GeometryInfoFactory::GeometryInfoFactory(const MatrixWorkspace &workspace)
: m_workspace(workspace), m_instrument(workspace.getInstrument()) {
// Note: This does not seem possible currently (the instrument objects is
// always allocated, even if it is empty), so this will not fail.
if (!m_instrument)
throw std::runtime_error("Workspace " + workspace.getName() +
" does not contain an instrument!");
}
/** Calculate smoothing of the data using the spline
* Wraps CubicSpline function1D
*
* @param inputWorkspace :: The input workspace
* @param outputWorkspace :: The output workspace
* @param row :: The row of spectra to use
*/
void SplineSmoothing::calculateSmoothing(const MatrixWorkspace &inputWorkspace,
MatrixWorkspace &outputWorkspace,
size_t row) const {
// define the spline's parameters
const auto &xIn = inputWorkspace.x(row);
const size_t nData = xIn.size();
const double *xValues = &(xIn[0]);
double *yValues = &(outputWorkspace.mutableY(row)[0]);
// calculate the smoothing
m_cspline->function1D(yValues, xValues, nData);
}
MatrixWorkspace_sptr MonteCarloAbsorption::createOutputWorkspace(
const MatrixWorkspace &inputWS) const {
MatrixWorkspace_sptr outputWS = inputWS.clone();
// The algorithm computes the signal values at bin centres so they should
// be treated as a distribution
outputWS->setDistribution(true);
outputWS->setYUnit("");
outputWS->setYUnitLabel("Attenuation factor");
return outputWS;
}
/** Calculate the derivatives of the newly smoothed data using the spline
* Wraps CubicSpline derivative1D
*
* @param inputWorkspace :: The input workspace
* @param outputWorkspace :: The output workspace
* @param order :: The order of derivatives to calculate
* @param row :: The row of spectra to use
*/
void SplineSmoothing::calculateDerivatives(
const MatrixWorkspace &inputWorkspace,
API::MatrixWorkspace &outputWorkspace, const int order,
const size_t row) const {
const auto &xIn = inputWorkspace.x(row);
const double *xValues = &(xIn[0]);
double *yValues = &(outputWorkspace.mutableY(order - 1)[0]);
const size_t nData = xIn.size();
m_cspline->derivative1D(yValues, xValues, nData, order);
}
/**
* Get log value from a workspace. Convert to double if possible.
*
* @param ws :: [Input] The input workspace.
* @return :: Log value.
* @throw :: std::invalid_argument if the log cannot be converted to a double or
*doesn't exist.
*/
double PlotAsymmetryByLogValue::getLogValue(MatrixWorkspace &ws) {
const Run &run = ws.run();
// Get the start & end time for the run
Mantid::Kernel::DateAndTime start, end;
if (run.hasProperty("run_start") && run.hasProperty("run_end")) {
start = run.getProperty("run_start")->value();
end = run.getProperty("run_end")->value();
}
auto *property = run.getLogData(m_logName);
if (!property) {
throw std::invalid_argument("Log " + m_logName + " does not exist.");
}
property->filterByTime(start, end);
double value = 0;
// try different property types
if (convertLogToDouble<double>(property, value, m_logFunc))
return value;
if (convertLogToDouble<float>(property, value, m_logFunc))
return value;
if (convertLogToDouble<int>(property, value, m_logFunc))
return value;
if (convertLogToDouble<long>(property, value, m_logFunc))
return value;
if (convertLogToDouble<long long>(property, value, m_logFunc))
return value;
if (convertLogToDouble<unsigned int>(property, value, m_logFunc))
return value;
if (convertLogToDouble<unsigned long>(property, value, m_logFunc))
return value;
if (convertLogToDouble<unsigned long long>(property, value, m_logFunc))
return value;
// try if it's a string and can be lexically cast to double
auto slog =
dynamic_cast<const Mantid::Kernel::PropertyWithValue<std::string> *>(
property);
if (slog) {
try {
value = boost::lexical_cast<double>(slog->value());
return value;
} catch (std::exception &) {
// do nothing, goto throw
}
}
throw std::invalid_argument("Log " + m_logName +
" cannot be converted to a double type.");
}
/**
* Fully masks one component named componentName
* @param ws :: workspace with the respective instrument assigned
* @param componentName :: must be a known CompAssembly.
*/
void CalculateEfficiency::maskComponent(MatrixWorkspace &ws,
const std::string &componentName) {
auto instrument = ws.getInstrument();
try {
boost::shared_ptr<const Geometry::ICompAssembly> component =
boost::dynamic_pointer_cast<const Geometry::ICompAssembly>(
instrument->getComponentByName(componentName));
if (!component) {
g_log.warning("Component " + componentName +
" expected to be a CompAssembly, e.g., a bank. Component " +
componentName + " not masked!");
return;
}
std::vector<detid_t> detectorList;
for (int x = 0; x < component->nelements(); x++) {
boost::shared_ptr<Geometry::ICompAssembly> xColumn =
boost::dynamic_pointer_cast<Geometry::ICompAssembly>((*component)[x]);
for (int y = 0; y < xColumn->nelements(); y++) {
boost::shared_ptr<Geometry::Detector> detector =
boost::dynamic_pointer_cast<Geometry::Detector>((*xColumn)[y]);
if (detector) {
auto detID = detector->getID();
detectorList.push_back(detID);
}
}
}
auto indexList = ws.getIndicesFromDetectorIDs(detectorList);
auto &spectrumInfo = ws.mutableSpectrumInfo();
for (const auto &idx : indexList) {
ws.getSpectrum(idx).clearData();
spectrumInfo.setMasked(idx, true);
}
} catch (std::exception &) {
g_log.warning("Expecting the component " + componentName +
" to be a CompAssembly, e.g., a bank. Component not masked!");
}
}
/**
* 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 lhsSpectrumInfo :: The LHS spectrum info object
* @param rhsSpectrumInfo :: The RHS spectrum info object
* @param index :: The workspace index to check
* @param out :: A pointer to the output workspace
* @param outSpectrumInfo :: The spectrum info object of `out`
* @returns True if further processing is not required on the spectra, false if
* the binary operation should be performed.
*/
bool BinaryOperation::propagateSpectraMask(const SpectrumInfo &lhsSpectrumInfo,
const SpectrumInfo &rhsSpectrumInfo,
const int64_t index,
MatrixWorkspace &out,
SpectrumInfo &outSpectrumInfo) {
bool continueOp(true);
if ((lhsSpectrumInfo.hasDetectors(index) &&
lhsSpectrumInfo.isMasked(index)) ||
(rhsSpectrumInfo.hasDetectors(index) &&
rhsSpectrumInfo.isMasked(index))) {
continueOp = false;
out.getSpectrum(index).clearData();
PARALLEL_CRITICAL(setMasked) { outSpectrumInfo.setMasked(index, true); }
}
void addFullInstrumentToWorkspace(MatrixWorkspace &workspace,
bool includeMonitors, bool startYNegative,
const std::string &instrumentName) {
auto instrument = boost::make_shared<Instrument>(instrumentName);
instrument->setReferenceFrame(
boost::make_shared<ReferenceFrame>(Y, Z, Right, ""));
workspace.setInstrument(instrument);
const double pixelRadius(0.05);
Object_sptr pixelShape = ComponentCreationHelper::createCappedCylinder(
pixelRadius, 0.02, V3D(0.0, 0.0, 0.0), V3D(0., 1.0, 0.), "tube");
const double detZPos(5.0);
// Careful! Do not use size_t or auto, the unisgned will break the -=2 below.
int ndets = static_cast<int>(workspace.getNumberHistograms());
if (includeMonitors)
ndets -= 2;
for (int i = 0; i < ndets; ++i) {
std::ostringstream lexer;
lexer << "pixel-" << i << ")";
Detector *physicalPixel =
new Detector(lexer.str(), workspace.getAxis(1)->spectraNo(i),
pixelShape, instrument.get());
int ycount(i);
if (startYNegative)
ycount -= 1;
const double ypos = ycount * 2.0 * pixelRadius;
physicalPixel->setPos(0.0, ypos, detZPos);
instrument->add(physicalPixel);
instrument->markAsDetector(physicalPixel);
workspace.getSpectrum(i).setDetectorID(physicalPixel->getID());
}
// Monitors last
if (includeMonitors) // These occupy the last 2 spectra
{
Detector *monitor1 =
new Detector("mon1", workspace.getAxis(1)->spectraNo(ndets),
Object_sptr(), instrument.get());
monitor1->setPos(0.0, 0.0, -9.0);
instrument->add(monitor1);
instrument->markAsMonitor(monitor1);
workspace.getSpectrum(ndets).setDetectorID(ndets + 1);
Detector *monitor2 =
new Detector("mon2", workspace.getAxis(1)->spectraNo(ndets) + 1,
Object_sptr(), instrument.get());
monitor2->setPos(0.0, 0.0, -2.0);
instrument->add(monitor2);
instrument->markAsMonitor(monitor2);
workspace.getSpectrum(ndets + 1).setDetectorID(ndets + 2);
}
// Define a source and sample position
// Define a source component
ObjComponent *source = new ObjComponent(
"moderator",
ComponentCreationHelper::createSphere(0.1, V3D(0, 0, 0), "1"),
instrument.get());
source->setPos(V3D(0.0, 0.0, -20.0));
instrument->add(source);
instrument->markAsSource(source);
// Define a sample as a simple sphere
ObjComponent *sample = new ObjComponent(
"samplePos",
ComponentCreationHelper::createSphere(0.1, V3D(0, 0, 0), "1"),
instrument.get());
instrument->setPos(0.0, 0.0, 0.0);
instrument->add(sample);
instrument->markAsSamplePos(sample);
// chopper position
Component *chop_pos = new Component("chopper-position",
Kernel::V3D(0, 0, -10), instrument.get());
instrument->add(chop_pos);
}
/** Defines the points used to make the spline by iteratively creating more
*smoothing points
* until all smoothing points fall within a certain error tolerance
*
* @param inputWorkspace :: The input workspace containing noisy data
* @param row :: The row of spectra to use
*/
void SplineSmoothing::selectSmoothingPoints(
const MatrixWorkspace &inputWorkspace, const size_t row) {
std::set<int> smoothPts;
const auto &xs = inputWorkspace.x(row);
const auto &ys = inputWorkspace.y(row);
// retrieving number of breaks
int maxBreaks = static_cast<int>(getProperty("MaxNumberOfBreaks"));
int xSize = static_cast<int>(xs.size());
// evenly space initial points over data set
int delta;
// if retrieved value is default zero/default
bool incBreaks = false;
if (maxBreaks != 0) {
// number of points to start with
int numSmoothPts(maxBreaks);
delta = xSize / numSmoothPts;
// include maxBreaks when != 0
incBreaks = true;
} else {
int numSmoothPts(M_START_SMOOTH_POINTS);
delta = xSize / numSmoothPts;
}
for (int i = 0; i < xSize; i += delta) {
smoothPts.insert(i);
}
smoothPts.insert(xSize - 1);
bool resmooth(true);
while (resmooth) {
if (incBreaks) {
if (smoothPts.size() > static_cast<unsigned>(maxBreaks + 2)) {
break;
}
} else if (!incBreaks) {
if (smoothPts.size() >= xs.size() - 1) {
break;
}
}
addSmoothingPoints(smoothPts, &xs[0], &ys[0]);
resmooth = false;
// calculate the spline and retrieve smoothed points
boost::shared_array<double> ysmooth(new double[xSize]);
m_cspline->function1D(ysmooth.get(), &xs[0], xSize);
// iterate over smoothing points
auto iter = smoothPts.cbegin();
int start = *iter;
for (++iter; iter != smoothPts.cend(); ++iter) {
int end = *iter;
// check each point falls within our range of error.
bool accurate = checkSmoothingAccuracy(start, end, &ys[0], ysmooth.get());
// if not, flag for resmoothing and add another point between these two
// data points
if (!accurate) {
resmooth = true;
smoothPts.insert((start + end) / 2);
}
start = end;
}
}
}
/** Initialize a workspace from its parent
* This sets values such as title, instrument, units, sample, spectramap.
* This does NOT copy any data.
*
* @deprecated Replaced by functions in MantidDataObjects/WorkspaceCreation.h
* @param parent :: the parent workspace
* @param child :: the child workspace
* @param differentSize :: A flag to indicate if the two workspace will be
*different sizes
*/
void WorkspaceFactoryImpl::initializeFromParent(
const MatrixWorkspace &parent, MatrixWorkspace &child,
const bool differentSize) const {
child.setTitle(parent.getTitle());
child.setComment(parent.getComment());
child.copyExperimentInfoFrom(&parent);
child.setYUnit(parent.m_YUnit);
child.setYUnitLabel(parent.m_YUnitLabel);
child.setDistribution(parent.isDistribution());
// Only copy the axes over if new sizes are not given
if (!differentSize) {
// Only copy mask map if same size for now. Later will need to check
// continued validity.
child.m_masks = parent.m_masks;
}
// Same number of histograms = copy over the spectra data
if (parent.getNumberHistograms() == child.getNumberHistograms()) {
child.m_isInitialized = false;
for (size_t i = 0; i < parent.getNumberHistograms(); ++i)
child.getSpectrum(i).copyInfoFrom(parent.getSpectrum(i));
child.m_isInitialized = true;
// We use this variant without ISpectrum update to avoid costly rebuilds
// triggered by setIndexInfo(). ISpectrum::copyInfoFrom sets invalid flags
// for spectrum definitions, so it is important to call this *afterwards*,
// since it clears the flags:
child.setIndexInfoWithoutISpectrumUpdate(parent.indexInfo());
}
// deal with axis
for (size_t i = 0; i < parent.m_axes.size(); ++i) {
if (parent.m_axes[i]->isSpectra()) {
// By default the child already has a spectra axis which
// does not need to get cloned from the parent.
continue;
}
const bool isBinEdge =
dynamic_cast<const BinEdgeAxis *const>(parent.m_axes[i]) != nullptr;
const size_t newAxisLength =
child.m_axes[i]->length() + (isBinEdge ? 1 : 0);
const size_t oldAxisLength = parent.m_axes[i]->length();
// Need to delete the existing axis created in init above
delete child.m_axes[i];
child.m_axes[i] = nullptr;
if (newAxisLength == oldAxisLength) {
// Now set to a copy of the parent workspace's axis
child.m_axes[i] = parent.m_axes[i]->clone(&child);
} else {
// Call the 'different length' clone variant
child.m_axes[i] = parent.m_axes[i]->clone(newAxisLength, &child);
}
}
}
