/** Divide each bin by the width of its q bin.
* @param outputWS :: The output workspace
* @param qAxis :: A vector of the q bin boundaries
*/
void SofQWCentre::makeDistribution(API::MatrixWorkspace_sptr outputWS,
const std::vector<double> qAxis) {
std::vector<double> widths(qAxis.size());
std::adjacent_difference(qAxis.begin(), qAxis.end(), widths.begin());
const size_t numQBins = outputWS->getNumberHistograms();
for (size_t i = 0; i < numQBins; ++i) {
auto &Y = outputWS->mutableY(i);
auto &E = outputWS->mutableE(i);
std::transform(Y.begin(), Y.end(), Y.begin(),
std::bind2nd(std::divides<double>(), widths[i + 1]));
std::transform(E.begin(), E.end(), E.begin(),
std::bind2nd(std::divides<double>(), widths[i + 1]));
}
}
/** Reads in the data corresponding to a single spectrum
* @param speFile :: The file handle
* @param workspace :: The output workspace
* @param index :: The index of the current spectrum
*/
void LoadSPE::readHistogram(FILE *speFile, API::MatrixWorkspace_sptr workspace,
size_t index) {
// First, there should be a comment line
char comment[100];
fgets(comment, 100, speFile);
if (comment[0] != '#')
reportFormatError(std::string(comment));
// Then it's the Y values
auto &Y = workspace->mutableY(index);
const size_t nbins = workspace->blocksize();
int retval;
for (size_t i = 0; i < nbins; ++i) {
retval = fscanf(speFile, "%10le", &Y[i]);
if (retval != 1) {
std::stringstream ss;
ss << "Reading data value" << i << " of histogram " << index;
reportFormatError(ss.str());
}
// -10^30 is the flag for not a number used in SPE files (from
// www.mantidproject.org/images/3/3d/Spe_file_format.pdf)
if (Y[i] == SaveSPE::MASK_FLAG) {
Y[i] = std::numeric_limits<double>::quiet_NaN();
}
}
// Read to EOL
fgets(comment, 100, speFile);
// Another comment line
fgets(comment, 100, speFile);
if (comment[0] != '#')
reportFormatError(std::string(comment));
// And then the error values
auto &E = workspace->mutableE(index);
for (size_t i = 0; i < nbins; ++i) {
retval = fscanf(speFile, "%10le", &E[i]);
if (retval != 1) {
std::stringstream ss;
ss << "Reading error value" << i << " of histogram " << index;
reportFormatError(ss.str());
}
}
// Read to EOL
fgets(comment, 100, speFile);
}
/** Zeroes all data points outside the X values given
* @param outputWorkspace :: The output workspace - data has already been
* copied
* @param inIndex :: The workspace index of the spectrum in the input
* workspace
* @param outIndex :: The workspace index of the spectrum in the output
* workspace
*/
void ExtractSpectra::cropRagged(API::MatrixWorkspace_sptr outputWorkspace,
int inIndex, int outIndex) {
auto &Y = outputWorkspace->mutableY(outIndex);
auto &E = outputWorkspace->mutableE(outIndex);
const size_t size = Y.size();
size_t startX = this->getXMin(inIndex);
if (startX > size)
startX = size;
for (size_t i = 0; i < startX; ++i) {
Y[i] = 0.0;
E[i] = 0.0;
}
size_t endX = this->getXMax(inIndex);
if (endX > 0)
endX -= m_histogram;
for (size_t i = endX; i < size; ++i) {
Y[i] = 0.0;
E[i] = 0.0;
}
}
API::MatrixWorkspace_sptr
CreateFloodWorkspace::removeBackground(API::MatrixWorkspace_sptr ws) {
g_log.information() << "Remove background "
<< getPropertyValue(Prop::BACKGROUND) << '\n';
auto fitWS = transpose(ws);
auto const &x = fitWS->x(0);
// Define the fitting interval
double startX = getProperty(Prop::START_X);
double endX = getProperty(Prop::END_X);
std::vector<double> excludeFromFit;
if (isDefault(Prop::START_X)) {
startX = x.front();
} else {
excludeFromFit.push_back(x.front());
excludeFromFit.push_back(startX);
}
if (isDefault(Prop::END_X)) {
endX = x.back();
} else {
excludeFromFit.push_back(endX);
excludeFromFit.push_back(x.back());
}
// Exclude any bad detectors.
for (auto i : m_excludedSpectra) {
excludeFromFit.push_back(i);
excludeFromFit.push_back(i);
}
std::string const function = getBackgroundFunction();
// Fit the data to determine unwanted background
auto alg = createChildAlgorithm("Fit", 0.9, 0.99);
alg->setProperty("Function", function);
alg->setProperty("InputWorkspace", fitWS);
alg->setProperty("WorkspaceIndex", 0);
if (!excludeFromFit.empty()) {
alg->setProperty("Exclude", excludeFromFit);
}
alg->setProperty("Output", "fit");
alg->execute();
IFunction_sptr func = alg->getProperty("Function");
g_log.information() << "Background function parameters:\n";
for (size_t i = 0; i < func->nParams(); ++i) {
g_log.information() << " " << func->parameterName(i) << ": "
<< func->getParameter(i) << '\n';
}
// Divide the workspace by the fitted curve to remove the background
// and scale to values around 1
MatrixWorkspace_sptr bkgWS = alg->getProperty("OutputWorkspace");
auto const &bkg = bkgWS->y(1);
auto const nHisto = static_cast<int>(ws->getNumberHistograms());
PARALLEL_FOR_IF(Kernel::threadSafe(*ws, *bkgWS))
for (int i = 0; i < nHisto; ++i) {
PARALLEL_START_INTERUPT_REGION
auto const xVal = x[i];
if (isExcludedSpectrum(xVal)) {
ws->mutableY(i)[0] = VERY_BIG_VALUE;
ws->mutableE(i)[0] = 0.0;
} else if (xVal >= startX && xVal <= endX) {
auto const background = bkg[i];
if (background <= 0.0) {
throw std::runtime_error(
"Background is expected to be positive, found value " +
std::to_string(background) + " at spectrum with workspace index " +
std::to_string(i));
}
ws->mutableY(i)[0] /= background;
ws->mutableE(i)[0] /= background;
} else {
ws->mutableY(i)[0] = 1.0;
ws->mutableE(i)[0] = 0.0;
}
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
// Remove the logs
ws->setSharedRun(make_cow<Run>());
return ws;
}
/** Forms the quadrature phase signal (squashogram)
* @param ws :: [input] workspace containing the measured spectra
* @param phase :: [input] table workspace containing the detector phases
* @param n0 :: [input] vector containing the normalization constants
* @return :: workspace containing the quadrature phase signal
*/
API::MatrixWorkspace_sptr
PhaseQuadMuon::squash(const API::MatrixWorkspace_sptr &ws,
const API::ITableWorkspace_sptr &phase,
const std::vector<double> &n0) {
// Poisson limit: below this number we consider we don't have enough
// statistics
// to apply sqrt(N). This is an arbitrary number used in the original code
// provided by scientists
double poissonLimit = 30.;
size_t nspec = ws->getNumberHistograms();
size_t npoints = ws->blocksize();
// Muon life time in microseconds
double muLife = PhysicalConstants::MuonLifetime * 1e6;
if (n0.size() != nspec) {
throw std::invalid_argument("Invalid normalization constants");
}
// Get the maximum asymmetry
double maxAsym = 0.;
for (size_t h = 0; h < nspec; h++) {
if (phase->Double(h, 1) > maxAsym) {
maxAsym = phase->Double(h, 1);
}
}
if (maxAsym == 0.0) {
throw std::invalid_argument("Invalid detector asymmetries");
}
std::vector<double> aj, bj;
{
// Calculate coefficients aj, bj
double sxx = 0;
double syy = 0;
double sxy = 0;
for (size_t h = 0; h < nspec; h++) {
double asym = phase->Double(h, 1) / maxAsym;
double phi = phase->Double(h, 2);
double X = n0[h] * asym * cos(phi);
double Y = n0[h] * asym * sin(phi);
sxx += X * X;
syy += Y * Y;
sxy += X * Y;
}
double lam1 = 2 * syy / (sxx * syy - sxy * sxy);
double mu1 = 2 * sxy / (sxy * sxy - sxx * syy);
double lam2 = 2 * sxy / (sxy * sxy - sxx * syy);
double mu2 = 2 * sxx / (sxx * syy - sxy * sxy);
for (size_t h = 0; h < nspec; h++) {
double asym = phase->Double(h, 1) / maxAsym;
double phi = phase->Double(h, 2);
double X = n0[h] * asym * cos(phi);
double Y = n0[h] * asym * sin(phi);
aj.push_back((lam1 * X + mu1 * Y) * 0.5);
bj.push_back((lam2 * X + mu2 * Y) * 0.5);
}
}
// First X value
double X0 = ws->x(0).front();
// Create and populate output workspace
API::MatrixWorkspace_sptr ows = API::WorkspaceFactory::Instance().create(
"Workspace2D", 2, npoints + 1, npoints);
// X
ows->setSharedX(0, ws->sharedX(0));
ows->setSharedX(1, ws->sharedX(0));
// Phase quadrature
auto &realY = ows->mutableY(0);
auto &imagY = ows->mutableY(1);
auto &realE = ows->mutableE(0);
auto &imagE = ows->mutableE(1);
for (size_t i = 0; i < npoints; i++) {
for (size_t h = 0; h < nspec; h++) {
// (X,Y,E) with exponential decay removed
const double X = ws->x(h)[i];
const double Y = ws->y(h)[i] - n0[h] * exp(-(X - X0) / muLife);
const double E = (ws->y(h)[i] > poissonLimit)
? ws->e(h)[i]
: sqrt(n0[h] * exp(-(X - X0) / muLife));
realY[i] += aj[h] * Y;
imagY[i] += bj[h] * Y;
realE[i] += aj[h] * aj[h] * E * E;
imagE[i] += bj[h] * bj[h] * E * E;
}
realE[i] = sqrt(realE[i]);
imagE[i] = sqrt(imagE[i]);
// Regain exponential decay
const double X = ws->getSpectrum(0).x()[i];
const double e = exp(-(X - X0) / muLife);
realY[i] /= e;
imagY[i] /= e;
realE[i] /= e;
imagE[i] /= e;
}
return ows;
}
/** Forms the quadrature phase signal (squashogram)
* @param ws :: [input] workspace containing the measured spectra
* @param phase :: [input] table workspace containing the detector phases
* @param n0 :: [input] vector containing the normalization constants
* @return :: workspace containing the quadrature phase signal
*/
API::MatrixWorkspace_sptr
PhaseQuadMuon::squash(const API::MatrixWorkspace_sptr &ws,
const API::ITableWorkspace_sptr &phase,
const std::vector<double> &n0) {
// Poisson limit: below this number we consider we don't have enough
// statistics
// to apply sqrt(N). This is an arbitrary number used in the original code
// provided by scientists
const double poissonLimit = 30.;
// Muon life time in microseconds
const double muLife = PhysicalConstants::MuonLifetime * 1e6;
const size_t nspec = ws->getNumberHistograms();
if (n0.size() != nspec) {
throw std::invalid_argument("Invalid normalization constants");
}
auto names = phase->getColumnNames();
for (auto &name : names) {
std::transform(name.begin(), name.end(), name.begin(), ::tolower);
}
auto phaseIndex = findName(phaseNames, names);
auto asymmetryIndex = findName(asymmNames, names);
// Get the maximum asymmetry
double maxAsym = 0.;
for (size_t h = 0; h < nspec; h++) {
if (phase->Double(h, asymmetryIndex) > maxAsym &&
phase->Double(h, asymmetryIndex) != ASYMM_ERROR) {
maxAsym = phase->Double(h, asymmetryIndex);
}
}
if (maxAsym == 0.0) {
throw std::invalid_argument("Invalid detector asymmetries");
}
std::vector<bool> emptySpectrum;
emptySpectrum.reserve(nspec);
std::vector<double> aj, bj;
{
// Calculate coefficients aj, bj
double sxx = 0.;
double syy = 0.;
double sxy = 0.;
for (size_t h = 0; h < nspec; h++) {
emptySpectrum.push_back(
std::all_of(ws->y(h).begin(), ws->y(h).end(),
[](double value) { return value == 0.; }));
if (!emptySpectrum[h]) {
const double asym = phase->Double(h, asymmetryIndex) / maxAsym;
const double phi = phase->Double(h, phaseIndex);
const double X = n0[h] * asym * cos(phi);
const double Y = n0[h] * asym * sin(phi);
sxx += X * X;
syy += Y * Y;
sxy += X * Y;
}
}
const double lam1 = 2 * syy / (sxx * syy - sxy * sxy);
const double mu1 = 2 * sxy / (sxy * sxy - sxx * syy);
const double lam2 = 2 * sxy / (sxy * sxy - sxx * syy);
const double mu2 = 2 * sxx / (sxx * syy - sxy * sxy);
for (size_t h = 0; h < nspec; h++) {
if (emptySpectrum[h]) {
aj.push_back(0.0);
bj.push_back(0.0);
} else {
const double asym = phase->Double(h, asymmetryIndex) / maxAsym;
const double phi = phase->Double(h, phaseIndex);
const double X = n0[h] * asym * cos(phi);
const double Y = n0[h] * asym * sin(phi);
aj.push_back((lam1 * X + mu1 * Y) * 0.5);
bj.push_back((lam2 * X + mu2 * Y) * 0.5);
}
}
}
const size_t npoints = ws->blocksize();
// Create and populate output workspace
API::MatrixWorkspace_sptr ows =
API::WorkspaceFactory::Instance().create(ws, 2, npoints + 1, npoints);
// X
ows->setSharedX(0, ws->sharedX(0));
ows->setSharedX(1, ws->sharedX(0));
// Phase quadrature
auto &realY = ows->mutableY(0);
auto &imagY = ows->mutableY(1);
auto &realE = ows->mutableE(0);
auto &imagE = ows->mutableE(1);
const auto xPointData = ws->histogram(0).points();
// First X value
const double X0 = xPointData.front();
// calculate exponential decay outside of the loop
std::vector<double> expDecay = xPointData.rawData();
std::transform(expDecay.begin(), expDecay.end(), expDecay.begin(),
[X0, muLife](double x) { return exp(-(x - X0) / muLife); });
for (size_t i = 0; i < npoints; i++) {
for (size_t h = 0; h < nspec; h++) {
if (!emptySpectrum[h]) {
// (X,Y,E) with exponential decay removed
const double X = ws->x(h)[i];
const double exponential = n0[h] * exp(-(X - X0) / muLife);
const double Y = ws->y(h)[i] - exponential;
const double E =
(ws->y(h)[i] > poissonLimit) ? ws->e(h)[i] : sqrt(exponential);
realY[i] += aj[h] * Y;
imagY[i] += bj[h] * Y;
realE[i] += aj[h] * aj[h] * E * E;
imagE[i] += bj[h] * bj[h] * E * E;
}
}
realE[i] = sqrt(realE[i]);
imagE[i] = sqrt(imagE[i]);
// Regain exponential decay
realY[i] /= expDecay[i];
imagY[i] /= expDecay[i];
realE[i] /= expDecay[i];
imagE[i] /= expDecay[i];
}
// New Y axis label
ows->setYUnit("Asymmetry");
return ows;
}
/** Carries out the bin-by-bin normalization
* @param inputWorkspace The input workspace
* @param outputWorkspace The result workspace
*/
void NormaliseToMonitor::normaliseBinByBin(
const API::MatrixWorkspace_sptr &inputWorkspace,
API::MatrixWorkspace_sptr &outputWorkspace) {
EventWorkspace_sptr inputEvent =
boost::dynamic_pointer_cast<EventWorkspace>(inputWorkspace);
// Only create output workspace if different to input one
if (outputWorkspace != inputWorkspace) {
if (inputEvent) {
outputWorkspace = inputWorkspace->clone();
} else
outputWorkspace = WorkspaceFactory::Instance().create(inputWorkspace);
}
auto outputEvent =
boost::dynamic_pointer_cast<EventWorkspace>(outputWorkspace);
// Get hold of the monitor spectrum
const auto &monX = m_monitor->binEdges(0);
auto monY = m_monitor->counts(0);
auto monE = m_monitor->countStandardDeviations(0);
// Calculate the overall normalization just the once if bins are all matching
if (m_commonBins)
this->normalisationFactor(monX, monY, monE);
const size_t numHists = inputWorkspace->getNumberHistograms();
auto specLength = inputWorkspace->blocksize();
// Flag set when a division by 0 is found
bool hasZeroDivision = false;
Progress prog(this, 0.0, 1.0, numHists);
// Loop over spectra
PARALLEL_FOR_IF(
Kernel::threadSafe(*inputWorkspace, *outputWorkspace, *m_monitor))
for (int64_t i = 0; i < int64_t(numHists); ++i) {
PARALLEL_START_INTERUPT_REGION
prog.report();
const auto &X = inputWorkspace->binEdges(i);
// If not rebinning, just point to our monitor spectra, otherwise create new
// vectors
auto Y = (m_commonBins ? monY : Counts(specLength));
auto E = (m_commonBins ? monE : CountStandardDeviations(specLength));
if (!m_commonBins) {
// ConvertUnits can give X vectors of all zeros - skip these, they cause
// problems
if (X.back() == 0.0 && X.front() == 0.0)
continue;
// Rebin the monitor spectrum to match the binning of the current data
// spectrum
VectorHelper::rebinHistogram(
monX.rawData(), monY.mutableRawData(), monE.mutableRawData(),
X.rawData(), Y.mutableRawData(), E.mutableRawData(), false);
// Recalculate the overall normalization factor
this->normalisationFactor(X, Y, E);
}
if (inputEvent) {
// ----------------------------------- EventWorkspace
// ---------------------------------------
EventList &outEL = outputEvent->getSpectrum(i);
outEL.divide(X.rawData(), Y.mutableRawData(), E.mutableRawData());
} else {
// ----------------------------------- Workspace2D
// ---------------------------------------
auto &YOut = outputWorkspace->mutableY(i);
auto &EOut = outputWorkspace->mutableE(i);
const auto &inY = inputWorkspace->y(i);
const auto &inE = inputWorkspace->e(i);
outputWorkspace->mutableX(i) = inputWorkspace->x(i);
// The code below comes more or less straight out of Divide.cpp
for (size_t k = 0; k < specLength; ++k) {
// Get the input Y's
const double leftY = inY[k];
const double rightY = Y[k];
if (rightY == 0.0) {
hasZeroDivision = true;
}
// Calculate result and store in local variable to avoid overwriting
// original data if
// output workspace is same as one of the input ones
const double newY = leftY / rightY;
if (fabs(rightY) > 1.0e-12 && fabs(newY) > 1.0e-12) {
const double lhsFactor = (inE[k] < 1.0e-12 || fabs(leftY) < 1.0e-12)
? 0.0
: pow((inE[k] / leftY), 2);
const double rhsFactor =
E[k] < 1.0e-12 ? 0.0 : pow((E[k] / rightY), 2);
EOut[k] = std::abs(newY) * sqrt(lhsFactor + rhsFactor);
}
// Now store the result
YOut[k] = newY;
} // end Workspace2D case
} // end loop over current spectrum
PARALLEL_END_INTERUPT_REGION
} // end loop over spectra
PARALLEL_CHECK_INTERUPT_REGION
if (hasZeroDivision) {
g_log.warning() << "Division by zero in some of the bins.\n";
}
}
