/**
* Mask the outlier values to get a better median value.
* @param medianvec The median value calculated from the current counts.
* @param countsWS The counts workspace. Any outliers will be masked here.
* @param indexmap Index map.
* @returns The number failed.
*/
int MedianDetectorTest::maskOutliers(const std::vector<double> medianvec, API::MatrixWorkspace_sptr countsWS,std::vector<std::vector<size_t> > indexmap)
{
// Fractions of the median
const double out_lo = getProperty("LowOutlier");
const double out_hi = getProperty("HighOutlier");
int numFailed(0);
bool checkForMask = false;
Geometry::Instrument_const_sptr instrument = countsWS->getInstrument();
if (instrument != NULL)
{
checkForMask = ((instrument->getSource() != NULL) && (instrument->getSample() != NULL));
}
for (size_t i=0; i<indexmap.size(); ++i)
{
std::vector<size_t> hists=indexmap.at(i);
double median=medianvec.at(i);
PARALLEL_FOR1(countsWS)
for(int j = 0; j < static_cast<int>(hists.size()); ++j)
{
const double value = countsWS->readY(hists.at(j))[0];
if ((value == 0.) && checkForMask)
{
const std::set<detid_t>& detids = countsWS->getSpectrum(hists.at(j))->getDetectorIDs();
if (instrument->isDetectorMasked(detids))
{
numFailed -= 1; // it was already masked
}
}
if( (value < out_lo*median) && (value > 0.0) )
{
countsWS->maskWorkspaceIndex(hists.at(j));
PARALLEL_ATOMIC
++numFailed;
}
else if( value > out_hi*median )
{
countsWS->maskWorkspaceIndex(hists.at(j));
PARALLEL_ATOMIC
++numFailed;
}
}
PARALLEL_CHECK_INTERUPT_REGION
}
return numFailed;
}
/**
* Checks if the spectra at the given index of either input workspace is masked. If so then the output spectra has zeroed data
* and is also masked.
* @param lhs :: A pointer to the left-hand operand
* @param rhs :: A pointer to the right-hand operand
* @param index :: The workspace index to check
* @param out :: A pointer to the output workspace
* @returns True if further processing is not required on the spectra, false if the binary operation should be performed.
*/
bool BinaryOperation::propagateSpectraMask(const API::MatrixWorkspace_const_sptr lhs, const API::MatrixWorkspace_const_sptr rhs,
const int64_t index, API::MatrixWorkspace_sptr out)
{
bool continueOp(true);
IDetector_const_sptr det_lhs, det_rhs;
try
{
det_lhs = lhs->getDetector(index);
det_rhs = rhs->getDetector(index);
}
catch(std::runtime_error &)
{
}
catch(std::domain_error &)
{
// try statement will throw a domain_error when the axis is not a spectra axis.
return continueOp;
}
if( (det_lhs && det_lhs->isMasked()) || ( det_rhs && det_rhs->isMasked()) )
{
continueOp = false;
out->maskWorkspaceIndex(index);
}
return continueOp;
}
/** Convert the workspace units using TOF as an intermediate step in the
* conversion
* @param fromUnit :: The unit of the input workspace
* @param outputWS :: The output workspace
*/
void ConvertUnitsUsingDetectorTable::convertViaTOF(
Kernel::Unit_const_sptr fromUnit, API::MatrixWorkspace_sptr outputWS) {
using namespace Geometry;
// Let's see if we are using a TableWorkspace to override parameters
TableWorkspace_sptr paramWS = getProperty("DetectorParameters");
// See if we have supplied a DetectorParameters Workspace
// TODO: Check if paramWS is NULL and if so throw an exception
// const std::string l1ColumnLabel("l1");
// Let's check all the columns exist and are readable
try {
auto spectraColumnTmp = paramWS->getColumn("spectra");
auto l1ColumnTmp = paramWS->getColumn("l1");
auto l2ColumnTmp = paramWS->getColumn("l2");
auto twoThetaColumnTmp = paramWS->getColumn("twotheta");
auto efixedColumnTmp = paramWS->getColumn("efixed");
auto emodeColumnTmp = paramWS->getColumn("emode");
} catch (...) {
throw Exception::InstrumentDefinitionError(
"DetectorParameter TableWorkspace is not defined correctly.");
}
// Now let's read them into some vectors.
auto l1Column = paramWS->getColVector<double>("l1");
auto l2Column = paramWS->getColVector<double>("l2");
auto twoThetaColumn = paramWS->getColVector<double>("twotheta");
auto efixedColumn = paramWS->getColVector<double>("efixed");
auto emodeColumn = paramWS->getColVector<int>("emode");
auto spectraColumn = paramWS->getColVector<int>("spectra");
EventWorkspace_sptr eventWS =
boost::dynamic_pointer_cast<EventWorkspace>(outputWS);
assert(static_cast<bool>(eventWS) == m_inputEvents); // Sanity check
Progress prog(this, 0.2, 1.0, m_numberOfSpectra);
int64_t numberOfSpectra_i =
static_cast<int64_t>(m_numberOfSpectra); // cast to make openmp happy
// Get the unit object for each workspace
Kernel::Unit_const_sptr outputUnit = outputWS->getAxis(0)->unit();
std::vector<double> emptyVec;
int failedDetectorCount = 0;
// ConstColumnVector<int> spectraNumber = paramWS->getVector("spectra");
// TODO: Check why this parallel stuff breaks
// Loop over the histograms (detector spectra)
// PARALLEL_FOR1(outputWS)
for (int64_t i = 0; i < numberOfSpectra_i; ++i) {
// Lets find what row this spectrum ID appears in our detector table.
// PARALLEL_START_INTERUPT_REGION
std::size_t wsid = i;
try {
double deg2rad = M_PI / 180.;
auto det = outputWS->getDetector(i);
int specid = det->getID();
// int spectraNumber = static_cast<int>(spectraColumn->toDouble(i));
// wsid = outputWS->getIndexFromSpectrumNumber(spectraNumber);
g_log.debug() << "###### Spectra #" << specid
<< " ==> Workspace ID:" << wsid << std::endl;
// Now we need to find the row that contains this spectrum
std::vector<int>::iterator specIter;
specIter = std::find(spectraColumn.begin(), spectraColumn.end(), specid);
if (specIter != spectraColumn.end()) {
size_t detectorRow = std::distance(spectraColumn.begin(), specIter);
double l1 = l1Column[detectorRow];
double l2 = l2Column[detectorRow];
double twoTheta = twoThetaColumn[detectorRow] * deg2rad;
double efixed = efixedColumn[detectorRow];
int emode = emodeColumn[detectorRow];
g_log.debug() << "specId from detector table = "
<< spectraColumn[detectorRow] << std::endl;
// l1 = l1Column->toDouble(detectorRow);
// l2 = l2Column->toDouble(detectorRow);
// twoTheta = deg2rad * twoThetaColumn->toDouble(detectorRow);
// efixed = efixedColumn->toDouble(detectorRow);
// emode = static_cast<int>(emodeColumn->toDouble(detectorRow));
g_log.debug() << "###### Spectra #" << specid
<< " ==> Det Table Row:" << detectorRow << std::endl;
g_log.debug() << "\tL1=" << l1 << ",L2=" << l2 << ",TT=" << twoTheta
<< ",EF=" << efixed << ",EM=" << emode << std::endl;
// Make local copies of the units. This allows running the loop in
// parallel
Unit *localFromUnit = fromUnit->clone();
Unit *localOutputUnit = outputUnit->clone();
/// @todo Don't yet consider hold-off (delta)
const double delta = 0.0;
// Convert the input unit to time-of-flight
localFromUnit->toTOF(outputWS->dataX(wsid), emptyVec, l1, l2, twoTheta,
emode, efixed, delta);
// Convert from time-of-flight to the desired unit
localOutputUnit->fromTOF(outputWS->dataX(wsid), emptyVec, l1, l2,
twoTheta, emode, efixed, delta);
// EventWorkspace part, modifying the EventLists.
if (m_inputEvents) {
eventWS->getEventList(wsid)
.convertUnitsViaTof(localFromUnit, localOutputUnit);
}
// Clear unit memory
delete localFromUnit;
delete localOutputUnit;
} else {
// Not found
g_log.debug() << "Spectrum " << specid << " not found!" << std::endl;
failedDetectorCount++;
outputWS->maskWorkspaceIndex(wsid);
}
} catch (Exception::NotFoundError &) {
// Get to here if exception thrown when calculating distance to detector
failedDetectorCount++;
// Since you usually (always?) get to here when there's no attached
// detectors, this call is
// the same as just zeroing out the data (calling clearData on the
// spectrum)
outputWS->maskWorkspaceIndex(i);
}
prog.report("Convert to " + m_outputUnit->unitID());
// PARALLEL_END_INTERUPT_REGION
} // loop over spectra
// PARALLEL_CHECK_INTERUPT_REGION
if (failedDetectorCount != 0) {
g_log.information() << "Something went wrong for " << failedDetectorCount
<< " spectra. Masking spectrum." << std::endl;
}
if (m_inputEvents)
eventWS->clearMRU();
}