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#ifndef MANTID_SINQ_POLDIINDEXKNOWNCOMPOUNDSTEST_H_
#define MANTID_SINQ_POLDIINDEXKNOWNCOMPOUNDSTEST_H_
#include <cxxtest/TestSuite.h>
#include "MantidSINQ/PoldiIndexKnownCompounds.h"
#include "MantidAPI/WorkspaceGroup.h"
#include "MantidSINQ/PoldiUtilities/PoldiMockInstrumentHelpers.h"
#include "MantidTestHelpers/WorkspaceCreationHelper.h"
#include "MantidKernel/V3D.h"
using namespace Mantid::Poldi;
using namespace Mantid::API;
class PoldiIndexKnownCompoundsTest : public CxxTest::TestSuite {
// This pair of boilerplate methods prevent the suite being created statically
// This means the constructor isn't called when running other tests
static PoldiIndexKnownCompoundsTest *createSuite() {
return new PoldiIndexKnownCompoundsTest();
}
static void destroySuite(PoldiIndexKnownCompoundsTest *suite) {
delete suite;
}
PoldiIndexKnownCompoundsTest() { FrameworkManager::Instance(); }
void test_Init() {
PoldiIndexKnownCompounds alg;
TS_ASSERT_THROWS_NOTHING(alg.initialize())
TS_ASSERT(alg.isInitialized())
}
void testExecOnePhase() {
/* In this test, peaks from PoldiMockInstrumentHelpers (Silicon)
* are indexed using theoretical Si-peaks.
*/
auto wsMeasuredSi =
PoldiPeakCollectionHelpers::createPoldiPeakTableWorkspace();
WorkspaceCreationHelper::storeWS("measured_SI", wsMeasuredSi);
auto wsSi =
PoldiPeakCollectionHelpers::createTheoreticalPeakCollectionSilicon()
->asTableWorkspace();
WorkspaceCreationHelper::storeWS("Si", wsSi);
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std::string outWSName("PoldiIndexKnownCompoundsTest_OutputWS");
PoldiIndexKnownCompounds alg;
TS_ASSERT_THROWS_NOTHING(alg.initialize())
TS_ASSERT(alg.isInitialized())
TS_ASSERT_THROWS_NOTHING(
alg.setPropertyValue("InputWorkspace", "measured_SI"));
TS_ASSERT_THROWS_NOTHING(alg.setPropertyValue("CompoundWorkspaces", "Si"));
TS_ASSERT_THROWS_NOTHING(alg.setPropertyValue("Tolerances", "0.005"));
TS_ASSERT_THROWS_NOTHING(
alg.setPropertyValue("ScatteringContributions", "1.0"));
TS_ASSERT_THROWS_NOTHING(
alg.setPropertyValue("OutputWorkspace", outWSName));
TS_ASSERT_THROWS_NOTHING(alg.execute(););
TS_ASSERT(alg.isExecuted());
Workspace_sptr ws;
TS_ASSERT_THROWS_NOTHING(
ws = AnalysisDataService::Instance().retrieveWS<Workspace>(outWSName));
TS_ASSERT(ws);
if (!ws)
return;
// Workspace is a group
WorkspaceGroup_sptr group = boost::dynamic_pointer_cast<WorkspaceGroup>(ws);
TS_ASSERT(group);
TS_ASSERT_EQUALS(group->getNumberOfEntries(), 2);
// Has two entries - indexed Si peaks and unindexed peaks
Workspace_sptr indexedSi = group->getItem(0);
TS_ASSERT(indexedSi);
// Table with peaks that can be attributed to Si
ITableWorkspace_sptr tableSi =
boost::dynamic_pointer_cast<ITableWorkspace>(indexedSi);
TS_ASSERT(tableSi);
TS_ASSERT_EQUALS(tableSi->getName(), "measured_SI_indexed_Si");
TS_ASSERT_EQUALS(tableSi->rowCount(), 4);
// Make sure unit cell and point group is carried over from compound ws
ITableWorkspace_sptr si =
AnalysisDataService::Instance().retrieveWS<ITableWorkspace>("Si");
TS_ASSERT_EQUALS(tableSi->getLogs()->getProperty("PointGroup")->value(),
si->getLogs()->getProperty("PointGroup")->value());
TS_ASSERT_EQUALS(tableSi->getLogs()->getProperty("UnitCell")->value(),
si->getLogs()->getProperty("UnitCell")->value());
Workspace_sptr unindexed = group->getItem(1);
TS_ASSERT(unindexed);
// Table with peaks that can be attributed to Si
ITableWorkspace_sptr tableUnindexed =
boost::dynamic_pointer_cast<ITableWorkspace>(unindexed);
TS_ASSERT(tableUnindexed);
TS_ASSERT_EQUALS(tableUnindexed->getName(), "measured_SI_unindexed");
TS_ASSERT_EQUALS(tableUnindexed->rowCount(), 0);
AnalysisDataService::Instance().remove(outWSName);
WorkspaceCreationHelper::removeWS("measured_SI");
WorkspaceCreationHelper::removeWS("Si");
}
void testSetMeasuredPeaks() {
PoldiPeakCollection_sptr silicon =
PoldiPeakCollectionHelpers::createPoldiPeakCollectionMaximum();
TestablePoldiIndexKnownCompounds alg;
alg.setMeasuredPeaks(silicon);
TS_ASSERT_EQUALS(alg.m_measuredPeaks, silicon)
}
void testSetExpectedPhases() {
std::vector<PoldiPeakCollection_sptr> expectedPeaks;
expectedPeaks.push_back(
PoldiPeakCollectionHelpers::createPoldiPeakCollectionMaximum());
expectedPeaks.push_back(
PoldiPeakCollectionHelpers::createPoldiPeakCollectionMaximum());
TestablePoldiIndexKnownCompounds alg;
alg.setExpectedPhases(expectedPeaks);
TS_ASSERT_EQUALS(alg.m_expectedPhases.size(), expectedPeaks.size());
for (size_t i = 0; i < expectedPeaks.size(); ++i) {
TS_ASSERT_EQUALS(alg.m_expectedPhases[i], expectedPeaks[i]);
void testInitializeUnindexedPeaks() {
TestablePoldiIndexKnownCompounds alg;
TS_ASSERT(!alg.m_unindexedPeaks);
TS_ASSERT(alg.m_unindexedPeaks);
}
void testInitializeIndexedPeaks() {
std::vector<PoldiPeakCollection_sptr> expectedPeaks;
expectedPeaks.push_back(
PoldiPeakCollectionHelpers::createPoldiPeakCollectionMaximum());
expectedPeaks.push_back(
PoldiPeakCollectionHelpers::createPoldiPeakCollectionMaximum());
TestablePoldiIndexKnownCompounds alg;
TS_ASSERT_EQUALS(alg.m_indexedPeaks.size(), 0);
TS_ASSERT_THROWS(alg.initializeIndexedPeaks(expectedPeaks),
std::runtime_error);
PoldiPeakCollection_sptr peaks =
PoldiPeakCollectionHelpers::createPoldiPeakCollectionMaximum();
alg.setMeasuredPeaks(peaks);
TS_ASSERT_THROWS_NOTHING(alg.initializeIndexedPeaks(expectedPeaks));
TS_ASSERT_EQUALS(alg.m_indexedPeaks.size(), expectedPeaks.size());
for (size_t i = 0; i < expectedPeaks.size(); ++i) {
TS_ASSERT(alg.m_indexedPeaks[i]);
TS_ASSERT_EQUALS(alg.m_indexedPeaks[i]->getProfileFunctionName(),
peaks->getProfileFunctionName());
TS_ASSERT_EQUALS(alg.m_indexedPeaks[i]->intensityType(),
peaks->intensityType());
void testGetWorkspaces() {
setupWorkspaceStructure();
TestablePoldiIndexKnownCompounds alg;
// test single workspaces
std::vector<std::string> singleWsNames =
getStringVector("test1,test3,test4");
TS_ASSERT_THROWS_NOTHING(alg.getWorkspaces(singleWsNames));
std::vector<Workspace_sptr> singleWs = alg.getWorkspaces(singleWsNames);
TS_ASSERT_EQUALS(singleWs.size(), 3);
// test group workspace
std::vector<std::string> groupWsName = getStringVector("group1");
TS_ASSERT_THROWS_NOTHING(alg.getWorkspaces(groupWsName));
std::vector<Workspace_sptr> groupWs = alg.getWorkspaces(groupWsName);
TS_ASSERT_EQUALS(groupWs.size(), 2);
// test 2 group workspaces
std::vector<std::string> groupWsNames = getStringVector("group1,group2");
TS_ASSERT_THROWS_NOTHING(alg.getWorkspaces(groupWsNames));
std::vector<Workspace_sptr> groupWs2 = alg.getWorkspaces(groupWsNames);
TS_ASSERT_EQUALS(groupWs2.size(), 4);
// test group of group workspaces
std::vector<std::string> groupsWsName = getStringVector("group3");
TS_ASSERT_THROWS_NOTHING(alg.getWorkspaces(groupsWsName));
std::vector<Workspace_sptr> groupsWs = alg.getWorkspaces(groupsWsName);
TS_ASSERT_EQUALS(groupsWs.size(), 4);
tearDownWorkspaceStructure();
}
void testGetWorkspaceNames() {
setupWorkspaceStructure();
std::vector<std::string> groupWsName = getStringVector("group1");
TestablePoldiIndexKnownCompounds alg;
std::vector<Workspace_sptr> groupWs = alg.getWorkspaces(groupWsName);
std::vector<std::string> workspaceNames = alg.getWorkspaceNames(groupWs);
TS_ASSERT_EQUALS(workspaceNames.size(), 2);
TS_ASSERT_EQUALS(workspaceNames.front(), "test1");
TS_ASSERT_EQUALS(workspaceNames.back(), "test2");
tearDownWorkspaceStructure();
}
void testGetPeakCollections() {
std::vector<Workspace_sptr> goodWorkspaces;
goodWorkspaces.push_back(
PoldiPeakCollectionHelpers::createPoldiPeakTableWorkspace());
goodWorkspaces.push_back(
PoldiPeakCollectionHelpers::createPoldiPeakTableWorkspace());
TestablePoldiIndexKnownCompounds alg;
TS_ASSERT_THROWS_NOTHING(alg.getPeakCollections(goodWorkspaces));
std::vector<Workspace_sptr> badWorkspaces;
badWorkspaces.push_back(
PoldiPeakCollectionHelpers::createPoldiPeakTableWorkspace());
badWorkspaces.push_back(
WorkspaceCreationHelper::create1DWorkspaceRand(10, true));
TS_ASSERT_THROWS(alg.getPeakCollections(badWorkspaces),
std::invalid_argument);
}
void testReshapeVector() {
std::vector<double> one(1, 0.1);
std::vector<double> two(2, 0.1);
two[1] = 0.2;
TestablePoldiIndexKnownCompounds alg;
TS_ASSERT_THROWS(alg.reshapeVector(empty, 1), std::invalid_argument);
TS_ASSERT_THROWS_NOTHING(alg.reshapeVector(one, 1));
TS_ASSERT_THROWS_NOTHING(alg.reshapeVector(one, 2));
TS_ASSERT_THROWS_NOTHING(alg.reshapeVector(two, 1));
TS_ASSERT_THROWS_NOTHING(alg.reshapeVector(two, 2));
TS_ASSERT_THROWS_NOTHING(alg.reshapeVector(two, 3));
TS_ASSERT_THROWS(alg.reshapeVector(one, 0), std::invalid_argument);
std::vector<double> t11 = alg.reshapeVector(one, 1);
TS_ASSERT_EQUALS(t11.size(), 1);
TS_ASSERT_EQUALS(t11[0], 0.1);
std::vector<double> t12 = alg.reshapeVector(one, 2);
TS_ASSERT_EQUALS(t12.size(), 2);
TS_ASSERT_EQUALS(t12[0], 0.1);
TS_ASSERT_EQUALS(t12[1], 0.1);
std::vector<double> t21 = alg.reshapeVector(two, 1);
TS_ASSERT_EQUALS(t21.size(), 1);
TS_ASSERT_EQUALS(t21[0], 0.1);
std::vector<double> t22 = alg.reshapeVector(two, 2);
TS_ASSERT_EQUALS(t22.size(), 2);
TS_ASSERT_EQUALS(t22[0], 0.1);
TS_ASSERT_EQUALS(t22[1], 0.2);
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std::vector<double> t23 = alg.reshapeVector(two, 3);
TS_ASSERT_EQUALS(t23.size(), 3);
TS_ASSERT_EQUALS(t23[0], 0.1);
TS_ASSERT_EQUALS(t23[1], 0.2);
TS_ASSERT_EQUALS(t23[2], 0.2);
}
void testGetTolerances() {
TestablePoldiIndexKnownCompounds alg;
alg.initialize();
alg.setPropertyValue("Tolerances", "");
TS_ASSERT_THROWS(alg.getTolerances(1), std::invalid_argument);
alg.setPropertyValue("Tolerances", "0.1");
TS_ASSERT_THROWS_NOTHING(alg.getTolerances(1));
TS_ASSERT_THROWS_NOTHING(alg.getTolerances(2));
alg.setPropertyValue("Tolerances", "0.1,0.2");
TS_ASSERT_THROWS_NOTHING(alg.getTolerances(1));
TS_ASSERT_THROWS_NOTHING(alg.getTolerances(2));
TS_ASSERT_THROWS_NOTHING(alg.getTolerances(3));
TS_ASSERT_THROWS(alg.getTolerances(0), std::invalid_argument);
}
void testGetContributions() {
TestablePoldiIndexKnownCompounds alg;
alg.initialize();
alg.setPropertyValue("ScatteringContributions", "");
TS_ASSERT_THROWS(alg.getContributions(1), std::invalid_argument);
alg.setPropertyValue("ScatteringContributions", "0.1");
TS_ASSERT_THROWS_NOTHING(alg.getContributions(1));
TS_ASSERT_THROWS_NOTHING(alg.getContributions(2));
alg.setPropertyValue("ScatteringContributions", "0.1,0.2");
TS_ASSERT_THROWS_NOTHING(alg.getContributions(1));
TS_ASSERT_THROWS_NOTHING(alg.getContributions(2));
TS_ASSERT_THROWS_NOTHING(alg.getContributions(3));
TS_ASSERT_THROWS(alg.getContributions(0), std::invalid_argument);
}
void testGetNormalizedContributions() {
std::vector<double> contributions;
contributions.push_back(4.0);
contributions.push_back(1.0);
TestablePoldiIndexKnownCompounds alg;
TS_ASSERT_THROWS_NOTHING(alg.getNormalizedContributions(contributions));
std::vector<double> normalized =
alg.getNormalizedContributions(contributions);
TS_ASSERT_EQUALS(normalized.size(), 2);
TS_ASSERT_EQUALS(normalized[0], 0.8);
TS_ASSERT_EQUALS(normalized[1], 0.2);
std::vector<double> empty;
TS_ASSERT_THROWS(alg.getNormalizedContributions(empty),
std::invalid_argument);
std::vector<double> negative(1, -2.0);
TS_ASSERT_THROWS(alg.getNormalizedContributions(negative),
std::invalid_argument);
}
void testScaleIntensityEstimates() {
TestablePoldiIndexKnownCompounds alg;
alg.initialize();
PoldiPeakCollection_sptr null;
TS_ASSERT_THROWS(alg.scaleIntensityEstimates(null, 0.1),
std::invalid_argument);
PoldiPeakCollection_sptr indexedSilicon =
PoldiPeakCollectionHelpers::createTheoreticalPeakCollectionSilicon();
TS_ASSERT_THROWS_NOTHING(alg.scaleIntensityEstimates(indexedSilicon, 2.0));
PoldiPeakCollection_sptr reference =
PoldiPeakCollectionHelpers::createTheoreticalPeakCollectionSilicon();
for (size_t i = 0; i < indexedSilicon->peakCount(); ++i) {
TS_ASSERT_EQUALS(indexedSilicon->peak(i)->intensity(),
2.0 * reference->peak(i)->intensity());
// test override with vectors
std::vector<PoldiPeakCollection_sptr> phases(4, indexedSilicon);
std::vector<double> goodContributions(4, 0.4);
std::vector<double> badContributions(2, 0.4);
TS_ASSERT_THROWS_NOTHING(
alg.scaleIntensityEstimates(phases, goodContributions));
TS_ASSERT_THROWS(alg.scaleIntensityEstimates(phases, badContributions),
std::invalid_argument);
}
void testFwhmSigmaConversion() {
double sigma = 1.0;
double fwhm = 2.354820045;
TS_ASSERT_DELTA(PoldiIndexKnownCompounds::sigmaToFwhm(sigma), fwhm, 1e-9);
TS_ASSERT_DELTA(PoldiIndexKnownCompounds::fwhmToSigma(fwhm), sigma, 1e-9);
TS_ASSERT_EQUALS(PoldiIndexKnownCompounds::sigmaToFwhm(
PoldiIndexKnownCompounds::fwhmToSigma(fwhm)),
fwhm);
}
void testAssignFwhmEstimates() {
TestablePoldiIndexKnownCompounds alg;
alg.initialize();
PoldiPeakCollection_sptr null;
TS_ASSERT_THROWS(alg.assignFwhmEstimates(null, 0.1), std::invalid_argument);
PoldiPeakCollection_sptr indexedSilicon =
PoldiPeakCollectionHelpers::createTheoreticalPeakCollectionSilicon();
TS_ASSERT_THROWS_NOTHING(alg.assignFwhmEstimates(indexedSilicon, 0.1));
for (size_t i = 0; i < indexedSilicon->peakCount(); ++i) {
TS_ASSERT_EQUALS(indexedSilicon->peak(i)->fwhm(PoldiPeak::Relative),
alg.sigmaToFwhm(0.1));
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// test override with vectors
std::vector<PoldiPeakCollection_sptr> phases(4, indexedSilicon);
std::vector<double> goodFwhms(4, 0.4);
std::vector<double> badFwhms(2, 0.4);
TS_ASSERT_THROWS_NOTHING(alg.assignFwhmEstimates(phases, goodFwhms));
TS_ASSERT_THROWS(alg.scaleIntensityEstimates(phases, badFwhms),
std::invalid_argument);
}
void testInPeakSet() {
PoldiPeak_sptr peak1 = PoldiPeak::create(1.0);
PoldiPeak_sptr peak2 = PoldiPeak::create(1.0);
PoldiPeak_sptr peak3 = PoldiPeak::create(1.0);
std::set<PoldiPeak_sptr> peakSet;
peakSet.insert(peak1);
peakSet.insert(peak2);
TestablePoldiIndexKnownCompounds alg;
TS_ASSERT(alg.inPeakSet(peakSet, peak1));
TS_ASSERT(alg.inPeakSet(peakSet, peak2));
TS_ASSERT(!alg.inPeakSet(peakSet, peak3));
}
void testIsCandidate() {
TestablePoldiIndexKnownCompounds alg;
PoldiPeak_sptr peak = PoldiPeak::create(Conversions::dToQ(2.0));
PoldiPeak_sptr candidate1 =
PoldiPeak::create(Conversions::dToQ(2.02)); // +2 * sigma
candidate1->setFwhm(UncertainValue(alg.sigmaToFwhm(0.01)),
PoldiPeak::AbsoluteD);
TS_ASSERT(alg.isCandidate(peak, candidate1));
PoldiPeak_sptr candidate2 =
PoldiPeak::create(Conversions::dToQ(1.971)); // -2.99 * sigma
candidate2->setFwhm(UncertainValue(alg.sigmaToFwhm(0.01)),
PoldiPeak::AbsoluteD);
TS_ASSERT(alg.isCandidate(peak, candidate2));
// More than 3sigma away - no candidate.
PoldiPeak_sptr candidate3 =
PoldiPeak::create(Conversions::dToQ(1.97)); // -3 sigma
candidate3->setFwhm(UncertainValue(alg.sigmaToFwhm(0.01)),
PoldiPeak::AbsoluteD);
TS_ASSERT(!alg.isCandidate(peak, candidate3));
// throw if one of the peaks is invalid
PoldiPeak_sptr null;
TS_ASSERT_THROWS(alg.isCandidate(null, candidate1), std::invalid_argument);
TS_ASSERT_THROWS(alg.isCandidate(peak, null), std::invalid_argument);
}
void testGetIndexCandidatePairs() {
PoldiPeakCollection_sptr measuredSi =
PoldiPeakCollectionHelpers::createPoldiPeakCollectionMaximum();
std::vector<PoldiPeakCollection_sptr> theoreticalSi(
2,
PoldiPeakCollectionHelpers::createTheoreticalPeakCollectionSilicon());
TestablePoldiIndexKnownCompounds alg;
alg.initialize();
alg.scaleIntensityEstimates(theoreticalSi, std::vector<double>(2, 1.0));
alg.assignFwhmEstimates(theoreticalSi, std::vector<double>(2, 0.005));
// Get candidates for one peak
std::vector<IndexCandidatePair> candidates =
alg.getIndexCandidatePairs(measuredSi->peak(0), theoreticalSi);
// Should be twice the same candidate from both collections
TS_ASSERT_EQUALS(candidates.size(), 2);
// Tolerance is too small, no candidates.
alg.assignFwhmEstimates(theoreticalSi, std::vector<double>(2, 0.00001));
candidates = alg.getIndexCandidatePairs(measuredSi->peak(0), theoreticalSi);
TS_ASSERT_EQUALS(candidates.size(), 0);
}
void testGetAllIndexCandidatePairs() {
PoldiPeakCollection_sptr measuredSi =
PoldiPeakCollectionHelpers::createPoldiPeakCollectionMaximum();
std::vector<PoldiPeakCollection_sptr> theoreticalSi(
2,
PoldiPeakCollectionHelpers::createTheoreticalPeakCollectionSilicon());
TestablePoldiIndexKnownCompounds alg;
alg.initialize();
alg.scaleIntensityEstimates(theoreticalSi, std::vector<double>(2, 1.0));
alg.assignFwhmEstimates(theoreticalSi, std::vector<double>(2, 0.005));
// Get candidates for all peaks
std::vector<IndexCandidatePair> candidates =
alg.getAllIndexCandidatePairs(measuredSi, theoreticalSi);
// Each peak has two candidates - one from each theoretical Si-collection
TS_ASSERT_EQUALS(candidates.size(),
measuredSi->peakCount() * theoreticalSi.size());
// Tolerance is too small, no candidates.
alg.assignFwhmEstimates(theoreticalSi, std::vector<double>(2, 0.00001));
/* unindexed peaks must be initialized, because they are sorted out by
* getAllCandidates() and placed in that collection, otherwise an exception
* is thrown.
*/
TS_ASSERT_THROWS(alg.getAllIndexCandidatePairs(measuredSi, theoreticalSi),
std::runtime_error);
// After initialization, everything is fine.
alg.initializeUnindexedPeaks();
candidates = alg.getAllIndexCandidatePairs(measuredSi, theoreticalSi);
TS_ASSERT_EQUALS(candidates.size(), 0);
}
void testCollectUnindexedPeak() {
TestablePoldiIndexKnownCompounds alg;
PoldiPeak_sptr peak = PoldiPeak::create(1.0);
TS_ASSERT_THROWS(alg.collectUnindexedPeak(peak), std::runtime_error);
alg.initializeUnindexedPeaks();
TS_ASSERT_THROWS_NOTHING(alg.collectUnindexedPeak(peak));
}
void testIndexCandidatePair() {
IndexCandidatePair defaultConstructed;
TS_ASSERT(!defaultConstructed.observed);
TS_ASSERT(!defaultConstructed.observed);
TS_ASSERT_EQUALS(defaultConstructed.positionMatch, 0.0);
TS_ASSERT_EQUALS(defaultConstructed.candidateCollectionIndex, 0);
}
void testIndexCandidatePairValues() {
TestablePoldiIndexKnownCompounds alg;
PoldiPeak_sptr null;
PoldiPeak_sptr noFwhm = PoldiPeak::create(3.0);
PoldiPeak_sptr peak = PoldiPeak::create(Conversions::dToQ(2.0));
/* Two candidates for indexing with different
* distances from the peak position, but equal tolerances.
*/
PoldiPeak_sptr candidate1 = PoldiPeak::create(Conversions::dToQ(2.04), 1.0);
candidate1->setFwhm(UncertainValue(alg.sigmaToFwhm(0.1)),
PoldiPeak::Relative);
PoldiPeak_sptr candidate2 = PoldiPeak::create(Conversions::dToQ(1.92), 1.0);
candidate2->setFwhm(UncertainValue(alg.sigmaToFwhm(0.1)),
PoldiPeak::Relative);
// Null peaks don't work
TS_ASSERT_THROWS(IndexCandidatePair(peak, null, 0), std::invalid_argument);
TS_ASSERT_THROWS(IndexCandidatePair(null, candidate1, 0),
std::invalid_argument);
// Range error when no fwhm is set (division by zero).
TS_ASSERT_THROWS(IndexCandidatePair(peak, noFwhm, 0), std::range_error);
IndexCandidatePair peakCandidate1(peak, candidate1, 1);
TS_ASSERT_EQUALS(peakCandidate1.observed, peak);
TS_ASSERT_EQUALS(peakCandidate1.candidate, candidate1);
TS_ASSERT_EQUALS(peakCandidate1.candidateCollectionIndex, 1);
IndexCandidatePair peakCandidate2(peak, candidate2, 1);
TS_ASSERT_EQUALS(peakCandidate2.observed, peak);
TS_ASSERT_EQUALS(peakCandidate2.candidate, candidate2);
TS_ASSERT_EQUALS(peakCandidate2.candidateCollectionIndex, 1);
// Test comparison operator
TS_ASSERT(peakCandidate2 < peakCandidate1);
TS_ASSERT(!(peakCandidate1 < peakCandidate2));
}
void testIndexPeaks() {
std::vector<PoldiPeakCollection_sptr> expected(
1,
PoldiPeakCollectionHelpers::createTheoreticalPeakCollectionSilicon());
PoldiPeakCollection_sptr measured =
PoldiPeakCollectionHelpers::createPoldiPeakCollectionMaximum();
// This peak does not exist in the pattern of Si. It will remain unindexed.
measured->addPeak(PoldiPeak::create(Conversions::dToQ(0.99111)));
/* This is very close to 422 (d=1.108539), but slightly further away than
* the one already present in the collection.
*/
measured->addPeak(PoldiPeak::create(Conversions::dToQ(1.10880)));
TestablePoldiIndexKnownCompounds alg;
alg.initialize();
alg.setMeasuredPeaks(measured);
alg.initializeUnindexedPeaks();
alg.initializeIndexedPeaks(expected);
alg.scaleIntensityEstimates(expected, std::vector<double>(1, 1.0));
alg.assignFwhmEstimates(expected, std::vector<double>(1, 0.005));
TS_ASSERT_THROWS_NOTHING(alg.indexPeaks(measured, expected));
TS_ASSERT_EQUALS(alg.m_unindexedPeaks->peakCount(), 2);
PoldiPeakCollection_sptr indexedSi =
alg.getIntensitySortedPeakCollection(alg.m_indexedPeaks[0]);
TS_ASSERT_EQUALS(indexedSi->peakCount(), 4);
// Peaks are ordered by intensity
TS_ASSERT_EQUALS(indexedSi->peak(3)->hkl(), MillerIndices(3, 3, 1));
// Make sure this is the correct peak (not the one introduced above)
TS_ASSERT_EQUALS(indexedSi->peak(2)->hkl(), MillerIndices(3, 1, 1));
TS_ASSERT_EQUALS(indexedSi->peak(1)->hkl(), MillerIndices(2, 2, 0));
TS_ASSERT_EQUALS(indexedSi->peak(0)->hkl(), MillerIndices(4, 2, 2));
TS_ASSERT_EQUALS(indexedSi->peak(0)->d(), 1.108644);
}
class TestablePoldiIndexKnownCompounds : public PoldiIndexKnownCompounds {
friend class PoldiIndexKnownCompoundsTest;
public:
TestablePoldiIndexKnownCompounds() : PoldiIndexKnownCompounds() {}
~TestablePoldiIndexKnownCompounds() override {}
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void setupWorkspaceStructure() {
/* Workspace structure:
* group3
* +----- group1
* | +----- test1
* | +----- test2
* |
* +----- group2
* +----- test3
* +----- test4
*/
std::vector<std::string> testWorkspaces =
getStringVector("test1,test2,test3,test4");
storeRandomWorkspaces(testWorkspaces);
WorkspaceGroup_sptr group1 = boost::make_shared<WorkspaceGroup>();
WorkspaceCreationHelper::storeWS("group1", group1);
group1->add("test1");
group1->add("test2");
WorkspaceGroup_sptr group2 = boost::make_shared<WorkspaceGroup>();
WorkspaceCreationHelper::storeWS("group2", group2);
group2->add("test3");
group2->add("test4");
WorkspaceGroup_sptr group3 = boost::make_shared<WorkspaceGroup>();
WorkspaceCreationHelper::storeWS("group3", group3);
group3->add("group1");
group3->add("group2");
}
void storeRandomWorkspaces(const std::vector<std::string> &wsNames) {
for (const auto &wsName : wsNames) {
auto ws = WorkspaceCreationHelper::create1DWorkspaceRand(10, true)
WorkspaceCreationHelper::storeWS(wsName, ws);
void tearDownWorkspaceStructure() {
removeRandomWorkspaces(getStringVector("test1,test2,test3,test4"));
WorkspaceCreationHelper::removeWS("group1");
WorkspaceCreationHelper::removeWS("group2");
WorkspaceCreationHelper::removeWS("group3");
}
void removeRandomWorkspaces(const std::vector<std::string> &wsNames) {
for (const auto &wsName : wsNames) {
WorkspaceCreationHelper::removeWS(wsName);
std::vector<std::string> getStringVector(const std::string &string) {
std::vector<std::string> stringVector;
boost::split(stringVector, string, boost::is_any_of(", "),
boost::token_compress_on);
};
#endif /* MANTID_SINQ_POLDIINDEXKNOWNCOMPOUNDSTEST_H_ */