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#include <catch2/catch_test_macros.hpp>
#include <catch2/catch_approx.hpp>
#include <QDebug>
#include <limits>
#include <pappsomspp/core/processing/filters/savgolfilter.h>
#include <pappsomspp/core/processing/combiners/mzintegrationparams.h>
#include <pappsomspp/core/utils.h>
using namespace pappso;
TEST_CASE("Constructing MzIntegrationParams objects.", "[MzIntegrationParams][constructors]")
{
SECTION("Construct a MzIntegrationParams", "[MzIntegrationParams]")
{
MzIntegrationParams mz_integration_params1;
PrecisionPtr precision_p = pappso::PrecisionFactory::getResInstance(40000);
REQUIRE(mz_integration_params1.getBinningType() == MzIntegrationParams::BinningType::ARBITRARY);
REQUIRE(precision_p == mz_integration_params1.getBinSizeModel());
double smallestMz = 1800.373856;
double greatestMz = 2600.956480;
MzIntegrationParams::BinningType binningType = MzIntegrationParams::BinningType::ARBITRARY;
int decimalPlaces = 3;
bool binSizeDivisor = 6;
bool removeZeroValDataPoints = true;
MzIntegrationParams mz_integration_params2(smallestMz,
greatestMz,
binningType,
precision_p,
binSizeDivisor,
decimalPlaces,
removeZeroValDataPoints);
REQUIRE(mz_integration_params2.getSmallestMz() == smallestMz);
REQUIRE(mz_integration_params2.getGreatestMz() == greatestMz);
REQUIRE(mz_integration_params2.getBinningType() == binningType);
REQUIRE(mz_integration_params2.getBinSizeModel() == precision_p);
REQUIRE(mz_integration_params2.getBinSizeDivisor() == binSizeDivisor);
REQUIRE(mz_integration_params2.getDecimalPlaces() == decimalPlaces);
REQUIRE(mz_integration_params2.isRemoveZeroValDataPoints() == removeZeroValDataPoints);
}
SECTION(
"Construct a MzIntegrationParams from another "
"MzIntegrationParams",
"[MzIntegrationParams]")
{
double smallestMz = 1800.373856;
double greatestMz = 2600.956480;
MzIntegrationParams::BinningType binningType = MzIntegrationParams::BinningType::ARBITRARY;
int decimalPlaces = 3;
PrecisionPtr precision_p = pappso::PrecisionFactory::getPpmInstance(20);
bool binSizeDivisor = 6;
bool removeZeroValDataPoints = true;
MzIntegrationParams mz_integration_params1(smallestMz,
greatestMz,
binningType,
precision_p,
binSizeDivisor,
decimalPlaces,
removeZeroValDataPoints);
MzIntegrationParams mz_integration_params2;
mz_integration_params2.initialize(mz_integration_params1);
REQUIRE(mz_integration_params2.getSmallestMz() == smallestMz);
REQUIRE(mz_integration_params2.getGreatestMz() == greatestMz);
REQUIRE(mz_integration_params2.getBinningType() == binningType);
REQUIRE(mz_integration_params2.getBinSizeModel() == precision_p);
REQUIRE(mz_integration_params2.getBinSizeDivisor() == binSizeDivisor);
REQUIRE(mz_integration_params2.getDecimalPlaces() == decimalPlaces);
REQUIRE(mz_integration_params2.isRemoveZeroValDataPoints() == removeZeroValDataPoints);
}
}
TEST_CASE("Create bins with Da-based bin size", "[MzIntegrationParams]")
{
double smallestMz = 1800.373856;
double greatestMz = 1800.373856;
MzIntegrationParams::BinningType binningType = MzIntegrationParams::BinningType::ARBITRARY;
int decimalPlaces = 3;
PrecisionPtr precision_p = pappso::PrecisionFactory::getDaltonInstance(0.05);
bool binSizeDivisor = 6;
bool removeZeroValDataPoints = true;
MzIntegrationParams mz_integration_params(smallestMz,
greatestMz,
binningType,
precision_p,
binSizeDivisor,
decimalPlaces,
removeZeroValDataPoints);
SECTION("Create bins in ARBITRARY mode", "[MzIntegrationParams]")
{
std::vector<double> bins = mz_integration_params.createBins();
// Do not forget that we round to 3 decimal places:
REQUIRE(bins.front() == 1800.374);
// We create two bins: the first mz value (1800.374) and a new one that is
// that mz value incremented by the delta (that is the size of the bin that
// is created using an increment of 0.05).
double manual_value = bins.front() + precision_p->delta(bins.front());
// Below: if abs(1.0 - 1.2) is less or equal to 0.2 -> success
// REQUIRE_THAT(1.0, Catch::Matchers::WithinAbs(1.2, 0.2)); // success
// REQUIRE_THAT(1.2, Catch::Matchers::WithinAbs(1.1, 0.2)); // success
// REQUIRE_THAT(1.0, Catch::Matchers::WithinAbs(1.3, 0.2)); // failure
// REQUIRE_THAT(1.3, Catch::Matchers::WithinAbs(1.0, 0.2)); // failure
REQUIRE(bins.back() == Catch::Approx(manual_value));
}
}
TEST_CASE("Create bins with ppm-based bin sizes", "[MzIntegrationParams]")
{
double smallestMz = 1800.373856;
double greatestMz = 1800.373856;
MzIntegrationParams::BinningType binningType = MzIntegrationParams::BinningType::ARBITRARY;
int decimalPlaces = 3;
PrecisionPtr precision_p = pappso::PrecisionFactory::getPpmInstance(20);
bool binSizeDivisor = 6;
bool removeZeroValDataPoints = true;
MzIntegrationParams mz_integration_params(smallestMz,
greatestMz,
binningType,
precision_p,
binSizeDivisor,
decimalPlaces,
removeZeroValDataPoints);
SECTION("Create bins in ARBITRARY mode", "[MzIntegrationParams]")
{
std::vector<double> bins = mz_integration_params.createBins();
// Do not forget that we round to 3 decimal places:
REQUIRE(bins.front() == 1800.374);
// Check that the precision delta is computed correctly:
double precision_delta = 1800.374 * 20 / 1000000;
REQUIRE(pappso::Utils::almostEqual(
precision_p->delta(1800.374), precision_delta, /*decimal_places*/ 15));
double rounded_precision_delta =
ceil((precision_delta * pow(10, decimalPlaces)) - 0.49) / pow(10, decimalPlaces);
// We create two bins: the first mz value (1800.374) and a new one that is
// that mz value incremented by the delta (that is the size of the bin that
// is created using relative proportion of 20 ppm).
REQUIRE(bins.back() == 1800.374 + rounded_precision_delta);
}
}
TEST_CASE("Create bins with res-based bin sizes", "[MzIntegrationParams]")
{
double smallestMz = 1800.373856;
double greatestMz = 1800.373856;
MzIntegrationParams::BinningType binningType = MzIntegrationParams::BinningType::ARBITRARY;
int decimalPlaces = 3;
PrecisionPtr precision_p = pappso::PrecisionFactory::getResInstance(20000);
bool binSizeDivisor = 6;
bool removeZeroValDataPoints = true;
MzIntegrationParams mz_integration_params(smallestMz,
greatestMz,
binningType,
precision_p,
binSizeDivisor,
decimalPlaces,
removeZeroValDataPoints);
SECTION("Create bins in ARBITRARY mode", "[MzIntegrationParams]")
{
std::vector<double> bins = mz_integration_params.createBins();
// Do not forget that we round to 3 decimal places:
REQUIRE(bins.front() == 1800.374);
// Check that the precision delta is computed correctly:
double precision_delta = 1800.374 / 20000;
REQUIRE(pappso::Utils::almostEqual(
precision_p->delta(1800.374), precision_delta, /*decimal_places*/ 15));
double rounded_precision_delta =
ceil((precision_delta * pow(10, decimalPlaces)) - 0.49) / pow(10, decimalPlaces);
// We create two bins: the first mz value (1800.374) and a new one that is
// that mz value incremented by the delta (that is the size of the bin that
// is created using relative proportion of 20 ppm).
REQUIRE(bins.back() == 1800.374 + rounded_precision_delta);
}
}
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