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//
// File: benchmark_mzcbor.cpp
// Created by: Olivier Langella
// Created on: 22/12/2025
//
/*******************************************************************************
* Copyright (c) 2025 Olivier Langella <Olivier.Langella@universite-paris-saclay.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/>.
*
******************************************************************************/
// ./tests/benchmarks/catch2-only-benchmarks [mzcbor] -s
// ./tests/benchmarks/catch2-only-benchmarks [mzcbor] -s --benchmark-samples 5
// ./tests/benchmarks/catch2-only-benchmarks [mzcborrandom] -s --benchmark-samples 5
// ./tests/benchmarks/catch2-only-benchmarks [mzcborxic] -s --benchmark-samples 5
#include <catch2/catch_test_macros.hpp>
#include <catch2/benchmark/catch_benchmark.hpp>
#include <pappsomspp/core/processing/uimonitor/uimonitorvoid.h>
#include <pappsomspp/core/msfile/msfileaccessor.h>
#include <pappsomspp/core/msrun/private/mzcbormsrunreader.h>
#include <pappsomspp/core/xicextractor/msrunxicextractorfactory.h>
#include <QDebug>
TEST_CASE("cbor psm map test suite.", "[mzcbor]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
SECTION("..:: PSM cbor features::..", "[mzml]")
{
pappso::MsFileAccessor file_access(
"/gorgone/pappso/moulon/raw/20250521_proteobench_dda_astral/"
"LFQ_Astral_DDA_15min_50ng_Condition_A_REP1.mzML",
"");
pappso::MsRunReaderSPtr msrunA01 = file_access.getMsRunReaderSPtrByRunId("", "runa01");
BENCHMARK("build TIC chromatogram from mzML")
{
msrunA01->getTicChromatogram();
};
BENCHMARK("build retention timeline from mzML")
{
msrunA01->getRetentionTimeLine();
};
}
SECTION("..:: PSM cbor features::..", "[mzcbor]")
{
pappso::MsFileAccessor file_access(
"/gorgone/pappso/moulon/raw/20250521_proteobench_dda_astral/mzcbor/"
"LFQ_Astral_DDA_15min_50ng_Condition_A_REP1.mzcbor",
"");
pappso::MsRunReaderSPtr msrunA01 = file_access.getMsRunReaderSPtrByRunId("", "runa01");
BENCHMARK("build TIC chromatogram from mzcbor")
{
msrunA01->getTicChromatogram();
};
BENCHMARK("build retention timeline from mzcbor")
{
msrunA01->getRetentionTimeLine();
};
}
}
TEST_CASE("cbor psm map test suite.", "[mzcborrandom]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
std::vector<double> relative_positions({0.9, 0.1, 0.5});
SECTION("..:: PSM cbor features::..", "[mzml]")
{
pappso::MsFileAccessor file_access(
"/gorgone/pappso/moulon/raw/20250521_proteobench_dda_astral/"
"LFQ_Astral_DDA_15min_50ng_Condition_A_REP1.mzML",
"");
pappso::MsRunReaderSPtr msrunA01 = file_access.getMsRunReaderSPtrByRunId("", "runa01");
std::size_t total_index = msrunA01.get()->spectrumListSize();
BENCHMARK("Random access in mzML")
{
for(double relative_position : relative_positions)
{
std::size_t index = relative_position * total_index;
pappso::QualifiedMassSpectrum qmass_spec =
msrunA01.get()->qualifiedMassSpectrum(index, true);
}
};
}
SECTION("..:: PSM cbor features::..", "[mzcbor]")
{
pappso::MsFileAccessor file_access(
"/gorgone/pappso/moulon/raw/20250521_proteobench_dda_astral/mzcbor/"
"LFQ_Astral_DDA_15min_50ng_Condition_A_REP1.mzcbor",
"");
pappso::MsRunReaderSPtr msrunA01 = file_access.getMsRunReaderSPtrByRunId("", "runa01");
std::size_t total_index = msrunA01.get()->spectrumListSize();
BENCHMARK("Random access in mzcbor")
{
for(double relative_position : relative_positions)
{
std::size_t index = relative_position * total_index;
pappso::QualifiedMassSpectrum qmass_spec =
msrunA01.get()->qualifiedMassSpectrum(index, true);
}
};
}
}
TEST_CASE("benchmark XIC extractor", "[mzcborxic]")
{
// Set the debugging message formatting pattern.
qSetMessagePattern(QString("%{file}@%{line}, %{function}(): %{message}"));
// pappso::MzRange mass_range(600, pappso::PrecisionFactory::getPpmInstance(10));
pappso::MsRunXicExtractorFactory::getInstance().setMsRunXicExtractorFactoryType(
pappso::MsRunXicExtractorFactoryType::direct);
std::vector<pappso::XicCoordSPtr> xic_coord_list;
pappso::XicCoord xic_coord;
for(double mz = 700; mz < 1200; mz += 10)
{
xic_coord_list.push_back(xic_coord.initializeAndClone());
xic_coord_list.back().get()->mzRange =
pappso::MzRange(mz, pappso::PrecisionFactory::getPpmInstance(10));
}
WARN(QString("benchmark for %1 XICs").arg(xic_coord_list.size()).toStdString());
SECTION("..:: benchmark XIC extractor mzML ::..", "[mzml]")
{
pappso::MsFileAccessor file_access(
"/gorgone/pappso/moulon/raw/20250521_proteobench_dda_astral/"
"LFQ_Astral_DDA_15min_50ng_Condition_A_REP1.mzML",
"");
pappso::MsRunReaderSPtr msrunA01 = file_access.getMsRunReaderSPtrByRunId("", "runa01");
auto direct_extractor =
pappso::MsRunXicExtractorFactory::getInstance().buildMsRunXicExtractorSp(msrunA01);
pappso::UiMonitorVoid mon_void;
BENCHMARK("XIC extractor on mzML")
{
direct_extractor.get()->extractXicCoordSPtrList(mon_void, xic_coord_list);
};
}
SECTION("..:: benchmark XIC extractor mzcbor ::..", "[mzcbor]")
{
pappso::MsFileAccessor file_access(
"/gorgone/pappso/moulon/raw/20250521_proteobench_dda_astral/mzcbor/"
"LFQ_Astral_DDA_15min_50ng_Condition_A_REP1.mzcbor",
"");
pappso::MsRunReaderSPtr msrunA01 = file_access.getMsRunReaderSPtrByRunId("", "runa01");
auto direct_extractor =
pappso::MsRunXicExtractorFactory::getInstance().buildMsRunXicExtractorSp(msrunA01);
pappso::UiMonitorVoid mon_void;
BENCHMARK("XIC extractor on mzcbor")
{
direct_extractor.get()->extractXicCoordSPtrList(mon_void, xic_coord_list);
};
}
}
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