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Commit 455e2a6c authored by Lynch, Vickie's avatar Lynch, Vickie
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Refs #21752 unit tests changed because formula for Zscore changed

parent fae29557
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Framework/Crystal/src/PeakStatisticsTools.cpp
View file @ 455e2a6c
......@@ -210,6 +210,8 @@ UniqueReflectionCollection::getReflections() const {
* group of equivalent reflections.
*
* @param uniqueReflections :: Map of unique reflections and peaks.
* @param equivalentIntensities :: Mean or median for statistics of equivalent peaks.
* @param sigmaCritical :: Number of standard deviations for outliers.
*/
void PeaksStatistics::calculatePeaksStatistics(
const std::map<V3D, UniqueReflection> &uniqueReflections,
......
Framework/Crystal/src/SortHKL.cpp
View file @ 455e2a6c
......@@ -128,11 +128,11 @@ void SortHKL::exec() {
auto wavelengths = unique.second.getWavelengths();
auto intensities = unique.second.getIntensities();
auto sigmas = unique.second.getSigmas();
std::cout << "HKL " << unique.second.getHKL() << "\n";
std::cout << "Intensities ";
for (const auto &e : intensities)
std::cout << e << " ";
std::cout << "\n";
//std::cout << "HKL " << unique.second.getHKL() << "\n";
//std::cout << "Intensities ";
//for (const auto &e : intensities)
//std::cout << e << " ";
//std::cout << "\n";
auto zScores = Kernel::getWeightedZscore(intensities, sigmas);
if (zScores.size() > maxPeaks)
maxPeaks = zScores.size();
......@@ -143,8 +143,8 @@ void SortHKL::exec() {
Kernel::getStatistics(outliersRemoved.getIntensities(),
StatOptions::Mean | StatOptions::Median);
std::cout << "Mean = " << intensityStatistics.mean
<< " Median = " << intensityStatistics.median << "\n";
//std::cout << "Mean = " << intensityStatistics.mean
//<< " Median = " << intensityStatistics.median << "\n";
// sort wavelengths & intensities
for (size_t i = 0; i < wavelengths.size(); i++) {
size_t i0 = i;
......@@ -161,7 +161,7 @@ void SortHKL::exec() {
intensities[i0] = intensities[i];
intensities[i] = temp;
}
std::cout << "Zscores ";
//std::cout << "Zscores ";
for (size_t i = 0; i < std::min(zScores.size(), static_cast<size_t>(20));
++i) {
UniqX[i] = wavelengths[i];
......@@ -172,14 +172,14 @@ void SortHKL::exec() {
UniqE[i] = intensityStatistics.mean - intensities[i];
else
UniqE[i] = intensityStatistics.median - intensities[i];
std::cout << zScores[i] << " ";
//std::cout << zScores[i] << " ";
}
for (size_t i = zScores.size(); i < 20; ++i) {
UniqX[i] = wavelengths[zScores.size() - 1];
UniqY[i] = intensities[zScores.size() - 1];
UniqE[i] = 0.0;
}
std::cout << "\n";
//std::cout << "\n";
}
}
......
Framework/Crystal/test/PeakStatisticsToolsTest.h
View file @ 455e2a6c
......@@ -161,21 +161,20 @@ public:
auto cleanReflection = reflection.removeOutliers();
TSM_ASSERT_EQUALS(
"UniqueReflection removed outlier although it should not.",
cleanReflection.count(), 4);
cleanReflection.count(), 3);
cleanReflection = reflection.removeOutliers(2.0);
TSM_ASSERT_EQUALS(
"UniqueReflection removed outlier although it should not.",
cleanReflection.count(), 4);
cleanReflection.count(), 2);
cleanReflection = reflection.removeOutliers(1.0);
TSM_ASSERT_EQUALS(
"UniqueReflection did not remove outliers although it should have.",
cleanReflection.count(), 2);
cleanReflection.count(), 1);
std::vector<double> cleanIntensities = cleanReflection.getIntensities();
TS_ASSERT_EQUALS(cleanIntensities[0], 32.0);
TS_ASSERT_EQUALS(cleanIntensities[1], 31.0);
}
void test_UniqueReflectionSetIntensityAndSigma() {
......@@ -263,7 +262,9 @@ public:
std::make_pair(V3D(1, 1, 1), UniqueReflection(V3D(1, 1, 1))));
MockUniqueReflectionCollection reflections(uniques);
PeaksStatistics statistics(reflections);
std::string statType = "Mean";
double sigmas = 3.0;
PeaksStatistics statistics(reflections, statType, sigmas);
TS_ASSERT_EQUALS(statistics.m_peaks.size(), 0);
TS_ASSERT_EQUALS(statistics.m_uniqueReflections, 0);
TS_ASSERT_EQUALS(statistics.m_redundancy, 0.0);
......@@ -278,7 +279,9 @@ public:
{{1, 1, 1}, getReflectionWithPeaks({56.0}, {4.5}, 1.0)}};
MockUniqueReflectionCollection reflections(uniques);
PeaksStatistics statistics(reflections);
std::string statType = "Mean";
double sigmas = 3.0;
PeaksStatistics statistics(reflections, statType, sigmas);
TS_ASSERT_EQUALS(statistics.m_peaks.size(), 1);
TS_ASSERT_EQUALS(statistics.m_uniqueReflections, 1);
TS_ASSERT_EQUALS(statistics.m_redundancy, 1.0);
......@@ -294,7 +297,9 @@ public:
{{1, 1, 2}, UniqueReflection(V3D(1, 1, 2))}};
MockUniqueReflectionCollection reflections(uniques);
PeaksStatistics statistics(reflections);
std::string statType = "Mean";
double sigmas = 3.0;
PeaksStatistics statistics(reflections, statType, sigmas);
TS_ASSERT_EQUALS(statistics.m_peaks.size(), 1);
TS_ASSERT_EQUALS(statistics.m_uniqueReflections, 1);
TS_ASSERT_EQUALS(statistics.m_redundancy, 1.0);
......@@ -311,7 +316,9 @@ public:
{{1, 1, 2}, getReflectionWithPeaks({20.0}, {1.0}, 2.0)}};
MockUniqueReflectionCollection reflections(uniques);
PeaksStatistics statistics(reflections);
std::string statType = "Mean";
double sigmas = 3.0;
PeaksStatistics statistics(reflections, statType, sigmas);
TS_ASSERT_EQUALS(statistics.m_peaks.size(), 2);
TS_ASSERT_EQUALS(statistics.m_uniqueReflections, 2);
TS_ASSERT_EQUALS(statistics.m_redundancy, 1.0);
......@@ -326,7 +333,9 @@ public:
{{1, 1, 1}, getReflectionWithPeaks({10.0, 20.0}, {0.1, 0.1}, 1.0)}};
MockUniqueReflectionCollection reflections(uniques);
PeaksStatistics statistics(reflections);
std::string statType = "Mean";
double sigmas = 3.0;
PeaksStatistics statistics(reflections, statType, sigmas);
TS_ASSERT_EQUALS(statistics.m_peaks.size(), 2);
TS_ASSERT_EQUALS(statistics.m_uniqueReflections, 1);
TS_ASSERT_EQUALS(statistics.m_redundancy, 2.0);
......@@ -344,7 +353,9 @@ public:
getReflectionWithPeaks({10.0, 20.0, 15.0}, {0.1, 0.1, 0.1}, 1.0)}};
MockUniqueReflectionCollection reflections(uniques);
PeaksStatistics statistics(reflections);
std::string statType = "Mean";
double sigmas = 3.0;
PeaksStatistics statistics(reflections, statType, sigmas);
TS_ASSERT_EQUALS(statistics.m_peaks.size(), 3);
TS_ASSERT_EQUALS(statistics.m_uniqueReflections, 1);
TS_ASSERT_EQUALS(statistics.m_redundancy, 3.0);
......
Framework/Crystal/test/StatisticsOfPeaksWorkspaceTest.h
View file @ 455e2a6c
......@@ -81,9 +81,9 @@ public:
TS_ASSERT_EQUALS(tableOut->String(0, 0), "Overall");
TS_ASSERT_EQUALS(tableOut->Int(0, 1), 3);
TS_ASSERT_DELTA(tableOut->Double(0, 2), 3.6, .1);
TS_ASSERT_DELTA(tableOut->Double(0, 3), 14.3, .1);
TS_ASSERT_DELTA(tableOut->Double(0, 4), 8., .1);
TS_ASSERT_DELTA(tableOut->Double(0, 5), 1.4195, .1);
TS_ASSERT_DELTA(tableOut->Double(0, 3), 14.03, .1);
TS_ASSERT_DELTA(tableOut->Double(0, 4), 5.3, .1);
TS_ASSERT_DELTA(tableOut->Double(0, 5), 1.25, .1);
TS_ASSERT_DELTA(tableOut->Double(0, 6), 0., .1);
TS_ASSERT_DELTA(tableOut->Double(0, 7), 0., .1);
......@@ -94,7 +94,7 @@ public:
TS_ASSERT(wsout);
if (!wsout)
return;
TS_ASSERT_EQUALS(wsout->getNumberPeaks(), 24);
TS_ASSERT_EQUALS(wsout->getNumberPeaks(), 16);
Peak p = wsout->getPeaks()[0];
TS_ASSERT_EQUALS(p.getH(), 1);
......
Framework/DataObjects/src/Peak.cpp
View file @ 455e2a6c
......@@ -890,7 +890,7 @@ void Peak::setCol(int m_col) { this->m_col = m_col; }
// -------------------------------------------------------------------------------------
/** Sets the unique peak number
* @param m_col :: col value */
* @param m_peakNumber :: unique peak number value */
void Peak::setPeakNumber(int m_peakNumber) {
this->m_peakNumber = m_peakNumber;
}
......
Framework/Geometry/test/MockObjects.h
View file @ 455e2a6c
......@@ -65,7 +65,9 @@ public:
MOCK_CONST_METHOD0(getDetector, Geometry::IDetector_const_sptr());
MOCK_CONST_METHOD0(getInstrument, Geometry::Instrument_const_sptr());
MOCK_CONST_METHOD0(getRunNumber, int());
MOCK_CONST_METHOD0(getPeakNumber, int());
MOCK_METHOD1(setRunNumber, void(int m_RunNumber));
MOCK_METHOD1(setPeakNumber, void(int m_PeakNumber));
MOCK_CONST_METHOD0(getMonitorCount, double());
MOCK_METHOD1(setMonitorCount, void(double m_MonitorCount));
MOCK_CONST_METHOD0(getH, double());
......
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