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Commit ada3d4d1 authored by Lynch, Vickie's avatar Lynch, Vickie
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Refs #21752 unique peak number visible in tables

parent ce3b323e
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Framework/Crystal/src/LoadIsawPeaks.cpp
View file @ ada3d4d1
......@@ -76,7 +76,8 @@ int LoadIsawPeaks::confidence(Kernel::FileDescriptor &descriptor) const {
getWord(in, false);
readToEndOfLine(in, true);
confidence = 95;
} catch (std::exception &) {
}
catch (std::exception &) {
}
return confidence;
......@@ -86,11 +87,11 @@ int LoadIsawPeaks::confidence(Kernel::FileDescriptor &descriptor) const {
/** Initialize the algorithm's properties.
*/
void LoadIsawPeaks::init() {
const std::vector<std::string> exts{".peaks", ".integrate"};
const std::vector<std::string> exts{ ".peaks", ".integrate" };
declareProperty(Kernel::make_unique<FileProperty>("Filename", "",
FileProperty::Load, exts),
"Path to an ISAW-style .peaks filename.");
declareProperty(make_unique<WorkspaceProperty<Workspace>>(
declareProperty(make_unique<WorkspaceProperty<Workspace> >(
"OutputWorkspace", "", Direction::Output),
"Name of the output workspace.");
}
......@@ -236,7 +237,8 @@ std::string LoadIsawPeaks::readHeader(PeaksWorkspace_sptr outWS,
if (!alg->execute())
throw std::runtime_error(
"MaskDetectors Child Algorithm has not executed successfully");
} catch (...) {
}
catch (...) {
g_log.error("Can't execute MaskBTP algorithm");
}
}
......@@ -334,6 +336,7 @@ DataObjects::Peak LoadIsawPeaks::readPeak(PeaksWorkspace_sptr outWS,
peak.setIntensity(Inti);
peak.setSigmaIntensity(SigI);
peak.setBinCount(IPK);
peak.setPeakNumber(seqNum);
// Return the peak
return peak;
}
......@@ -510,7 +513,8 @@ void LoadIsawPeaks::appendFile(PeaksWorkspace_sptr outWS,
peak.setWavelength(wl.singleFromTOF(tof));
// Add the peak to workspace
outWS->addPeak(peak);
} catch (std::runtime_error &e) {
}
catch (std::runtime_error &e) {
g_log.error() << "Error reading peak SEQN " << seqNum << " : " << e.what()
<< '\n';
throw std::runtime_error("Corrupted input file. ");
......
Framework/Crystal/src/SaveHKL.cpp
View file @ ada3d4d1
......@@ -33,11 +33,11 @@ DECLARE_ALGORITHM(SaveHKL)
/** Initialize the algorithm's properties.
*/
void SaveHKL::init() {
declareProperty(make_unique<WorkspaceProperty<PeaksWorkspace>>(
declareProperty(make_unique<WorkspaceProperty<PeaksWorkspace> >(
"InputWorkspace", "", Direction::Input),
"An input PeaksWorkspace.");
auto mustBePositive = boost::make_shared<BoundedValidator<double>>();
auto mustBePositive = boost::make_shared<BoundedValidator<double> >();
mustBePositive->setLower(0.0);
declareProperty("ScalePeaks", 1.0, mustBePositive,
"Multiply FSQ and sig(FSQ) by scaleFactor");
......@@ -69,7 +69,7 @@ void SaveHKL::init() {
make_unique<FileProperty>("Filename", "", FileProperty::Save, ".hkl"),
"Path to an hkl file to save.");
std::vector<std::string> histoTypes{"Bank", "RunNumber", ""};
std::vector<std::string> histoTypes{ "Bank", "RunNumber", "" };
declareProperty("SortBy", histoTypes[2],
boost::make_shared<StringListValidator>(histoTypes),
"Sort the histograms by bank, run number or both (default).");
......@@ -78,7 +78,7 @@ void SaveHKL::init() {
declareProperty("WidthBorder", EMPTY_INT(), "Width of border of detectors");
declareProperty("MinIntensity", EMPTY_DBL(), mustBePositive,
"The minimum Intensity");
declareProperty(make_unique<WorkspaceProperty<PeaksWorkspace>>(
declareProperty(make_unique<WorkspaceProperty<PeaksWorkspace> >(
"OutputWorkspace", "SaveHKLOutput", Direction::Output),
"Output PeaksWorkspace");
declareProperty(
......@@ -88,7 +88,7 @@ void SaveHKL::init() {
"DirectionCosines", false,
"Extra columns (22 total) in file if true for direction cosines.\n"
"If false, original 14 columns (default).");
const std::vector<std::string> exts{".mat", ".ub", ".txt"};
const std::vector<std::string> exts{ ".mat", ".ub", ".txt" };
declareProperty(Kernel::make_unique<FileProperty>(
"UBFilename", "", FileProperty::OptionalLoad, exts),
"Path to an ISAW-style UB matrix text file only needed for "
......@@ -185,7 +185,7 @@ void SaveHKL::exec() {
std::string bankPart = "?";
// We must sort the peaks first by run, then bank #, and save the list of
// workspace indices of it
typedef std::map<int, std::vector<size_t>> bankMap_t;
typedef std::map<int, std::vector<size_t> > bankMap_t;
typedef std::map<int, bankMap_t> runMap_t;
std::set<int> uniqueBanks;
std::set<int> uniqueRuns;
......@@ -221,8 +221,8 @@ void SaveHKL::exec() {
}
bool correctPeaks = getProperty("ApplyAnvredCorrections");
std::vector<std::vector<double>> spectra;
std::vector<std::vector<double>> time;
std::vector<std::vector<double> > spectra;
std::vector<std::vector<double> > time;
int iSpec = 0;
m_smu = getProperty("LinearScatteringCoef"); // in 1/cm
m_amu = getProperty("LinearAbsorptionCoef"); // in 1/cm
......@@ -345,6 +345,7 @@ void SaveHKL::exec() {
continue;
}
int run = p.getRunNumber();
int seqNum = p.getPeakNumber();
int bank = 0;
std::string bankName = p.getBankName();
int nCols, nRows;
......@@ -546,7 +547,7 @@ void SaveHKL::exec() {
out << std::setw(6) << run;
out << std::setw(6) << wi + 1;
out << std::setw(6) << seqNum;
out << std::setw(7) << std::fixed << std::setprecision(4)
<< transmission;
......@@ -687,8 +688,8 @@ double SaveHKL::absor_sphere(double &twoth, double &wl, double &tbar) {
}
double SaveHKL::spectrumCalc(double TOF, int iSpec,
std::vector<std::vector<double>> time,
std::vector<std::vector<double>> spectra,
std::vector<std::vector<double> > time,
std::vector<std::vector<double> > spectra,
size_t id) {
double spect = 0;
if (iSpec == 1) {
......@@ -716,9 +717,9 @@ double SaveHKL::spectrumCalc(double TOF, int iSpec,
for (i = 1; i < spectra[id].size(); ++i)
if (TOF < time[id][i])
break;
spect = spectra[id][i - 1] +
(TOF - time[id][i - 1]) / (time[id][i] - time[id][i - 1]) *
(spectra[id][i] - spectra[id][i - 1]);
spect = spectra[id][i - 1] + (TOF - time[id][i - 1]) /
(time[id][i] - time[id][i - 1]) *
(spectra[id][i] - spectra[id][i - 1]);
}
return spect;
......
Framework/Crystal/src/SaveIsawPeaks.cpp
View file @ ada3d4d1
......@@ -27,7 +27,7 @@ DECLARE_ALGORITHM(SaveIsawPeaks)
/** Initialize the algorithm's properties.
*/
void SaveIsawPeaks::init() {
declareProperty(make_unique<WorkspaceProperty<PeaksWorkspace>>(
declareProperty(make_unique<WorkspaceProperty<PeaksWorkspace> >(
"InputWorkspace", "", Direction::Input,
boost::make_shared<InstrumentValidator>()),
"An input PeaksWorkspace with an instrument.");
......@@ -35,13 +35,13 @@ void SaveIsawPeaks::init() {
declareProperty("AppendFile", false, "Append to file if true.\n"
"If false, new file (default).");
const std::vector<std::string> exts{".peaks", ".integrate"};
const std::vector<std::string> exts{ ".peaks", ".integrate" };
declareProperty(Kernel::make_unique<FileProperty>("Filename", "",
FileProperty::Save, exts),
"Path to an ISAW-style peaks or integrate file to save.");
declareProperty(
make_unique<WorkspaceProperty<Workspace2D>>(
make_unique<WorkspaceProperty<Workspace2D> >(
"ProfileWorkspace", "", Direction::Input, PropertyMode::Optional),
"An optional Workspace2D of profiles from integrating cylinder.");
}
......@@ -62,9 +62,9 @@ void SaveIsawPeaks::exec() {
// We must sort the peaks first by run, then bank #, and save the list of
// workspace indices of it
typedef std::map<int, std::vector<size_t>> bankMap_t;
typedef std::map<int, std::vector<size_t> > bankMap_t;
typedef std::map<int, bankMap_t> runMap_t;
std::set<int, std::less<int>> uniqueBanks;
std::set<int, std::less<int> > uniqueBanks;
if (!inst)
throw std::runtime_error(
"No instrument in the Workspace. Cannot save DetCal file.");
......@@ -310,7 +310,7 @@ void SaveIsawPeaks::exec() {
Peak &p = peaks[wi];
// Sequence (run) number
out << "3" << std::setw(7) << seqNum;
out << "3" << std::setw(7) << p.getPeakNumber();
// HKL's are flipped by -1 because of the internal Q convention
// unless Crystallography convention
......
Framework/Crystal/src/SortHKL.cpp
View file @ ada3d4d1
......@@ -133,6 +133,8 @@ void SortHKL::exec() {
std::cout << e << " ";
std::cout << "\n";
auto zScores = Kernel::getZscore(intensities);
if (zScores.size() > maxPeaks)
maxPeaks = zScores.size();
// Possibly remove outliers.
auto outliersRemoved = unique.second.removeOutliers(sigmaCritical);
......@@ -183,7 +185,7 @@ void SortHKL::exec() {
MatrixWorkspace_sptr UniqWksp2 =
Mantid::API::WorkspaceFactory::Instance().create("Workspace2D", counter,
20, 20);
maxPeaks, maxPeaks);
for (int64_t i = 0; i < counter; ++i) {
auto &outSpec = UniqWksp2->getSpectrum(i);
const auto &inSpec = UniqWksp->getSpectrum(i);
......
Framework/DataObjects/inc/MantidDataObjects/Peak.h
View file @ ada3d4d1
......@@ -111,12 +111,12 @@ public:
Mantid::Kernel::V3D getDetectorPosition() const override;
Mantid::Kernel::V3D getDetectorPositionNoCheck() const override;
void setQSampleFrame(
const Mantid::Kernel::V3D &QSampleFrame,
boost::optional<double> detectorDistance = boost::none) override;
void
setQLabFrame(const Mantid::Kernel::V3D &QLabFrame,
boost::optional<double> detectorDistance = boost::none) override;
void setQSampleFrame(const Mantid::Kernel::V3D &QSampleFrame,
boost::optional<double> detectorDistance =
boost::none) override;
void setQLabFrame(const Mantid::Kernel::V3D &QLabFrame,
boost::optional<double> detectorDistance =
boost::none) override;
void setWavelength(double wavelength) override;
double getWavelength() const override;
......@@ -149,6 +149,8 @@ public:
int getCol() const override;
void setRow(int m_row);
void setCol(int m_col);
void setPeakNumber(int m_peakNumber);
int getPeakNumber() const override;
virtual Mantid::Kernel::V3D getDetPos() const override;
double getL1() const override;
......@@ -242,6 +244,9 @@ private:
double m_orig_K;
double m_orig_L;
// keep peak number
int m_peakNumber;
/// List of contributing detectors IDs
std::set<int> m_detIDs;
......
Framework/DataObjects/src/Peak.cpp
View file @ ada3d4d1
......@@ -29,7 +29,7 @@ Peak::Peak()
m_finalEnergy(0.), m_GoniometerMatrix(3, 3, true),
m_InverseGoniometerMatrix(3, 3, true), m_runNumber(0), m_monitorCount(0),
m_row(-1), m_col(-1), m_orig_H(0), m_orig_K(0), m_orig_L(0),
m_peakShape(boost::make_shared<NoShape>()) {
m_peakNumber(0), m_peakShape(boost::make_shared<NoShape>()) {
convention = Kernel::ConfigService::Instance().getString("Q.convention");
}
......@@ -169,7 +169,7 @@ Peak::Peak(const Geometry::Instrument_const_sptr &m_inst, double scattering,
m_binCount(0), m_GoniometerMatrix(3, 3, true),
m_InverseGoniometerMatrix(3, 3, true), m_runNumber(0), m_monitorCount(0),
m_row(-1), m_col(-1), m_orig_H(0), m_orig_K(0), m_orig_L(0),
m_peakShape(boost::make_shared<NoShape>()) {
m_peakNumber(0), m_peakShape(boost::make_shared<NoShape>()) {
convention = Kernel::ConfigService::Instance().getString("Q.convention");
this->setInstrument(m_inst);
this->setWavelength(m_Wavelength);
......@@ -197,8 +197,9 @@ Peak::Peak(const Peak &other)
m_row(other.m_row), m_col(other.m_col), sourcePos(other.sourcePos),
samplePos(other.samplePos), detPos(other.detPos),
m_orig_H(other.m_orig_H), m_orig_K(other.m_orig_K),
m_orig_L(other.m_orig_L), m_detIDs(other.m_detIDs),
m_peakShape(other.m_peakShape->clone()), convention(other.convention) {}
m_orig_L(other.m_orig_L), m_peakNumber(other.m_peakNumber),
m_detIDs(other.m_detIDs), m_peakShape(other.m_peakShape->clone()),
convention(other.convention) {}
//----------------------------------------------------------------------------------------------
/** Constructor making a Peak from IPeak interface
......@@ -218,7 +219,7 @@ Peak::Peak(const Geometry::IPeak &ipeak)
m_runNumber(ipeak.getRunNumber()),
m_monitorCount(ipeak.getMonitorCount()), m_row(ipeak.getRow()),
m_col(ipeak.getCol()), m_orig_H(0.), m_orig_K(0.), m_orig_L(0.),
m_peakShape(boost::make_shared<NoShape>()) {
m_peakNumber(0), m_peakShape(boost::make_shared<NoShape>()) {
convention = Kernel::ConfigService::Instance().getString("Q.convention");
if (fabs(m_InverseGoniometerMatrix.Invert()) < 1e-8)
throw std::invalid_argument(
......@@ -870,6 +871,11 @@ int Peak::getRow() const { return m_row; }
* Returns -1 if it could not find it. */
int Peak::getCol() const { return m_col; }
// -------------------------------------------------------------------------------------
/**Returns the unique peak number
* Returns -1 if it could not find it. */
int Peak::getPeakNumber() const { return m_peakNumber; }
// -------------------------------------------------------------------------------------
/** For RectangularDetectors only, sets the row (y) of the pixel of the
* detector.
......@@ -882,6 +888,13 @@ void Peak::setRow(int m_row) { this->m_row = m_row; }
* @param m_col :: col value */
void Peak::setCol(int m_col) { this->m_col = m_col; }
// -------------------------------------------------------------------------------------
/** Sets the unique peak number
* @param m_col :: col value */
void Peak::setPeakNumber(int m_peakNumber) {
this->m_peakNumber = m_peakNumber;
}
// -------------------------------------------------------------------------------------
/** Return the detector position vector */
Mantid::Kernel::V3D Peak::getDetPos() const { return detPos; }
......
Framework/DataObjects/src/PeakColumn.cpp
View file @ ada3d4d1
......@@ -31,7 +31,7 @@ const std::string typeFromName(const std::string &name) {
// We should enter the critical section if the map has not been fully filled.
// Be sure to keep the value tested against in sync with the number of inserts
// below
if (TYPE_INDEX.size() != 17) {
if (TYPE_INDEX.size() != 18) {
PARALLEL_CRITICAL(fill_column_index_map) {
if (TYPE_INDEX.empty()) // check again inside the critical block
{
......@@ -53,6 +53,7 @@ const std::string typeFromName(const std::string &name) {
TYPE_INDEX.emplace("Col", "double");
TYPE_INDEX.emplace("QLab", "V3D");
TYPE_INDEX.emplace("QSample", "V3D");
TYPE_INDEX.emplace("PeakNumber", "int");
// If adding an entry, be sure to increment the size comparizon in the
// first line
}
......@@ -152,6 +153,8 @@ void PeakColumn::print(size_t index, std::ostream &s) const {
s << std::fixed << std::setprecision(m_hklPrec) << peak.getK();
} else if (m_name == "l") {
s << std::fixed << std::setprecision(m_hklPrec) << peak.getL();
} else if (m_name == "PeakNumber") {
s << peak.getPeakNumber();
} else
s << peak.getValueByColName(m_name);
s.flags(fflags);
......
Framework/DataObjects/src/PeaksWorkspace.cpp
View file @ ada3d4d1
......@@ -630,6 +630,7 @@ void PeaksWorkspace::initColumns() {
addPeakColumn("Col");
addPeakColumn("QLab");
addPeakColumn("QSample");
addPeakColumn("PeakNumber");
}
//---------------------------------------------------------------------------------------------
......@@ -694,6 +695,7 @@ void PeaksWorkspace::saveNexus(::NeXus::File *file) const {
std::vector<double> dSpacing(np);
std::vector<double> TOF(np);
std::vector<int> runNumber(np);
std::vector<int> peakNumber(np);
std::vector<double> goniometerMatrix(9 * np);
std::vector<std::string> shapes(np);
......@@ -715,6 +717,7 @@ void PeaksWorkspace::saveNexus(::NeXus::File *file) const {
dSpacing[i] = p.getDSpacing();
TOF[i] = p.getTOF();
runNumber[i] = p.getRunNumber();
peakNumber[i] = p.getPeakNumber();
{
Matrix<double> gm = p.getGoniometerMatrix();
goniometerMatrix[9 * i] = gm[0][0];
......@@ -861,6 +864,14 @@ void PeaksWorkspace::saveNexus(::NeXus::File *file) const {
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Peak Number column
file->writeData("column_20", peakNumber);
file->openData("column_20");
file->putAttr("name", "Peak Number");
file->putAttr("interpret_as", specifyInteger);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Goniometer Matrix Column
std::vector<int> array_dims;
array_dims.push_back(static_cast<int>(peaks.size()));
......
Framework/Geometry/inc/MantidGeometry/Crystal/IPeak.h
View file @ ada3d4d1
......@@ -76,6 +76,9 @@ public:
virtual double getBinCount() const = 0;
virtual void setBinCount(double m_BinCount) = 0;
virtual int getPeakNumber() const = 0;
virtual void setPeakNumber(int m_PeakNumber) = 0;
virtual Mantid::Kernel::Matrix<double> getGoniometerMatrix() const = 0;
virtual void setGoniometerMatrix(
const Mantid::Kernel::Matrix<double> &m_GoniometerMatrix) = 0;
......
Framework/Kernel/src/Statistics.cpp
View file @ ada3d4d1
......@@ -68,7 +68,7 @@ double getMedian(const vector<TYPE> &data, const size_t num_data,
// return the average
return (left + right) / 2.;
} else
// Odd number
// Odd number
{
if (sorted) {
// If sorted and odd, just return the centre value
......@@ -100,9 +100,10 @@ std::vector<double> getZscore(const vector<TYPE> &data) {
std::vector<double> Zscore(data.size(), 0.);
return Zscore;
}
double divisor = stats.standard_deviation / data.size();
for (auto it = data.cbegin(); it != data.cend(); ++it) {
double tmp = static_cast<double>(*it);
Zscore.push_back(fabs((tmp - stats.mean) / stats.standard_deviation));
Zscore.push_back(fabs(stats.mean - tmp) / divisor;
}
return Zscore;
}
......@@ -158,7 +159,7 @@ Statistics getStatistics(const vector<TYPE> &data, const unsigned int flags) {
(flags & StatOptions::CorrectedStdDev));
if (stddev) {
using namespace boost::accumulators;
accumulator_set<double, stats<tag::min, tag::max, tag::variance>> acc;
accumulator_set<double, stats<tag::min, tag::max, tag::variance> > acc;
for (auto &value : data) {
acc(static_cast<double>(value));
}
......@@ -175,7 +176,7 @@ Statistics getStatistics(const vector<TYPE> &data, const unsigned int flags) {
} else if (flags & StatOptions::Mean) {
using namespace boost::accumulators;
accumulator_set<double, stats<tag::mean>> acc;
accumulator_set<double, stats<tag::mean> > acc;
for (auto &value : data) {
acc(static_cast<double>(value));
}
......
Framework/MDAlgorithms/inc/MantidMDAlgorithms/FindPeaksMD.h
View file @ ada3d4d1
......@@ -100,6 +100,8 @@ private:
Mantid::Geometry::Instrument_const_sptr inst;
/// Run number of the peaks
int m_runNumber;
/// Unique peak number
int m_peakNumber;
/// Dimension type
eDimensionType dimType;
/// Goniometer matrix
......
Framework/MDAlgorithms/src/FindPeaksMD.cpp
View file @ ada3d4d1
......@@ -114,30 +114,30 @@ const std::string FindPeaksMD::numberOfEventsNormalization =
FindPeaksMD::FindPeaksMD()
: peakWS(), peakRadiusSquared(), DensityThresholdFactor(0.0), m_maxPeaks(0),
m_addDetectors(true), m_densityScaleFactor(1e-6), prog(nullptr), inst(),
m_runNumber(-1), dimType(), m_goniometer() {}
m_runNumber(-1), m_peakNumber(1), dimType(), m_goniometer() {}
//----------------------------------------------------------------------------------------------
/** Initialize the algorithm's properties.
*/
void FindPeaksMD::init() {
declareProperty(make_unique<WorkspaceProperty<IMDWorkspace>>(
declareProperty(make_unique<WorkspaceProperty<IMDWorkspace> >(
"InputWorkspace", "", Direction::Input),
"An input MDEventWorkspace or MDHistoWorkspace with at least "
"3 dimensions.");
declareProperty(
make_unique<PropertyWithValue<double>>("PeakDistanceThreshold", 0.1,
Direction::Input),
make_unique<PropertyWithValue<double> >("PeakDistanceThreshold", 0.1,
Direction::Input),
"Threshold distance for rejecting peaks that are found to be too close "
"from each other.\n"
"This should be some multiple of the radius of a peak. Default: 0.1.");
declareProperty(make_unique<PropertyWithValue<int64_t>>("MaxPeaks", 500,
Direction::Input),
declareProperty(make_unique<PropertyWithValue<int64_t> >("MaxPeaks", 500,
Direction::Input),
"Maximum number of peaks to find. Default: 500.");
std::vector<std::string> strategy = {volumeNormalization,
numberOfEventsNormalization};
std::vector<std::string> strategy = { volumeNormalization,
numberOfEventsNormalization };
declareProperty(
"PeakFindingStrategy", volumeNormalization,
boost::make_shared<StringListValidator>(strategy),
......@@ -156,7 +156,7 @@ void FindPeaksMD::init() {
"be larger than 1. Note that this approach does not work for event-based "
"raw data.\n");
declareProperty(make_unique<PropertyWithValue<double>>(
declareProperty(make_unique<PropertyWithValue<double> >(
"DensityThresholdFactor", 10.0, Direction::Input),
"The overall signal density of the workspace will be "
"multiplied by this factor \n"
......@@ -170,7 +170,7 @@ void FindPeaksMD::init() {
Mantid::Kernel::ePropertyCriterion::IS_EQUAL_TO,
volumeNormalization));
declareProperty(make_unique<PropertyWithValue<double>>(
declareProperty(make_unique<PropertyWithValue<double> >(
"SignalThresholdFactor", 1.5, Direction::Input),
"The overal signal value (not density!) normalized by the "
"number of events is compared to the specified signal "
......@@ -193,7 +193,7 @@ void FindPeaksMD::init() {
"only) for a constant wavelength. This only works for Q "
"sample workspaces.");
auto nonNegativeDbl = boost::make_shared<BoundedValidator<double>>();
auto nonNegativeDbl = boost::make_shared<BoundedValidator<double> >();
nonNegativeDbl->setLower(0);
declareProperty("Wavelength", DBL_MAX, nonNegativeDbl,
"Wavelength to use when calculating goniometer angle");
......@@ -203,7 +203,7 @@ void FindPeaksMD::init() {
"CalculateGoniometerForCW",
Mantid::Kernel::ePropertyCriterion::IS_NOT_DEFAULT));
declareProperty(make_unique<WorkspaceProperty<PeaksWorkspace>>(
declareProperty(make_unique<WorkspaceProperty<PeaksWorkspace> >(
"OutputWorkspace", "", Direction::Output),
"An output PeaksWorkspace with the peaks' found positions.");
......@@ -212,7 +212,7 @@ void FindPeaksMD::init() {
"if it exists. \n"
"If unchecked, the output workspace is replaced (Default).");
auto nonNegativeInt = boost::make_shared<BoundedValidator<int>>();
auto nonNegativeInt = boost::make_shared<BoundedValidator<int> >();
nonNegativeInt->setLower(0);
declareProperty("EdgePixels", 0, nonNegativeInt,
"Remove peaks that are at pixels this close to edge. ");
......@@ -246,7 +246,8 @@ void FindPeaksMD::readExperimentInfo(const ExperimentInfo_sptr &ei,
Mantid::Kernel::Matrix<double>(3, 3, true); // Default IDENTITY matrix
try {
m_goniometer = ei->mutableRun().getGoniometerMatrix();
} catch (std::exception &e) {
}
catch (std::exception &e) {
g_log.warning() << "Error finding goniometer matrix. It will not be set in "
"the peaks found.\n";
g_log.warning() << e.what() << '\n';
......@@ -270,7 +271,8 @@ void FindPeaksMD::addPeak(const V3D &Q, const double binCount,
}
if (p->getDetectorID() != -1)
peakWS->addPeak(*p);
} catch (std::exception &e) {
}
catch (std::exception &e) {
g_log.notice() << "Error creating peak at " << Q << " because of '"
<< e.what() << "'. Peak will be skipped.\n";
}
......@@ -304,9 +306,9 @@ FindPeaksMD::createPeak(const Mantid::Kernel::V3D &Q, const double binCount,
// Solve to find rotation matrix, assuming only rotation around y-axis
// A * X = B
Matrix<double> A({Q[0], Q[2], Q[2], -Q[0]}, 2, 2);
Matrix<double> A({ Q[0], Q[2], Q[2], -Q[0] }, 2, 2);
A.Invert();
std::vector<double> B{Q_lab[0], Q_lab[2]};
std::vector<double> B{ Q_lab[0], Q_lab[2] };
std::vector<double> X = A * B;
double rot = atan2(X[1], X[0]);
g_log.information() << "Found goniometer rotation to be "
......@@ -330,7 +332,8 @@ FindPeaksMD::createPeak(const Mantid::Kernel::V3D &Q, const double binCount,
try { // Look for a detector
p->findDetector(tracer);
} catch (...) { /* Ignore errors in ray-tracer */
}
catch (...) { /* Ignore errors in ray-tracer */
}
p->setBinCount(binCount);
......@@ -500,8 +503,8 @@ void FindPeaksMD::findPeaks(typename MDEventWorkspace<MDE, nd>::sptr ws) {
if (nexp > 1) {
MDBox<MDE, nd> *mdbox = dynamic_cast<MDBox<MDE, nd> *>(box);
typename std::vector<MDE> &events = mdbox->getEvents();
if (std::none_of(events.cbegin(), events.cend(), [&iexp, &nexp](
MDE event) {
if (std::none_of(events.cbegin(), events.cend(),
[&iexp, &nexp](MDE event) {
return event.getRunIndex() == iexp || event.getRunIndex() >= nexp;
}))
continue;
......@@ -545,7 +548,8 @@ void FindPeaksMD::findPeaks(typename MDEventWorkspace<MDE, nd>::sptr ws) {
g_log.information() << "Add new peak with Q-center = " << Q[0] << ", "
<< Q[1] << ", " << Q[2] << "\n";
}
} catch (std::exception &e) {
}
catch (std::exception &e) {
g_log.notice() << "Error creating peak at " << Q << " because of '"
<< e.what() << "'. Peak will be skipped.\n";
}
......@@ -564,8 +568,8 @@ void FindPeaksMD::findPeaks(typename MDEventWorkspace<MDE, nd>::sptr ws) {
*
* @param ws :: MDHistoWorkspace
*/
void FindPeaksMD::findPeaksHisto(
Mantid::DataObjects::MDHistoWorkspace_sptr ws) {
void
FindPeaksMD::findPeaksHisto(Mantid::DataObjects::MDHistoWorkspace_sptr ws) {
size_t nd = ws->getNumDims();
if (nd < 3)
throw std::invalid_argument("Workspace must have at least 3 dimensions.");
......@@ -740,12 +744,16 @@ void FindPeaksMD::exec() {
}