/**
* Calculate detector efficiency given a formula, the efficiency at the elastic line,
* and a vector with energies.
* Efficiency = f(Ei-DeltaE) / f(Ei)
* Hope all compilers supports the NRVO (otherwise will copy the output vector)
* @param eff0 :: calculated eff0
* @param formula :: formula to calculate efficiency (parsed from IDF)
* @param xIn :: Energy bins vector (X axis)
* @return a vector with the efficiencies
*/
MantidVec DetectorEfficiencyCorUser::calculateEfficiency(double eff0,
const std::string& formula, const MantidVec& xIn) {
MantidVec effOut(xIn.size() - 1); // x are bins and have more one value than y
try {
double e;
mu::Parser p;
p.DefineVar("e", &e);
p.SetExpr(formula);
// copied from Jaques Ollivier Code
bool conditionForEnergy = std::min( std::abs( *std::min_element(xIn.begin(), xIn.end()) ) , m_Ei) < m_Ei;
MantidVec::const_iterator xIn_it = xIn.begin(); // DeltaE
MantidVec::iterator effOut_it = effOut.begin();
for (; effOut_it != effOut.end(); ++xIn_it, ++effOut_it) {
if (conditionForEnergy ) {
// cppcheck cannot see that this is used by reference by muparser
e = std::fabs(m_Ei + *xIn_it);
}
else {
// cppcheck cannot see that this is used by reference by muparser
// cppcheck-suppress unreadVariable
e = std::fabs(m_Ei - *xIn_it);
}
double eff = p.Eval();
*effOut_it = eff / eff0;
}
return effOut;
} catch (mu::Parser::exception_type &e) {
throw Kernel::Exception::InstrumentDefinitionError(
"Error calculating formula from string. Muparser error message is: "
+ e.GetMsg());
}
}
/** Calculates Sn as estimator of scale for given vector
*
* This method implements a naive calculation of Sn, as defined by Rousseeuw and Croux (http://dx.doi.org/10.2307%2F2291267).
* In contrast to standard deviation, this is more robust towards outliers.
*
* @param begin :: Beginning of vector.
* @param end :: End of vector.
* @return Sn of supplied data.
*/
double PoldiPeakSearch::getSn(MantidVec::const_iterator begin, MantidVec::const_iterator end) const
{
size_t numberOfPoints = std::distance(begin, end);
MantidVec absoluteDifferenceMedians(numberOfPoints);
PARALLEL_FOR_NO_WSP_CHECK()
for(int i = 0; i < static_cast<int>(numberOfPoints); ++i) {
double currentValue = *(begin + i);
MantidVec temp;
temp.reserve(numberOfPoints - 1);
for(int j = 0; j < static_cast<int>(numberOfPoints); ++j) {
if(j != i) {
temp.push_back(fabs(*(begin + j) - currentValue));
}
}
std::sort(temp.begin(), temp.end());
absoluteDifferenceMedians[i] = getMedianFromSortedVector(temp.begin(), temp.end());
}
std::sort(absoluteDifferenceMedians.begin(), absoluteDifferenceMedians.end());
return 1.1926 * getMedianFromSortedVector(absoluteDifferenceMedians.begin(), absoluteDifferenceMedians.end());
}
/** Retrieves a vector with all counts that belong to the background
*
* In this method, a vector is assembled which contains all count data that is
*considered to be background.
* Whether a point is considered background depends on its distance to the
*given peak positions.
*
* @param peakPositions :: Peak positions.
* @param correlationCounts :: Vector with the complete correlation spectrum.
* @return Vector only with counts that belong to the background.
*/
MantidVec PoldiPeakSearch::getBackground(
std::list<MantidVec::const_iterator> peakPositions,
const MantidVec &correlationCounts) const {
size_t backgroundPoints =
getNumberOfBackgroundPoints(peakPositions, correlationCounts);
MantidVec background;
background.reserve(backgroundPoints);
for (MantidVec::const_iterator point = correlationCounts.begin() + 1;
point != correlationCounts.end() - 1; ++point) {
if (distanceToPeaksGreaterThanMinimum(peakPositions, point)) {
background.push_back(*point);
}
}
return background;
}
/** Write data in SLOG format
*/
void SaveGSS::writeSLOGdata(const int bank, const bool MultiplyByBinWidth,
std::stringstream &out, const MantidVec &X,
const MantidVec &Y, const MantidVec &E) const {
const size_t datasize = Y.size();
double bc1 = X.front(); // minimum TOF in microseconds
if (bc1 <= 0.) {
throw std::runtime_error(
"Cannot write out logarithmic data starting at zero");
}
double bc2 = 0.5 * (*(X.rbegin()) +
*(X.rbegin() + 1)); // maximum TOF (in microseconds?)
double bc3 = (*(X.begin() + 1) - bc1) / bc1; // deltaT/T
g_log.debug() << "SaveGSS(): Min TOF = " << bc1 << std::endl;
writeBankLine(out, "SLOG", bank, datasize);
out << std::fixed << " " << std::setprecision(0) << std::setw(10) << bc1
<< std::fixed << " " << std::setprecision(0) << std::setw(10) << bc2
<< std::fixed << " " << std::setprecision(7) << std::setw(10) << bc3
<< std::fixed << " 0 FXYE" << std::endl;
for (size_t i = 0; i < datasize; i++) {
double y = Y[i];
double e = E[i];
if (MultiplyByBinWidth) {
// Multiple by bin width as
double delta = X[i + 1] - X[i];
y *= delta;
e *= delta;
}
e = fixErrorValue(e);
out << " " << std::fixed << std::setprecision(9) << std::setw(20)
<< 0.5 * (X[i] + X[i + 1]) << " " << std::fixed << std::setprecision(9)
<< std::setw(20) << y << " " << std::fixed << std::setprecision(9)
<< std::setw(20) << e << std::setw(12) << " "
<< "\n"; // let it flush its own buffer
}
out << std::flush;
return;
}
/**
* Copy over the metadata from the input matrix workspace to output MDEventWorkspace
* @param mdEventWS :: The output MDEventWorkspace where metadata are copied to. The source of the metadata is the input matrix workspace
*
*/
void ConvertToMD::copyMetaData(API::IMDEventWorkspace_sptr &mdEventWS) const
{
// found detector which is not a monitor to get proper bin boundaries.
size_t spectra_index(0);
bool dector_found(false);
for(size_t i=0;i<m_InWS2D->getNumberHistograms(); ++i)
{
try
{
auto det=m_InWS2D->getDetector(i);
if (!det->isMonitor())
{
spectra_index=i;
dector_found = true;
g_log.debug()<<"Using spectra N "<<i<< " as the source of the bin boundaries for the resolution corrections \n";
break;
}
}
catch(...)
{}
}
if (!dector_found)
g_log.warning()<<"No detectors in the workspace are associated with spectra. Using spectrum 0 trying to retrieve the bin boundaries \n";
// retrieve representative bin boundaries
MantidVec binBoundaries = m_InWS2D->readX(spectra_index);
// check if the boundaries transformation is necessary
if (m_Convertor->getUnitConversionHelper().isUnitConverted())
{
if( !dynamic_cast<DataObjects::EventWorkspace *>(m_InWS2D.get()))
{
g_log.information()<<" ConvertToMD converts input workspace units, but the bin boundaries are copied from the first workspace spectra. The resolution estimates can be incorrect if unit conversion depends on spectra number.\n";
UnitsConversionHelper &unitConv = m_Convertor->getUnitConversionHelper();
unitConv.updateConversion(spectra_index);
for(size_t i=0;i<binBoundaries.size();i++)
{
binBoundaries[i] =unitConv.convertUnits(binBoundaries[i]);
}
}
// sort bin boundaries in case if unit transformation have swapped them.
if (binBoundaries[0]>binBoundaries[binBoundaries.size()-1])
{
g_log.information()<<"Bin boundaries are not arranged monotonously. Sorting performed\n";
std::sort(binBoundaries.begin(),binBoundaries.end());
}
}
// Replacement for SpectraDetectorMap::createIDGroupsMap using the ISpectrum objects instead
auto mapping = boost::make_shared<det2group_map>();
for ( size_t i = 0; i < m_InWS2D->getNumberHistograms(); ++i )
{
const auto& dets = m_InWS2D->getSpectrum(i)->getDetectorIDs();
if(!dets.empty())
{
std::vector<detid_t> id_vector;
std::copy(dets.begin(), dets.end(), std::back_inserter(id_vector));
mapping->insert(std::make_pair(id_vector.front(), id_vector));
}
}
uint16_t nexpts = mdEventWS->getNumExperimentInfo();
for(uint16_t i = 0; i < nexpts; ++i)
{
ExperimentInfo_sptr expt = mdEventWS->getExperimentInfo(i);
expt->mutableRun().storeHistogramBinBoundaries(binBoundaries);
expt->cacheDetectorGroupings(*mapping);
}
}
/** Corrects a spectra for the detector efficiency calculated from detector information
Gets the detector information and uses this to calculate its efficiency
* @param spectraIn :: index of the spectrum to get the efficiency for
* @throw invalid_argument if the shape of a detector is isn't a cylinder aligned along one axis
* @throw runtime_error if the SpectraDetectorMap has not been filled
* @throw NotFoundError if the detector or its gas pressure or wall thickness were not found
*/
void DetectorEfficiencyCor::correctForEfficiency(int64_t spectraIn)
{
IDetector_const_sptr det = m_inputWS->getDetector(spectraIn);
if( det->isMonitor() || det->isMasked() )
{
return;
}
MantidVec & yout = m_outputWS->dataY(spectraIn);
MantidVec & eout = m_outputWS->dataE(spectraIn);
// Need the original values so this is not a reference
const MantidVec yValues = m_inputWS->readY(spectraIn);
const MantidVec eValues = m_inputWS->readE(spectraIn);
// get a pointer to the detectors that created the spectrum
const std::set<detid_t> dets = m_inputWS->getSpectrum(spectraIn)->getDetectorIDs();
std::set<detid_t>::const_iterator it = dets.begin();
std::set<detid_t>::const_iterator iend = dets.end();
if ( it == iend )
{
throw Exception::NotFoundError("No detectors found", spectraIn);
}
// Storage for the reciprocal wave vectors that are calculated as the
//correction proceeds
std::vector<double> oneOverWaveVectors(yValues.size());
for( ; it != iend ; ++it )
{
IDetector_const_sptr det_member = m_inputWS->getInstrument()->getDetector(*it);
Parameter_sptr par = m_paraMap->get(det_member.get(),"3He(atm)");
if ( !par )
{
throw Exception::NotFoundError("3He(atm)", spectraIn);
}
const double atms = par->value<double>();
par = m_paraMap->get(det_member.get(),"wallT(m)");
if ( !par )
{
throw Exception::NotFoundError("wallT(m)", spectraIn);
}
const double wallThickness = par->value<double>();
double detRadius(0.0);
V3D detAxis;
getDetectorGeometry(det_member, detRadius, detAxis);
// now get the sin of the angle, it's the magnitude of the cross product of unit vector along the detector tube axis and a unit vector directed from the sample to the detector centre
V3D vectorFromSample = det_member->getPos() - m_samplePos;
vectorFromSample.normalize();
Quat rot = det_member->getRotation();
// rotate the original cylinder object axis to get the detector axis in the actual instrument
rot.rotate(detAxis);
detAxis.normalize();
// Scalar product is quicker than cross product
double cosTheta = detAxis.scalar_prod(vectorFromSample);
double sinTheta = std::sqrt(1.0 - cosTheta*cosTheta);
// Detector constant
const double det_const = g_helium_prefactor*(detRadius - wallThickness)*atms/sinTheta;
MantidVec::const_iterator yinItr = yValues.begin();
MantidVec::const_iterator einItr = eValues.begin();
MantidVec::iterator youtItr = yout.begin();
MantidVec::iterator eoutItr = eout.begin();
MantidVec::const_iterator xItr = m_inputWS->readX(spectraIn).begin();
std::vector<double>::iterator wavItr = oneOverWaveVectors.begin();
for( ; youtItr != yout.end(); ++youtItr, ++eoutItr)
{
if( it == dets.begin() )
{
*youtItr = 0.0;
*eoutItr = 0.0;
*wavItr = calculateOneOverK(*xItr, *(xItr + 1 ));
}
const double oneOverWave = *wavItr;
const double factor = 1.0/detectorEfficiency(det_const*oneOverWave);
*youtItr += (*yinItr)*factor;
*eoutItr += (*einItr)*factor;
++yinItr; ++einItr;
++xItr; ++wavItr;
}
}
}
/** Subtracts a constant from the data values in the given workspace
* @param Y :: The vector from which to subtract
* @param value :: The value to subtract from each data point
*/
void IQTransform::subtractBackgroundValue(MantidVec& Y, const double value)
{
g_log.debug() << "Subtracting the background value " << value << " from the input workspace.\n";
std::transform(Y.begin(),Y.end(),Y.begin(),std::bind2nd(std::minus<double>(),value));
}
void PoldiPeakSearch::exec() {
g_log.information() << "PoldiPeakSearch:" << std::endl;
Workspace2D_sptr correlationWorkspace = getProperty("InputWorkspace");
MantidVec correlationQValues = correlationWorkspace->readX(0);
MantidVec correlatedCounts = correlationWorkspace->readY(0);
g_log.information() << " Auto-correlation data read." << std::endl;
Unit_sptr xUnit = correlationWorkspace->getAxis(0)->unit();
if (xUnit->caption() == "") {
g_log.information()
<< " Workspace does not have unit, defaulting to MomentumTransfer."
<< std::endl;
xUnit = UnitFactory::Instance().create("MomentumTransfer");
} else {
g_log.information() << " Unit of workspace is " << xUnit->caption() << "."
<< std::endl;
}
setMinimumDistance(getProperty("MinimumPeakSeparation"));
setMinimumPeakHeight(getProperty("MinimumPeakHeight"));
setMaximumPeakNumber(getProperty("MaximumPeakNumber"));
if (m_doubleMinimumDistance > static_cast<int>(correlatedCounts.size())) {
throw(std::runtime_error("MinimumPeakSeparation is smaller than number of "
"spectrum points - no peaks possible."));
}
g_log.information() << " Parameters set." << std::endl;
MantidVec summedNeighborCounts = getNeighborSums(correlatedCounts);
g_log.information() << " Neighboring counts summed, contains "
<< summedNeighborCounts.size() << " data points."
<< std::endl;
std::list<MantidVec::const_iterator> peakPositionsSummed =
findPeaks(summedNeighborCounts.begin(), summedNeighborCounts.end());
g_log.information() << " Peaks detected in summed spectrum: "
<< peakPositionsSummed.size() << std::endl;
/* This step is required because peaks are actually searched in the
* "sum-of-neighbors"-spectrum.
* The mapping removes the offset from the peak position which results from
* different beginning
* of this vector compared to the original correlation counts.
*/
std::list<MantidVec::const_iterator> peakPositionsCorrelation =
mapPeakPositionsToCorrelationData(peakPositionsSummed,
summedNeighborCounts.begin(),
correlatedCounts.begin());
g_log.information() << " Peak positions transformed to original spectrum."
<< std::endl;
/* Since intensities are required for filtering, they are extracted from the
* original count data,
* along with the Q-values.
*/
std::vector<PoldiPeak_sptr> peakCoordinates =
getPeaks(correlatedCounts.begin(), correlatedCounts.end(),
peakPositionsCorrelation, correlationQValues, xUnit);
g_log.information()
<< " Extracted peak positions in Q and intensity guesses." << std::endl;
UncertainValue backgroundWithSigma =
getBackgroundWithSigma(peakPositionsCorrelation, correlatedCounts);
g_log.information() << " Calculated average background and deviation: "
<< UncertainValueIO::toString(backgroundWithSigma)
<< std::endl;
if ((*getProperty("MinimumPeakHeight")).isDefault()) {
setMinimumPeakHeight(minimumPeakHeightFromBackground(backgroundWithSigma));
}
std::vector<PoldiPeak_sptr> intensityFilteredPeaks(peakCoordinates.size());
auto newEnd = std::remove_copy_if(
peakCoordinates.begin(), peakCoordinates.end(),
intensityFilteredPeaks.begin(),
boost::bind(&PoldiPeakSearch::isLessThanMinimum, this, _1));
intensityFilteredPeaks.resize(
std::distance(intensityFilteredPeaks.begin(), newEnd));
g_log.information() << " Peaks above minimum intensity ("
<< m_minimumPeakHeight
<< "): " << intensityFilteredPeaks.size() << std::endl;
std::sort(intensityFilteredPeaks.begin(), intensityFilteredPeaks.end(),
boost::bind<bool>(&PoldiPeak::greaterThan, _1, _2,
&PoldiPeak::intensity));
for (std::vector<PoldiPeak_sptr>::const_iterator peak =
intensityFilteredPeaks.begin();
peak != intensityFilteredPeaks.end(); ++peak) {
m_peaks->addPeak(*peak);
}
/* The derived background error is set as error in the workspace containing
* correlation data, so it may be used as weights for peak fitting later on.
*/
setErrorsOnWorkspace(correlationWorkspace, backgroundWithSigma.error());
setProperty("OutputWorkspace", m_peaks->asTableWorkspace());
}
void LoadDaveGrp::exec()
{
const std::string filename = this->getProperty("Filename");
int yLength = 0;
MantidVec *xAxis = new MantidVec();
MantidVec *yAxis = new MantidVec();
std::vector<MantidVec *> data;
std::vector<MantidVec *> errors;
this->ifile.open(filename.c_str());
if (this->ifile.is_open())
{
// Size of x axis
this->getAxisLength(this->xLength);
// Size of y axis
this->getAxisLength(yLength);
// This is also the number of groups (spectra)
this->nGroups = yLength;
// Read in the x axis values
this->getAxisValues(xAxis, static_cast<std::size_t>(this->xLength));
// Read in the y axis values
this->getAxisValues(yAxis, static_cast<std::size_t>(yLength));
// Read in the data
this->getData(data, errors);
}
this->ifile.close();
// Scale the x-axis if it is in micro-eV to get it to meV
const bool isUeV = this->getProperty("IsMicroEV");
if (isUeV)
{
MantidVec::iterator iter;
for (iter = xAxis->begin(); iter != xAxis->end(); ++iter)
{
*iter /= 1000.0;
}
}
// Create workspace
API::MatrixWorkspace_sptr outputWorkspace = \
boost::dynamic_pointer_cast<API::MatrixWorkspace>\
(API::WorkspaceFactory::Instance().create("Workspace2D", this->nGroups,
this->xLength, yLength));
// Force the workspace to be a distribution
outputWorkspace->isDistribution(true);
// Set the x-axis units
outputWorkspace->getAxis(0)->unit() = Kernel::UnitFactory::Instance().create(this->getProperty("XAxisUnits"));
API::Axis* const verticalAxis = new API::NumericAxis(yLength);
// Set the y-axis units
verticalAxis->unit() = Kernel::UnitFactory::Instance().create(this->getProperty("YAxisUnits"));
outputWorkspace->replaceAxis(1, verticalAxis);
for(int i = 0; i < this->nGroups; i++)
{
outputWorkspace->dataX(i) = *xAxis;
outputWorkspace->dataY(i) = *data[i];
outputWorkspace->dataE(i) = *errors[i];
verticalAxis->setValue(i, yAxis->at(i));
delete data[i];
delete errors[i];
}
delete xAxis;
delete yAxis;
outputWorkspace->mutableRun().addProperty("Filename",filename);
this->setProperty("OutputWorkspace", outputWorkspace);
}
/** Finds the index in an ordered vector which follows the given value
* @param value :: The value to search for
* @param vec :: The vector to search
* @return The index (will give vec.size()+1 if the value is past the end of the vector)
*/
int RemoveBins::findIndex(const double& value, const MantidVec& vec)
{
MantidVec::const_iterator pos = std::lower_bound(vec.begin(),vec.end(),value);
return static_cast<int>(pos-vec.begin());
}
/**
* Loads data from a selection of the FITS files into the workspace
* @param workspace The workspace to insert data into
* @param yVals Reference to a pre-allocated vector to hold data values for the workspace
* @param eVals Reference to a pre-allocated vector to hold error values for the workspace
* @param bufferAny Pointer to an allocated memory region which will hold a files worth of data
* @param x Vector holding the X bin values
* @param spectraCount Number of data points in each file
* @param bitsPerPixel Number of bits used to represent one data point
* @param binChunkStartIndex Index for the first file to be processed in this chunk
*/
void LoadFITS::loadChunkOfBinsFromFile(MatrixWorkspace_sptr &workspace, vector<vector<double> > &yVals, vector<vector<double> > &eVals, void *&bufferAny, MantidVecPtr &x, size_t spectraCount, int bitsPerPixel, size_t binChunkStartIndex)
{
size_t binsThisChunk = m_binChunkSize;
if((binChunkStartIndex + m_binChunkSize) > m_allHeaderInfo.size())
{
// No need to do extra processing if number of bins to process is lower than m_binChunkSize
// Also used to prevent out of bounds error where a greater number of elements have been reserved.
binsThisChunk = static_cast<size_t>(m_allHeaderInfo.size() - binChunkStartIndex);
}
uint8_t *buffer8 = NULL;
uint16_t *buffer16 = NULL;
uint32_t *buffer32 = NULL;
// create pointer of correct data type to void pointer of the buffer:
buffer8 = static_cast<uint8_t*>(bufferAny);
buffer16 = static_cast<uint16_t*>(bufferAny);
buffer32 = static_cast<uint32_t*>(bufferAny);
for(size_t i=binChunkStartIndex; i < binChunkStartIndex+binsThisChunk ; ++i)
{
// Read Data
bool fileErr = false;
FILE * currFile = fopen ( m_allHeaderInfo[i].filePath.c_str(), "rb" );
if (currFile==NULL) fileErr = true;
size_t result = 0;
if(!fileErr)
{
fseek (currFile , FIXED_HEADER_SIZE , SEEK_CUR);
result = fread(bufferAny, bitsPerPixel/8, spectraCount, currFile);
}
if (result != spectraCount) fileErr = true;
if(fileErr)
{
throw std::runtime_error("Error reading file; possibly invalid data.");
}
for(size_t j=0; j<spectraCount;++j)
{
double val = 0;
if(bitsPerPixel == 8) val = static_cast<double>(buffer8[j]);
if(bitsPerPixel == 16) val = static_cast<double>(buffer16[j]);
if(bitsPerPixel == 32) val = static_cast<double>(buffer32[j]);
yVals[j][i-binChunkStartIndex] = val;
eVals[j][i-binChunkStartIndex] = sqrt(val);
}
// Clear memory associated with the file load
fclose (currFile);
}
// Now load chunk into workspace
PARALLEL_FOR1(workspace)
for (int64_t wi = 0; wi < static_cast<int64_t>(spectraCount); ++wi)
{
workspace->setX(wi, x);
MantidVec *currY = &workspace->dataY(wi);
MantidVec *currE = &workspace->dataE(wi);
std::copy(yVals[wi].begin(), yVals[wi].end()-(m_binChunkSize-binsThisChunk), currY->begin()+binChunkStartIndex );
std::copy(eVals[wi].begin(), eVals[wi].end()-(m_binChunkSize-binsThisChunk), currE->begin()+binChunkStartIndex );
// I expect this will be wanted once IDF is in a more useful state.
//workspace->getSpectrum(wi)->setDetectorID(detid_t(wi));
//workspace->getSpectrum(wi)->setSpectrumNo(specid_t(wi+1));
}
}