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/*******************************************************************************
* Copyright (c) 2023 Olivier Langella <Olivier.Langella@u-psud.fr>.
*
* This file is part of the PAPPSOms++ library.
*
* PAPPSOms++ is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* PAPPSOms++ is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
*
******************************************************************************/
// cmake .. -DCMAKE_BUILD_TYPE=Debug -DMAKE_TESTS=1 -DUSEPAPPSOTREE=1
//./tests/catch2-only-tests [MsRunReader] -s
//./tests/catch2-only-tests [MsRunReaderPerf] -s
//./tests/catch2-only-tests [MsRunReaderPerf] -s --benchmark-samples 5
#define CATCH_CONFIG_MAIN // This tells Catch to provide a main() - only do
// this in one cpp file
#define CATCH_CONFIG_ENABLE_BENCHMARKING
#include <catch2/catch_test_macros.hpp>
#include <catch2/benchmark/catch_benchmark.hpp>
#include <iostream>
#include <pappsomspp/core/pappsoexception.h>
#include <pappsomspp/core/exception/exceptionnotpossible.h>
#include <pappsomspp/core/msfile/msfileaccessor.h>
#include <pappsomspp/core/msrun/output/mzxmloutput.h>
#include <pappsomspp/core/processing/uimonitor/uimonitorvoid.h>
#include <pappsomspp/core/msrun/private/timsframesmsrunreader.h>
#include <QDebug>
#include <QtCore>
#include <QFile>
#include <QtConcurrent>
#include "tests/tests-config.h"
// #include "common.h"
using namespace std;
TEST_CASE("Test MsRunReader new API performance", "[MsRunReaderPerf]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
#if USEPAPPSOTREE == 1
SECTION("..:: MsRunReader performance check ::..")
{
qDebug();
pappso::MsFileAccessor file_access_A01(
"/gorgone/pappso/versions_logiciels_pappso/bruker/"
"200ngHeLaPASEF_2min_compressed.d",
"");
file_access_A01.setPreferredFileReaderType(pappso::Enums::MsDataFormat::brukerTims,
pappso::Enums::FileReaderType::tims_frames);
pappso::MsRunReaderSPtr msrunA01 = file_access_A01.getMsRunReaderSPtrByRunId("", "runa01");
pappso::MsRunReadConfig config;
// config.setRetentionTimeStartInSeconds(2490);
// config.setRetentionTimeEndInSeconds(2600);
config.setParameterValue(pappso::MsRunReadConfigParameter::TimsFrameIonMobScanIndexBegin, 100);
config.setParameterValue(pappso::MsRunReadConfigParameter::TimsFrameIonMobScanIndexEnd, 200);
config.setNeedPeakList(true);
config.setMsLevels({1});
// msrunA01.get()->setMonoThread(false);
pappso::MsRunQualifiedSpectrumLoader spectrum_list_reader;
BENCHMARK("without mz merge")
{
msrunA01.get()->readSpectrumCollection2(config, spectrum_list_reader);
};
// REQUIRE(spectrum_list_reader.getQualifiedMassSpectrumList().size() ==
// 33);
config.setParameterValue(pappso::MsRunReadConfigParameter::TimsFrameMzIndexMergeWindow, 7);
BENCHMARK("with TimsFramesMsRunReader_mz_index_merge_window 7")
{
msrunA01.get()->readSpectrumCollection2(config, spectrum_list_reader);
};
config.setParameterValue(pappso::MsRunReadConfigParameter::TimsFrameMzIndexMergeWindow, 15);
BENCHMARK("with TimsFramesMsRunReader_mz_index_merge_window 15")
{
msrunA01.get()->readSpectrumCollection2(config, spectrum_list_reader);
};
config.setParameterValue(pappso::MsRunReadConfigParameter::TimsFrameMzIndexMergeWindow, 30);
BENCHMARK("with TimsFramesMsRunReader_mz_index_merge_window 30")
{
msrunA01.get()->readSpectrumCollection2(config, spectrum_list_reader);
};
config.setParameterValue(pappso::MsRunReadConfigParameter::TimsFrameMzIndexMergeWindow, 600);
BENCHMARK("with TimsFramesMsRunReader_mz_index_merge_window 600")
{
msrunA01.get()->readSpectrumCollection2(config, spectrum_list_reader);
};
}
#endif
}
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