/** Read the specified number of entries from input file into the
* the array that is passed
* @param[in] nEntries the number of numbers to read
* @param[out] output the contents of this will be replaced by the data read from the file
*/
void LoadRKH::readNumEntrys(const int nEntries, MantidVec & output)
{
output.resize(nEntries);
for( int i = 0; i < nEntries; ++i )
{
m_fileIn >> output[i];
}
}
/** Load the event_workspace field
*
* @param wksp_cls
* @param progressStart
* @param progressRange
* @return
*/
API::MatrixWorkspace_sptr LoadNexusProcessed::loadEventEntry(NXData & wksp_cls, NXDouble & xbins,
const double& progressStart, const double& progressRange)
{
NXDataSetTyped<int64_t> indices_data = wksp_cls.openNXDataSet<int64_t>("indices");
indices_data.load();
boost::shared_array<int64_t> indices = indices_data.sharedBuffer();
int numspec = indices_data.dim0()-1;
int num_xbins = xbins.dim0();
if (num_xbins < 2) num_xbins = 2;
EventWorkspace_sptr ws = boost::dynamic_pointer_cast<EventWorkspace>
(WorkspaceFactory::Instance().create("EventWorkspace", numspec, num_xbins, num_xbins-1));
// Set the YUnit label
ws->setYUnit(indices_data.attributes("units"));
std::string unitLabel = indices_data.attributes("unit_label");
if (unitLabel.empty()) unitLabel = indices_data.attributes("units");
ws->setYUnitLabel(unitLabel);
//Handle optional fields.
// TODO: Handle inconsistent sizes
boost::shared_array<int64_t> pulsetimes;
if (wksp_cls.isValid("pulsetime"))
{
NXDataSetTyped<int64_t> pulsetime = wksp_cls.openNXDataSet<int64_t>("pulsetime");
pulsetime.load();
pulsetimes = pulsetime.sharedBuffer();
}
boost::shared_array<double> tofs;
if (wksp_cls.isValid("tof"))
{
NXDouble tof = wksp_cls.openNXDouble("tof");
tof.load();
tofs = tof.sharedBuffer();
}
boost::shared_array<float> error_squareds;
if (wksp_cls.isValid("error_squared"))
{
NXFloat error_squared = wksp_cls.openNXFloat("error_squared");
error_squared.load();
error_squareds = error_squared.sharedBuffer();
}
boost::shared_array<float> weights;
if (wksp_cls.isValid("weight"))
{
NXFloat weight = wksp_cls.openNXFloat("weight");
weight.load();
weights = weight.sharedBuffer();
}
// What type of event lists?
EventType type = TOF;
if (tofs && pulsetimes && weights && error_squareds)
type = WEIGHTED;
else if ((tofs && weights && error_squareds))
type = WEIGHTED_NOTIME;
else if (pulsetimes && tofs)
type = TOF;
else
throw std::runtime_error("Could not figure out the type of event list!");
// Create all the event lists
PARALLEL_FOR_NO_WSP_CHECK()
for (int wi=0; wi < numspec; wi++)
{
PARALLEL_START_INTERUPT_REGION
int64_t index_start = indices[wi];
int64_t index_end = indices[wi+1];
if (index_end >= index_start)
{
EventList & el = ws->getEventList(wi);
el.switchTo(type);
// Allocate all the required memory
el.reserve(index_end - index_start);
el.clearDetectorIDs();
for (long i=index_start; i<index_end; i++)
switch (type)
{
case TOF:
el.addEventQuickly( TofEvent( tofs[i], DateAndTime(pulsetimes[i])) );
break;
case WEIGHTED:
el.addEventQuickly( WeightedEvent( tofs[i], DateAndTime(pulsetimes[i]), weights[i], error_squareds[i]) );
break;
case WEIGHTED_NOTIME:
el.addEventQuickly( WeightedEventNoTime( tofs[i], weights[i], error_squareds[i]) );
break;
}
// Set the X axis
if (this->m_shared_bins)
el.setX(this->m_xbins);
else
{
MantidVec x;
x.resize(xbins.dim0());
for (int i=0; i < xbins.dim0(); i++)
x[i] = xbins(wi, i);
el.setX(x);
}
}
progress(progressStart + progressRange*(1.0/numspec));
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
// Clean up some stuff
ws->doneAddingEventLists();
return ws;
}
void Qxy::exec()
{
MatrixWorkspace_const_sptr inputWorkspace = getProperty("InputWorkspace");
MatrixWorkspace_const_sptr waveAdj = getProperty("WavelengthAdj");
MatrixWorkspace_const_sptr pixelAdj = getProperty("PixelAdj");
const bool doGravity = getProperty("AccountForGravity");
const bool doSolidAngle = getProperty("SolidAngleWeighting");
//throws if we don't have common binning or another incompatibility
Qhelper helper;
helper.examineInput(inputWorkspace, waveAdj, pixelAdj);
g_log.debug() << "All input workspaces were found to be valid\n";
// Create the output Qx-Qy grid
MatrixWorkspace_sptr outputWorkspace = this->setUpOutputWorkspace(inputWorkspace);
// Will also need an identically-sized workspace to hold the solid angle/time bin masked weight
MatrixWorkspace_sptr weights = WorkspaceFactory::Instance().create(outputWorkspace);
// Copy the X values from the output workspace to the solidAngles one
cow_ptr<MantidVec> axis;
axis.access() = outputWorkspace->readX(0);
for ( size_t i = 0; i < weights->getNumberHistograms(); ++i ) weights->setX(i,axis);
const size_t numSpec = inputWorkspace->getNumberHistograms();
const size_t numBins = inputWorkspace->blocksize();
// the samplePos is often not (0, 0, 0) because the instruments components are moved to account for the beam centre
const V3D samplePos = inputWorkspace->getInstrument()->getSample()->getPos();
// Set the progress bar (1 update for every one percent increase in progress)
Progress prog(this, 0.05, 1.0, numSpec);
// PARALLEL_FOR2(inputWorkspace,outputWorkspace)
for (int64_t i = 0; i < int64_t(numSpec); ++i)
{
// PARALLEL_START_INTERUPT_REGION
// Get the pixel relating to this spectrum
IDetector_const_sptr det;
try {
det = inputWorkspace->getDetector(i);
} catch (Exception::NotFoundError&) {
g_log.warning() << "Spectrum index " << i << " has no detector assigned to it - discarding" << std::endl;
// Catch if no detector. Next line tests whether this happened - test placed
// outside here because Mac Intel compiler doesn't like 'continue' in a catch
// in an openmp block.
}
// If no detector found or if it's masked or a monitor, skip onto the next spectrum
if ( !det || det->isMonitor() || det->isMasked() ) continue;
//get the bins that are included inside the RadiusCut/WaveCutcut off, those to calculate for
const size_t wavStart = helper.waveLengthCutOff(inputWorkspace, getProperty("RadiusCut"), getProperty("WaveCut"), i);
if (wavStart >= inputWorkspace->readY(i).size())
{
// all the spectra in this detector are out of range
continue;
}
V3D detPos = det->getPos()-samplePos;
// these will be re-calculated if gravity is on but without gravity there is no need
double phi = atan2(detPos.Y(),detPos.X());
double a = cos(phi);
double b = sin(phi);
double sinTheta = sin( inputWorkspace->detectorTwoTheta(det)/2.0 );
// Get references to the data for this spectrum
const MantidVec& X = inputWorkspace->readX(i);
const MantidVec& Y = inputWorkspace->readY(i);
const MantidVec& E = inputWorkspace->readE(i);
const MantidVec& axis = outputWorkspace->readX(0);
// the solid angle of the detector as seen by the sample is used for normalisation later on
double angle = det->solidAngle(samplePos);
// some bins are masked completely or partially, the following vector will contain the fractions
MantidVec maskFractions;
if ( inputWorkspace->hasMaskedBins(i) )
{
// go through the set and convert it to a vector
const MatrixWorkspace::MaskList& mask = inputWorkspace->maskedBins(i);
maskFractions.resize(numBins, 1.0);
MatrixWorkspace::MaskList::const_iterator it, itEnd(mask.end());
for (it = mask.begin(); it != itEnd; ++it)
{
// The weight for this masked bin is 1 minus the degree to which this bin is masked
maskFractions[it->first] -= it->second;
}
}
double maskFraction(1);
// this object is not used if gravity correction is off, but it is only constructed once per spectrum
GravitySANSHelper grav;
if (doGravity)
{
grav = GravitySANSHelper(inputWorkspace, det);
}
for (int j = static_cast<int>(numBins)-1; j >= static_cast<int>(wavStart); --j)
{
if( j < 0 ) break; // Be careful with counting down. Need a better fix but this will work for now
const double binWidth = X[j+1]-X[j];
// Calculate the wavelength at the mid-point of this bin
const double wavLength = X[j]+(binWidth)/2.0;
if (doGravity)
{
// SANS instruments must have their y-axis pointing up, show the detector position as where the neutron would be without gravity
sinTheta = grav.calcComponents(wavLength, a, b);
}
// Calculate |Q| for this bin
const double Q = 4.0*M_PI*sinTheta/wavLength;
// Now get the x & y components of Q.
const double Qx = a*Q;
// Test whether they're in range, if not go to next spectrum.
if ( Qx < axis.front() || Qx >= axis.back() ) break;
const double Qy = b*Q;
if ( Qy < axis.front() || Qy >= axis.back() ) break;
// Find the indices pointing to the place in the 2D array where this bin's contents should go
const MantidVec::difference_type xIndex = std::upper_bound(axis.begin(),axis.end(),Qx) - axis.begin() - 1;
const int yIndex = static_cast<int>(
std::upper_bound(axis.begin(),axis.end(),Qy) - axis.begin() - 1);
// PARALLEL_CRITICAL(qxy) /* Write to shared memory - must protect */
{
// the data will be copied to this bin in the output array
double & outputBinY = outputWorkspace->dataY(yIndex)[xIndex];
double & outputBinE = outputWorkspace->dataE(yIndex)[xIndex];
if ( boost::math::isnan(outputBinY))
{
outputBinY = outputBinE = 0;
}
// Add the contents of the current bin to the 2D array.
outputBinY += Y[j];
// add the errors in quadranture
outputBinE = std::sqrt( (outputBinE*outputBinE) + (E[j]*E[j]) );
// account for masked bins
if ( ! maskFractions.empty() )
{
maskFraction = maskFractions[j];
}
// add the total weight for this bin in the weights workspace,
// in an equivalent bin to where the data was stored
// first take into account the product of contributions to the weight which have
// no errors
double weight = 0.0;
if(doSolidAngle)
weight = maskFraction*angle;
else
weight = maskFraction;
// then the product of contributions which have errors, i.e. optional
// pixelAdj and waveAdj contributions
if (pixelAdj && waveAdj)
{
weights->dataY(yIndex)[xIndex] += weight*pixelAdj->readY(i)[0]*waveAdj->readY(0)[j];
const double pixelYSq = pixelAdj->readY(i)[0]*pixelAdj->readY(i)[0];
const double pixelESq = pixelAdj->readE(i)[0]*pixelAdj->readE(i)[0];
const double waveYSq = waveAdj->readY(0)[j]*waveAdj->readY(0)[j];
const double waveESq = waveAdj->readE(0)[j]*waveAdj->readE(0)[j];
// add product of errors from pixelAdj and waveAdj (note no error on weight is assumed)
weights->dataE(yIndex)[xIndex] += weight*weight*(waveESq*pixelYSq + pixelESq*waveYSq);
}
else if (pixelAdj)
{
weights->dataY(yIndex)[xIndex] += weight*pixelAdj->readY(i)[0];
const double pixelE = weight*pixelAdj->readE(i)[0];
// add error from pixelAdj
weights->dataE(yIndex)[xIndex] += pixelE*pixelE;
}
else if(waveAdj)
{
weights->dataY(yIndex)[xIndex] += weight*waveAdj->readY(0)[j];
const double waveE = weight*waveAdj->readE(0)[j];
// add error from waveAdj
weights->dataE(yIndex)[xIndex] += waveE*waveE;
}
else
weights->dataY(yIndex)[xIndex] += weight;
}
} // loop over single spectrum
prog.report("Calculating Q");
// PARALLEL_END_INTERUPT_REGION
} // loop over all spectra
// PARALLEL_CHECK_INTERUPT_REGION
// take sqrt of error weight values
// left to be executed here for computational efficiency
size_t numHist = weights->getNumberHistograms();
for (size_t i = 0; i < numHist; i++)
{
for (size_t j = 0; j < weights->dataE(i).size(); j++)
{
weights->dataE(i)[j] = sqrt(weights->dataE(i)[j]);
}
}
bool doOutputParts = getProperty("OutputParts");
if (doOutputParts)
{
// copy outputworkspace before it gets further modified
MatrixWorkspace_sptr ws_sumOfCounts = WorkspaceFactory::Instance().create(outputWorkspace);
for (size_t i = 0; i < ws_sumOfCounts->getNumberHistograms(); i++)
{
ws_sumOfCounts->dataX(i) = outputWorkspace->dataX(i);
ws_sumOfCounts->dataY(i) = outputWorkspace->dataY(i);
ws_sumOfCounts->dataE(i) = outputWorkspace->dataE(i);
}
helper.outputParts(this, ws_sumOfCounts, weights);
}
// Divide the output data by the solid angles
outputWorkspace /= weights;
outputWorkspace->isDistribution(true);
// Count of the number of empty cells
MatrixWorkspace::const_iterator wsIt(*outputWorkspace);
int emptyBins = 0;
for (;wsIt != wsIt.end(); ++wsIt)
{
if (wsIt->Y() < 1.0e-12) ++emptyBins;
}
// Log the number of empty bins
g_log.notice() << "There are a total of " << emptyBins << " ("
<< (100*emptyBins)/(outputWorkspace->size()) << "%) empty Q bins.\n";
}
/** Reads the header information from a file containing 2D data
* @param[in] initalLine the second line in the file
* @param[out] outWrksp the workspace that the data will be writen to
* @param[out] axis0Data x-values for the workspace
* @return a progress bar object
* @throw NotFoundError if there is compulsulary data is missing from the file
* @throw invalid_argument if there is an inconsistency in the header information
*/
Progress LoadRKH::read2DHeader(const std::string & initalLine, MatrixWorkspace_sptr & outWrksp, MantidVec & axis0Data)
{
const std::string XUnit(readUnit(initalLine));
std::string fileLine;
std::getline(m_fileIn, fileLine);
const std::string YUnit(readUnit(fileLine));
std::getline(m_fileIn, fileLine);
const std::string intensityUnit(readUnit(fileLine));
// the next line should contain just "1", but I'm not enforcing that
std::getline(m_fileIn, fileLine);
std::string title;
std::getline(m_fileIn, title);
std::getline(m_fileIn, fileLine);
boost::trim(fileLine);
const int nAxis0Boundaries = boost::lexical_cast<int>(fileLine);
axis0Data.resize(nAxis0Boundaries);
readNumEntrys(nAxis0Boundaries, axis0Data);
std::getline(m_fileIn, fileLine);
boost::trim(fileLine);
int nAxis1Boundaries;
try
{
nAxis1Boundaries = boost::lexical_cast<int>(fileLine);
}
catch(boost::bad_lexical_cast &)
{
// using readNumEntrys() above broke the sequence of getline()s and so try again in case we just read the end of a line
std::getline(m_fileIn, fileLine);
boost::trim(fileLine);
nAxis1Boundaries = boost::lexical_cast<int>(fileLine);
}
MantidVec axis1Data(nAxis1Boundaries);
readNumEntrys(nAxis1Boundaries, axis1Data);
std::getline(m_fileIn, fileLine);
// check for the file pointer being left at the end of a line
if ( fileLine.size() < 5 )
{
std::getline(m_fileIn, fileLine);
}
Poco::StringTokenizer wsDimensions(fileLine, " ",
Poco::StringTokenizer::TOK_TRIM);
if ( wsDimensions.count() < 2 )
{
throw Exception::NotFoundError("Input file", "dimensions");
}
const int nAxis0Values = boost::lexical_cast<int>(wsDimensions[0]);
const int nAxis1Values = boost::lexical_cast<int>(wsDimensions[1]);
Progress prog(this, 0.05, 1.0, 2*nAxis1Values);
// we now have all the data we need to create the output workspace
outWrksp = WorkspaceFactory::Instance().create(
"Workspace2D", nAxis1Values, nAxis0Boundaries, nAxis0Values);
outWrksp->getAxis(0)->unit() = UnitFactory::Instance().create(XUnit);
outWrksp->setYUnitLabel(intensityUnit);
NumericAxis* const axis1 = new Mantid::API::NumericAxis(nAxis1Boundaries);
axis1->unit() = Mantid::Kernel::UnitFactory::Instance().create(YUnit);
outWrksp->replaceAxis(1, axis1);
for ( int i = 0; i < nAxis1Boundaries; ++i )
{
axis1->setValue(i, axis1Data[i]);
}
outWrksp->setTitle(title);
// move over the next line which is there to help with loading from Fortran routines
std::getline(m_fileIn, fileLine);
return prog;
}
/**
* Get a data array covering the specified range of data, at the specified
* resolution. NOTE: The calling code is responsible for deleting the
* DataArray that is constructed in and returned by this method.
*
* @param xMin Left edge of region to be covered.
* @param xMax Right edge of region to be covered.
* @param yMin Bottom edge of region to be covered.
* @param yMax Top edge of region to be covered.
* @param numRows Number of rows to return. If the number of rows is less
* than the actual number of data rows in [yMin,yMax], the
* data will be subsampled, and only the specified number
* of rows will be returned.
* @param numCols The specrum data will be rebinned using the specified
* number of colums.
* @param isLogX Flag indicating whether or not the data should be
* binned logarithmically.
*/
DataArray_const_sptr MatrixWSDataSource::getDataArray( double xMin, double xMax,
double yMin, double yMax,
size_t numRows, size_t numCols,
bool isLogX )
{
/* Since we're rebinning, the columns can be arbitrary */
/* but rows must be aligned to get whole spectra */
size_t first_row;
SVUtils::CalculateInterval( m_totalYMin, m_totalYMax, m_totalRows,
first_row, yMin, yMax, numRows );
std::vector<float> newData(numRows * numCols);
MantidVec xScale;
xScale.resize(numCols + 1);
if ( isLogX )
{
for ( size_t i = 0; i < numCols+1; i++ )
{
xScale[i] = xMin * exp ( (double)i / (double)numCols * log(xMax/xMin) );
}
}
else
{
double dx = (xMax - xMin) / ((double)numCols + 1.0);
for ( size_t i = 0; i < numCols+1; i++ )
{
xScale[i] = xMin + (double)i * dx;
}
}
// Choose spectra from required range of spectrum indexes
double yStep = (yMax - yMin) / (double)numRows;
double dYIndex;
MantidVec yVals;
MantidVec err;
yVals.resize(numCols);
err.resize(numCols);
size_t index = 0;
for ( size_t i = 0; i < numRows; i++ )
{
double midY = yMin + ((double)i + 0.5) * yStep;
SVUtils::Interpolate( m_totalYMin, m_totalYMax, midY,
0.0, (double)m_totalRows, dYIndex );
size_t sourceRow = (size_t)dYIndex;
yVals.clear();
err.clear();
yVals.resize(numCols, 0);
err.resize(numCols, 0);
m_matWs->generateHistogram( sourceRow, xScale, yVals, err, true );
for ( size_t col = 0; col < numCols; col++ )
{
newData[index] = (float)yVals[col];
index++;
}
}
// The calling code is responsible for deleting the DataArray when it is done with it
DataArray_const_sptr newDataArray( new DataArray( xMin, xMax, yMin, yMax,
isLogX,
numRows, numCols,
newData) );
return newDataArray;
}