FeatureDetectorTuningTest.cpp

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//
// $Id: FeatureDetectorTuningTest.cpp 4129 2012-11-20 00:05:37Z chambm $
//
//
// Original author: Darren Kessner <darren@proteowizard.org>
//
// Copyright 2009 Center for Applied Molecular Medicine
//   University of Southern California, Los Angeles, CA
//
// 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.
//


#include "PeakExtractor.hpp"
#include "PeakelGrower.hpp"
#include "PeakelPicker.hpp"
#include "pwiz/data/msdata/MSDataFile.hpp"
#include "pwiz/analysis/passive/MSDataCache.hpp"
#include "pwiz/utility/misc/unit.hpp"
#include "boost/filesystem/path.hpp"
#include "pwiz/utility/misc/Std.hpp"

using namespace pwiz::util;
using namespace pwiz::analysis;
using namespace pwiz::data;
using namespace pwiz::data::peakdata;
using namespace pwiz::msdata;
namespace bfs = boost::filesystem;


ostream* os_ = 0;


shared_ptr<PeakExtractor> createPeakExtractor()
{
    shared_ptr<NoiseCalculator> noiseCalculator(new NoiseCalculator_2Pass);

    PeakFinder_SNR::Config pfsnrConfig;
    pfsnrConfig.windowRadius = 2;
    pfsnrConfig.zValueThreshold = 3;

    shared_ptr<PeakFinder> peakFinder(new PeakFinder_SNR(noiseCalculator, pfsnrConfig));

    PeakFitter_Parabola::Config pfpConfig;
    pfpConfig.windowRadius = 1; // (windowRadius != 1) is not good for real data
    shared_ptr<PeakFitter> peakFitter(new PeakFitter_Parabola(pfpConfig));

    return shared_ptr<PeakExtractor>(new PeakExtractor(peakFinder, peakFitter));
}


struct SetRetentionTime
{
    double rt;
    SetRetentionTime(double _rt) : rt(_rt) {}
    void operator()(Peak& peak) {peak.retentionTime = rt;}
};


vector< vector<Peak> > extractPeaks(const MSData& msd, const PeakExtractor& peakExtractor)
{
    MSDataCache msdCache;
    msdCache.open(msd);

    const size_t spectrumCount = msdCache.size();
    vector< vector<Peak> > result(spectrumCount);

    for (size_t index=0; index<spectrumCount; index++)
    {
        const SpectrumInfo& spectrumInfo = msdCache.spectrumInfo(index, true);

        vector<Peak>& peaks = result[index];
        peakExtractor.extractPeaks(spectrumInfo.data, peaks);
        for_each(peaks.begin(), peaks.end(), SetRetentionTime(spectrumInfo.retentionTime));

        if (os_)
        {
            *os_ << "index: " << index << endl;
            *os_ << "peaks: " << peaks.size() << endl; 
            copy(peaks.begin(), peaks.end(), ostream_iterator<Peak>(*os_, "\n"));
        }
    }

    return result;
}


shared_ptr<PeakelGrower> createPeakelGrower()
{
    PeakelGrower_Proximity::Config config;
    config.mzTolerance = .01;
    config.rtTolerance = 10; // seconds

    return shared_ptr<PeakelGrower>(new PeakelGrower_Proximity(config));
}


void print(ostream& os, const string& label, vector<PeakelPtr> v)
{
    os << label << ":\n";
    for (vector<PeakelPtr>::const_iterator it=v.begin(); it!=v.end(); ++it)
        os << **it << endl;
}


void verifyBombesinPeakels(const PeakelField& peakelField)
{
    // TODO: assert # peaks/peakel, verify metadata

    // charge state 2

    vector<PeakelPtr> bombesin_2_0 = peakelField.find(810.41, .01, RTMatches_Contains<Peakel>(1870));
    if (os_) print(*os_, "bombesin_2_0", bombesin_2_0);
    unit_assert(bombesin_2_0.size() == 1);

    vector<PeakelPtr> bombesin_2_1 = peakelField.find(810.91, .01, RTMatches_Contains<Peakel>(1870));
    if (os_) print(*os_, "bombesin_2_1", bombesin_2_1);
    unit_assert(bombesin_2_1.size() == 1);

    vector<PeakelPtr> bombesin_2_2 = peakelField.find(811.41, .01, RTMatches_Contains<Peakel>(1870));
    if (os_) print(*os_, "bombesin_2_2", bombesin_2_2);
    unit_assert(bombesin_2_2.size() == 1);

    vector<PeakelPtr> bombesin_2_3 = peakelField.find(811.91, .01, RTMatches_Contains<Peakel>(1870,10));
    if (os_) print(*os_, "bombesin_2_3", bombesin_2_3);
    unit_assert(bombesin_2_3.size() == 1);

    // charge state 3

    vector<PeakelPtr> bombesin_3_0 = peakelField.find(540.61, .01, RTMatches_Contains<Peakel>(1870));
    if (os_) print(*os_, "bombesin_3_0", bombesin_3_0);
    unit_assert(bombesin_3_0.size() == 1);

    vector<PeakelPtr> bombesin_3_1 = peakelField.find(540.61 + 1./3., .02, RTMatches_Contains<Peakel>(1865));
    if (os_) print(*os_, "bombesin_3_1", bombesin_3_1);
    unit_assert(bombesin_3_1.size() == 1);

    vector<PeakelPtr> bombesin_3_2 = peakelField.find(540.61 + 2./3., .02, RTMatches_Contains<Peakel>(1865,5));
    if (os_) print(*os_, "bombesin_3_2", bombesin_3_2);
    unit_assert(bombesin_3_2.size() == 1);
    // TODO: verify peaks.size() == 1
}


shared_ptr<PeakelPicker> createPeakelPicker()
{
    PeakelPicker_Basic::Config config;
    //config.log = os_;
    config.minMonoisotopicPeakelSize = 2;

    return shared_ptr<PeakelPicker>(new PeakelPicker_Basic(config));
}


void verifyBombesinFeatures(const FeatureField& featureField)
{
    const double epsilon = .01;

    const double mz_bomb2 = 810.415;
    vector<FeaturePtr> bombesin_2_found = featureField.find(mz_bomb2, epsilon, 
        RTMatches_Contains<Feature>(1865));
    unit_assert(bombesin_2_found.size() == 1);
    const Feature& bombesin_2 = *bombesin_2_found[0];
    unit_assert(bombesin_2.charge == 2);
    unit_assert(bombesin_2.peakels.size() == 5);
    unit_assert_equal(bombesin_2.peakels[0]->mz, mz_bomb2, epsilon);
    unit_assert_equal(bombesin_2.peakels[1]->mz, mz_bomb2+.5, epsilon);
    unit_assert_equal(bombesin_2.peakels[2]->mz, mz_bomb2+1, epsilon);
    unit_assert_equal(bombesin_2.peakels[3]->mz, mz_bomb2+1.5, epsilon);
    unit_assert_equal(bombesin_2.peakels[4]->mz, mz_bomb2+2, epsilon);
    //TODO: verify feature metadata

    const double mz_bomb3 = 540.612;
    vector<FeaturePtr> bombesin_3_found = featureField.find(mz_bomb3, epsilon, 
        RTMatches_Contains<Feature>(1865));
    unit_assert(bombesin_3_found.size() == 1);
    const Feature& bombesin_3 = *bombesin_3_found[0];
    unit_assert(bombesin_3.charge == 3);
    unit_assert(bombesin_3.peakels.size() == 3);
    unit_assert_equal(bombesin_3.peakels[0]->mz, mz_bomb3, epsilon);
    unit_assert_equal(bombesin_3.peakels[1]->mz, mz_bomb3+1./3, epsilon);
    unit_assert_equal(bombesin_3.peakels[2]->mz, mz_bomb3+2./3, epsilon);
    //TODO: verify feature metadata
}


void testBombesin(const string& filename)
{
    if (os_) *os_ << "testBombesin()" << endl;

    // open data file and check sanity

    MSDataFile msd(filename);
    unit_assert(msd.run.spectrumListPtr.get());
    unit_assert(msd.run.spectrumListPtr->size() == 8);

    // instantiate PeakExtractor and extract peaks

    shared_ptr<PeakExtractor> peakExtractor = createPeakExtractor();
    vector< vector<Peak> > peaks = extractPeaks(msd, *peakExtractor);
    unit_assert(peaks.size() == 8);

    // grow peakels
    shared_ptr<PeakelGrower> peakelGrower = createPeakelGrower();
    PeakelField peakelField;
    peakelGrower->sowPeaks(peakelField, peaks);

    if (os_) *os_ << "peakelField:\n" << peakelField << endl;
    verifyBombesinPeakels(peakelField);

    // pick peakels

    shared_ptr<PeakelPicker> peakelPicker = createPeakelPicker();
    FeatureField featureField;
    peakelPicker->pick(peakelField, featureField);

    if (os_) *os_ << "featureField:\n" << featureField << endl;
    verifyBombesinFeatures(featureField);
}


void test(const bfs::path& datadir)
{
    testBombesin((datadir / "FeatureDetectorTest_Bombesin.mzML").string());
}


int main(int argc, char* argv[])
{
    TEST_PROLOG(argc, argv)

    try
    {
        bfs::path datadir = ".";

        for (int i=1; i<argc; i++)
        {
            if (!strcmp(argv[i],"-v")) 
                os_ = &cout;
            else
                // hack to allow running unit test from a different directory:
                // Jamfile passes full path to specified input file.
                // we want the path, so we can ignore filename
                datadir = bfs::path(argv[i]).branch_path(); 
        }   
        
        test(datadir);
    }
    catch (exception& e)
    {
        TEST_FAILED(e.what())
    }
    catch (...)
    {
        TEST_FAILED("Caught unknown exception.")
    }

    TEST_EPILOG
}