment< OutputPeakType >& ms_exp,bool real2D=true)))
//******************************************************************
//test exception with unequal number of scans
{
MSExperiment<Peak1D> exp_in;
exp_in.resize(1);
MSExperiment<Peak1D>::const_iterator first1 = exp_in.begin();
MSExperiment<Peak1D>::const_iterator last1 = exp_in.end();
MSExperiment<> exp_out;
TwoDOptimization opt1;
TEST_EXCEPTION(Exception::IllegalArgument, opt1.optimize(first1,last1,exp_out));
}
//******************************************************************
//test exception when meta data is missing
{
MSExperiment<Peak1D> exp_in;
exp_in.resize(1);
MSExperiment<Peak1D>::const_iterator first1 = exp_in.begin();
MSExperiment<Peak1D>::const_iterator last1 = exp_in.end();
MSExperiment<> exp_out;
exp_out.resize(1);
TwoDOptimization opt1;
TEST_EXCEPTION(Exception::IllegalArgument, opt1.optimize(first1,last1,exp_out));
}
//******************************************************************
// test for 2D optimization
TOLERANCE_ABSOLUTE(0.04)
MSSpectrum<> peaks;
peaks.getFloatDataArrays().resize(6);
peaks.getFloatDataArrays()[1].setName("maximumIntensity");
peaks.getFloatDataArrays()[1].push_back(700.); //intensity
peaks.getFloatDataArrays()[3].setName("leftWidth");
peaks.getFloatDataArrays()[3].push_back(12.5f); //left width
peaks.getFloatDataArrays()[4].setName("rightWidth");
peaks.getFloatDataArrays()[4].push_back(12.5f); //right width
peaks.getFloatDataArrays()[5].setName("peakShape");
peaks.getFloatDataArrays()[5].push_back(0); //shape
peaks.getFloatDataArrays()[1].push_back(700.); //intensity
peaks.getFloatDataArrays()[3].push_back(12.5f); //left width
peaks.getFloatDataArrays()[4].push_back(12.5f); //right width
peaks.getFloatDataArrays()[5].push_back(0); //shape
MSSpectrum<> peaks2;
peaks2.getFloatDataArrays().resize(6);
peaks2.getFloatDataArrays()[1].setName("maximumIntensity");
peaks2.getFloatDataArrays()[1].push_back(700.); //intensity
peaks2.getFloatDataArrays()[3].setName("leftWidth");
peaks2.getFloatDataArrays()[3].push_back(12.5f); //left width
peaks2.getFloatDataArrays()[4].setName("rightWidth");
peaks2.getFloatDataArrays()[4].push_back(12.5f); //right width
peaks2.getFloatDataArrays()[5].setName("peakShape");
peaks2.getFloatDataArrays()[5].push_back(0); //shape
peaks2.getFloatDataArrays()[1].push_back(700.); //intensity
peaks2.getFloatDataArrays()[3].push_back(12.5f); //left width
peaks2.getFloatDataArrays()[4].push_back(12.5f); //right width
peaks2.getFloatDataArrays()[5].push_back(0); //shape
Peak1D peak;
PeakShape peak_shape,peak_shape2;
peak.setMZ(500.);
peak.setIntensity(171.69f);
peak_shape.mz_position = 500;
peak_shape.left_width = 12.5;
peak_shape.right_width = 12.5;
peak_shape.area = 171.69;
peak_shape.height = 700;
peak_shape.type = PeakShape::LORENTZ_PEAK;
peaks.push_back(peak);
peak.setMZ(501.);
peak.setIntensity(171.69f);
peak_shape2.mz_position = 501;
peak_shape2.left_width = 12.5;
peak_shape2.right_width = 12.5;
peak_shape2.area = 171.69;
peak_shape2.height = 700;
peak_shape2.type = PeakShape::LORENTZ_PEAK;
peaks.push_back(peak);
MSExperiment<> ms_exp;
ms_exp.addSpectrum(peaks);
ms_exp.begin()->setRT(100);
float origin = 499;
float spacing = 0.1f;
MSSpectrum<Peak1D > raw_spec;
for (Size i = 0; i < 20 ;++i)
{
Peak1D data_point;
data_point.setMZ(origin +i*spacing);
data_point.setIntensity(peak_shape(origin +i*spacing)+peak_shape2(origin +i*spacing));
raw_spec.push_back(data_point);
}
peak.setMZ(500.02);
peak.setIntensity(171.69f);
peak_shape.mz_position = 500;
peak_shape.left_width = 12.5;
peak_shape.right_width = 12.5;
peak_shape.area = 171.69;
peak_shape.height = 700;
peak_shape.type = PeakShape::LORENTZ_PEAK;
peaks2.push_back(peak);
peak.setMZ(501);
peak.setIntensity(171.69f);
peak_shape2.mz_position = 501;
peak_shape2.left_width = 12.5;
peak_shape2.right_width = 12.5;
peak_shape2.area = 171.69;
peak_shape2.height = 700;
peak_shape2.type = PeakShape::LORENTZ_PEAK;
peaks2.push_back(peak);
ms_exp.addSpectrum(peaks2);
(ms_exp.begin()+1)->setRT(101);
MSSpectrum<Peak1D > raw_spec2;
for (Size i = 0; i < 20 ;++i)
{
Peak1D data_point;
data_point.setMZ(origin +i*spacing);
data_point.setIntensity(peak_shape(origin +i*spacing)+peak_shape2(origin +i*spacing));
raw_spec2.push_back(data_point);
}
MSExperiment<Peak1D > raw_exp;
raw_exp.addSpectrum(raw_spec);
raw_exp.addSpectrum(raw_spec2);
raw_exp.begin()->setRT(100);
(raw_exp.begin()+1)->setRT(101);
String file = OPENMS_GET_TEST_DATA_PATH("TwoDOptimization.xml");
Param param;
ParamXMLFile paramFile;
paramFile.load(file, param);
MSExperiment<Peak1D >::const_iterator first,last;
first = raw_exp.begin();
last = raw_exp.end();
TwoDOptimization opt_2d;
opt_2d.setParameters(param);
opt_2d.optimize(first,last,ms_exp,true);
TEST_REAL_SIMILAR(ms_exp[0][0].getMZ(),500)
TEST_REAL_SIMILAR(ms_exp[0].getFloatDataArrays()[3][0],12.5)
TEST_REAL_SIMILAR(ms_exp[0].getFloatDataArrays()[4][0],12.5)
TEST_REAL_SIMILAR(ms_exp[0][0].getIntensity(),171.69)
TEST_REAL_SIMILAR(ms_exp[0][1].getMZ(),501)
TEST_REAL_SIMILAR(ms_exp[0].getFloatDataArrays()[3][1],12.5)
TEST_REAL_SIMILAR(ms_exp[0].getFloatDataArrays()[4][1],12.5)
TEST_REAL_SIMILAR(ms_exp[0][1].getIntensity(),171.69)
TEST_REAL_SIMILAR(ms_exp[1][0].getMZ(),500)
TEST_REAL_SIMILAR(ms_exp[1].getFloatDataArrays()[3][0],12.5)
TEST_REAL_SIMILAR(ms_exp[1].getFloatDataArrays()[4][0],12.5)
TEST_REAL_SIMILAR(ms_exp[1][0].getIntensity(),171.69)
TEST_REAL_SIMILAR(ms_exp[1][1].getMZ(),501)
TEST_REAL_SIMILAR(ms_exp[1].getFloatDataArrays()[3][1],12.5)
TEST_REAL_SIMILAR(ms_exp[1].getFloatDataArrays()[4][1],12.5)
TEST_REAL_SIMILAR(ms_exp[1][1].getIntensity(),171.69)
peaks2.clear(false);
peaks2.getFloatDataArrays()[3][0]=12.5; //left width
peaks2.getFloatDataArrays()[4][0]=12.5; //right width
peaks2.getFloatDataArrays()[3][1]=12.5; //left width
peaks2.getFloatDataArrays()[4][1]=12.5; //right width
peaks2.getFloatDataArrays()[1][0]=700.; //intensity
peaks2.getFloatDataArrays()[1][1]=800.; //intensity
peak.setMZ(900);
peak.setIntensity(105.79f);
peak_shape.mz_position = 900;
peak_shape.left_width = 12.5;
peak_shape.right_width = 12.5;
peak_shape.area = 171.69;
peak_shape.height = 700;
peak_shape.type = PeakShape::LORENTZ_PEAK;
peaks2.push_back(peak);
peak.setMZ(901);
peak.setIntensity(105.79f);
peak_shape2.mz_position = 901;
peak_shape2.left_width = 12.5;
peak_shape2.right_width = 12.5;
peak_shape2.area = 171.69;
peak_shape2.height = 700;
peak_shape2.type = PeakShape::LORENTZ_PEAK;
peaks2.push_back(peak);
ms_exp.addSpectrum(peaks2);
(ms_exp.begin()+2)->setRT(102);
raw_spec2.clear(true);
origin = 899;
for (Size i = 0; i < 20 ;++i)
{
Peak1D data_point;
data_point.setMZ(origin +i*spacing);
data_point.setIntensity(peak_shape(origin +i*spacing)+peak_shape2(origin +i*spacing));
raw_spec2.push_back(data_point);
}
raw_exp.addSpectrum(raw_spec2);
(raw_exp.begin()+2)->setRT(102);
first = raw_exp.begin();
last = raw_exp.end();
TwoDOptimization opt_1d;
opt_1d.setParameters(param);
opt_1d.optimize(first,last,ms_exp,false); // test 1D optimization
TEST_REAL_SIMILAR(ms_exp[0][0].getMZ(),500)
TEST_REAL_SIMILAR(ms_exp[0].getFloatDataArrays()[3][0],12.5)
TEST_REAL_SIMILAR(ms_exp[0].getFloatDataArrays()[4][0],12.5)
TEST_REAL_SIMILAR(ms_exp[0][0].getIntensity(),171.69)
TEST_REAL_SIMILAR(ms_exp[0][1].getMZ(),501)
TEST_REAL_SIMILAR(ms_exp[0].getFloatDataArrays()[3][1],12.5)
TEST_REAL_SIMILAR(ms_exp[0].getFloatDataArrays()[4][1],12.5)
TEST_REAL_SIMILAR(ms_exp[0][1].getIntensity(),171.69)
TEST_REAL_SIMILAR(ms_exp[1][0].getMZ(),500)
TEST_REAL_SIMILAR(ms_exp[1].getFloatDataArrays()[3][0],12.5)
TEST_REAL_SIMILAR(ms_exp[1].getFloatDataArrays()[4][0],12.5)
TEST_REAL_SIMILAR(ms_exp[1][0].getIntensity(),171.69)
TEST_REAL_SIMILAR(ms_exp[1][1].getMZ(),501)
TEST_REAL_SIMILAR(ms_exp[1].getFloatDataArrays()[3][1],12.5)
TEST_REAL_SIMILAR(ms_exp[1].getFloatDataArrays()[4][1],12.5)
TEST_REAL_SIMILAR(ms_exp[1][1].getIntensity(),171.69)
TEST_REAL_SIMILAR(ms_exp[2][0].getMZ(),900)
TEST_REAL_SIMILAR(ms_exp[2].getFloatDataArrays()[3][0],12.5)
TEST_REAL_SIMILAR(ms_exp[2].getFloatDataArrays()[4][0],12.5)
TEST_REAL_SIMILAR(ms_exp[2][0].getIntensity(),171.69)
TEST_REAL_SIMILAR(ms_exp[2][1].getMZ(),901)
TEST_REAL_SIMILAR(ms_exp[2].getFloatDataArrays()[3][1],12.5)
TEST_REAL_SIMILAR(ms_exp[2].getFloatDataArrays()[4][1],12.5)
TEST_REAL_SIMILAR(ms_exp[2][1].getIntensity(),171.69)
END_SECTION
START_SECTION((void setMaxAbsError(DoubleReal eps_abs)))
TOLERANCE_ABSOLUTE(0.0001)
DoubleReal abs_err = 0.01;
TwoDOptimization opt_2d;
opt_2d.setMaxAbsError(abs_err);
TEST_REAL_SIMILAR(abs_err, opt_2d.getMaxAbsError())
END_SECTION
START_SECTION((void setMaxRelError(DoubleReal eps_rel)))
TOLERANCE_ABSOLUTE(0.0001)
DoubleReal rel_err = 0.01;
TwoDOptimization opt_2d;
opt_2d.setMaxRelError(rel_err);
TEST_REAL_SIMILAR(rel_err, opt_2d.getMaxRelError())
END_SECTION
START_SECTION((DoubleReal getMaxAbsError() const))
TOLERANCE_ABSOLUTE(0.0001)
DoubleReal abs_err = 0.01;
TwoDOptimization opt_2d;
opt_2d.setMaxAbsError(abs_err);
TEST_REAL_SIMILAR(abs_err, opt_2d.getMaxAbsError())
END_SECTION
START_SECTION((DoubleReal getMaxRelError() const))
TOLERANCE_ABSOLUTE(0.0001)
DoubleReal rel_err = 0.01;
TwoDOptimization opt_2d;
opt_2d.setMaxRelError(rel_err);
TEST_REAL_SIMILAR(rel_err, opt_2d.getMaxRelError())
END_SECTION
START_SECTION((void setMaxPeakDistance(DoubleReal max_peak_distance)))
TOLERANCE_ABSOLUTE(0.0001)
DoubleReal max_peak_distance = 0.01;
TwoDOptimization opt_2d;
opt_2d.setMaxPeakDistance(max_peak_distance);
TEST_REAL_SIMILAR(max_peak_distance, opt_2d.getMaxPeakDistance())
END_SECTION
START_SECTION((DoubleReal getMaxPeakDistance() const))
TOLERANCE_ABSOLUTE(0.0001)
DoubleReal max_peak_distance = 0.01;
TwoDOptimization opt_2d;
opt_2d.setMaxPeakDistance(max_peak_distance);
TEST_REAL_SIMILAR(max_peak_distance, opt_2d.getMaxPeakDistance())
END_SECTION
START_SECTION((void setMZTolerance(DoubleReal tolerance_mz)))
TOLERANCE_ABSOLUTE(0.0001)
DoubleReal mz_tolerance = 0.01;
TwoDOptimization opt_2d;
opt_2d.setMZTolerance(mz_tolerance);
TEST_REAL_SIMILAR(mz_tolerance, opt_2d.getMZTolerance())
END_SECTION
START_SECTION((DoubleReal getMZTolerance() const))
TOLERANCE_ABSOLUTE(0.0001)
DoubleReal mz_tolerance = 0.01;
TwoDOptimization opt_2d;
opt_2d.setMZTolerance(mz_tolerance);
TEST_REAL_SIMILAR(mz_tolerance, opt_2d.getMZTolerance())
END_SECTION
START_SECTION((void setMaxIterations(UInt max_iteration)))
UInt number = 20;
TwoDOptimization opt_2d;
opt_2d.setMaxIterations(number);
TEST_EQUAL(number == opt_2d.getMaxIterations(), true)
END_SECTION
START_SECTION((UInt getMaxIterations() const))
UInt number = 20;
TwoDOptimization opt_2d;
opt_2d.setMaxIterations(number);
TEST_EQUAL(number == opt_2d.getMaxIterations(), true)
END_SECTION
START_SECTION((void setPenalties(OptimizationFunctions::PenaltyFactorsIntensity& penalties)))
TOLERANCE_ABSOLUTE(0.0001)
struct OptimizationFunctions::PenaltyFactorsIntensity penalties;
penalties.pos = 0;
penalties.lWidth = 1;
penalties.rWidth = 2;
penalties.height = 3;
TwoDOptimization opt_2d;
opt_2d.setPenalties(penalties);
TEST_REAL_SIMILAR(penalties.pos,opt_2d.getPenalties().pos)
TEST_REAL_SIMILAR(penalties.lWidth,opt_2d.getPenalties().lWidth)
TEST_REAL_SIMILAR(penalties.rWidth,opt_2d.getPenalties().rWidth)
TEST_REAL_SIMILAR(penalties.height,opt_2d.getPenalties().height)
END_SECTION
START_SECTION((const OptimizationFunctions::PenaltyFactorsIntensity& getPenalties() const))
TOLERANCE_ABSOLUTE(0.0001)
struct OptimizationFunctions::PenaltyFactorsIntensity penalties;
penalties.pos = 0;
penalties.lWidth = 1;
penalties.rWidth = 2;
penalties.height = 3;
TwoDOptimization opt_2d;
opt_2d.setPenalties(penalties);
TEST_REAL_SIMILAR(penalties.pos,opt_2d.getPenalties().pos)
TEST_REAL_SIMILAR(penalties.lWidth,opt_2d.getPenalties().lWidth)
TEST_REAL_SIMILAR(penalties.rWidth,opt_2d.getPenalties().rWidth)
TEST_REAL_SIMILAR(penalties.height,opt_2d.getPenalties().height)
END_SECTION
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
|
