/** Do the initial copy of the data from the input to the output workspace for histogram workspaces.
* Takes out the bin width if necessary.
* @param inputWS The input workspace
* @param outputWS The output workspace
*/
void ConvertUnits::fillOutputHist(const API::MatrixWorkspace_const_sptr inputWS, const API::MatrixWorkspace_sptr outputWS)
{
const int size = static_cast<int>(inputWS->blocksize());
// Loop over the histograms (detector spectra)
Progress prog(this,0.0,0.2,m_numberOfSpectra);
int64_t numberOfSpectra_i = static_cast<int64_t>(m_numberOfSpectra); // cast to make openmp happy
PARALLEL_FOR2(inputWS,outputWS)
for (int64_t i = 0; i < numberOfSpectra_i; ++i)
{
PARALLEL_START_INTERUPT_REGION
// Take the bin width dependency out of the Y & E data
if (m_distribution)
{
for (int j = 0; j < size; ++j)
{
const double width = std::abs( inputWS->dataX(i)[j+1] - inputWS->dataX(i)[j] );
outputWS->dataY(i)[j] = inputWS->dataY(i)[j]*width;
outputWS->dataE(i)[j] = inputWS->dataE(i)[j]*width;
}
}
else
{
// Just copy over
outputWS->dataY(i) = inputWS->dataY(i);
outputWS->dataE(i) = inputWS->dataE(i);
}
// Copy over the X data
outputWS->setX( i, inputWS->refX(i) );
prog.report("Convert to " + m_outputUnit->unitID());
PARALLEL_END_INTERUPT_REGION
}
PARALLEL_CHECK_INTERUPT_REGION
}
/** Execute the algorithm.
*/
void DampSq::exec()
{
// TODO Auto-generated execute stub
// 1. Generate new workspace
API::MatrixWorkspace_const_sptr isqspace = getProperty("InputWorkspace");
API::MatrixWorkspace_sptr osqspace = WorkspaceFactory::Instance().create(isqspace, 1, isqspace->size(), isqspace->size());
int mode = getProperty("Mode");
double qmax = getProperty("QMax");
if (mode < 1 || mode > 4) {
g_log.error("Damp mode can only be 1, 2, 3, or 4");
return;
}
// 2. Get access to all
const MantidVec& iQVec = isqspace->dataX(0);
const MantidVec& iSVec = isqspace->dataY(0);
const MantidVec& iEVec = isqspace->dataE(0);
MantidVec& oQVec = osqspace->dataX(0);
MantidVec& oSVec = osqspace->dataY(0);
MantidVec& oEVec = osqspace->dataE(0);
// 3. Calculation
double dqmax = qmax - iQVec[0];
double damp;
for (unsigned int i = 0; i < iQVec.size(); i ++) {
// a) calculate damp coefficient
switch (mode) {
case 1:
damp = dampcoeff1(iQVec[i], qmax, dqmax);
break;
case 2:
damp = dampcoeff2(iQVec[i], qmax, dqmax);;
break;
case 3:
damp = dampcoeff3(iQVec[i], qmax, dqmax);;
break;
case 4:
damp = dampcoeff4(iQVec[i], qmax, dqmax);;
break;
default:
damp = 0;
break;
}
// b) calculate new S(q)
oQVec[i] = iQVec[i];
oSVec[i] = 1 + damp*(iSVec[i]-1);
oEVec[i] = damp*iEVec[i];
} // i
// 4. Over
setProperty("OutputWorkspace", osqspace);
return;
}
/** Initialization method:
@param bkgWS -- shared pointer to the workspace which contains background
@param sourceWS -- shared pointer to the workspace to remove background from
@param emode -- energy conversion mode used during internal units conversion
(0 -- elastic, 1-direct, 2 indirect, as defined in Units conversion
@param pLog -- pointer to the logger class which would report errors
@param nThreads -- number of threads to be used for background removal
@param inPlace -- if the background removal occurs from the existing workspace
or target workspace has to be cloned.
*/
void BackgroundHelper::initialize(const API::MatrixWorkspace_const_sptr &bkgWS,
const API::MatrixWorkspace_sptr &sourceWS,
int emode, Kernel::Logger *pLog, int nThreads,
bool inPlace) {
m_bgWs = bkgWS;
m_wkWS = sourceWS;
m_Emode = emode;
m_pgLog = pLog;
m_inPlace = inPlace;
std::string bgUnits = bkgWS->getAxis(0)->unit()->unitID();
if (bgUnits != "TOF")
throw std::invalid_argument(" Background Workspace: " + bkgWS->getName() +
" should be in the units of TOF");
if (!(bkgWS->getNumberHistograms() == 1 ||
sourceWS->getNumberHistograms() == bkgWS->getNumberHistograms()))
throw std::invalid_argument(" Background Workspace: " + bkgWS->getName() +
" should have the same number of spectra as "
"source workspace or be a single histogram "
"workspace");
auto WSUnit = sourceWS->getAxis(0)->unit();
if (!WSUnit)
throw std::invalid_argument(" Source Workspace: " + sourceWS->getName() +
" should have units");
Geometry::IComponent_const_sptr source =
sourceWS->getInstrument()->getSource();
m_Sample = sourceWS->getInstrument()->getSample();
if ((!source) || (!m_Sample))
throw std::invalid_argument(
"Instrument on Source workspace:" + sourceWS->getName() +
"is not sufficiently defined: failed to get source and/or sample");
m_L1 = source->getDistance(*m_Sample);
// just in case.
this->deleteUnitsConverters();
// allocate the array of units converters to avoid units reallocation within a
// loop
m_WSUnit.assign(nThreads, NULL);
for (int i = 0; i < nThreads; i++) {
m_WSUnit[i] = WSUnit->clone();
}
m_singleValueBackground = false;
if (bkgWS->getNumberHistograms() == 0)
m_singleValueBackground = true;
const MantidVec &dataX = bkgWS->dataX(0);
const MantidVec &dataY = bkgWS->dataY(0);
// const MantidVec& dataE = bkgWS->dataE(0);
m_NBg = dataY[0];
m_dtBg = dataX[1] - dataX[0];
// m_ErrSq = dataE[0]*dataE[0]; // needs further clarification
m_Efix = this->getEi(sourceWS);
}
double BivariateNormal::initCommon() {
double penalty = 0;
bool ParamsOK = true;
bool CommonsOK = true;
if (!expVals)
CommonsOK = false;
API::MatrixWorkspace_const_sptr ws = getMatrixWorkspace();
MantidVec D = ws->dataY(0);
MantidVec X = ws->dataY(1);
MantidVec Y = ws->dataY(2);
if (NCells < 0) {
NCells =
(int)std::min<size_t>(D.size(), std::min<size_t>(X.size(), Y.size()));
CommonsOK = false;
}
double Attrib[12] = {0.0};
double MinX, MinY, MaxX, MaxY, MaxD, MinD;
MinX = MaxX = X[0];
MinY = MaxY = Y[0];
MaxD = MinD = D[0];
if (!CommonsOK) {
for (int i = 0; i < NCells; i++) {
Attrib[S_int] += D[i];
Attrib[S_xint] += D[i] * X[i];
Attrib[S_yint] += D[i] * Y[i];
Attrib[S_x2int] += D[i] * X[i] * X[i];
Attrib[S_y2int] += D[i] * Y[i] * Y[i];
Attrib[S_xyint] += D[i] * X[i] * Y[i];
Attrib[S_y] += Y[i];
Attrib[S_x] += X[i];
Attrib[S_x2] += X[i] * X[i];
Attrib[S_y2] += Y[i] * Y[i];
Attrib[S_xy] += X[i] * Y[i];
Attrib[S_1] += 1.0;
if (X[i] < MinX)
MinX = X[i];
if (X[i] > MaxX)
MaxX = X[i];
if (Y[i] < MinY)
MinY = Y[i];
if (Y[i] > MaxY)
MaxY = Y[i];
if (D[i] < MinD)
MinD = D[i];
if (D[i] > MaxD)
MaxD = D[i];
}
mIx = Attrib[S_xint] / Attrib[S_int];
mIy = Attrib[S_yint] / Attrib[S_int];
mx = Attrib[S_x] / Attrib[S_1];
my = Attrib[S_y] / Attrib[S_1];
SIxx = Attrib[S_x2int] - (Attrib[S_xint] * Attrib[S_xint]) / Attrib[S_int];
SIyy =
Attrib[S_y2int] - (Attrib[S_yint]) * (Attrib[S_yint]) / Attrib[S_int];
SIxy =
Attrib[S_xyint] - (Attrib[S_xint]) * (Attrib[S_yint]) / Attrib[S_int];
Sxx = Attrib[S_x2] - (Attrib[S_x]) * (Attrib[S_x]) / Attrib[S_1];
Syy = Attrib[S_y2] - (Attrib[S_y]) * (Attrib[S_y]) / Attrib[S_1];
Sxy = Attrib[S_xy] - (Attrib[S_x]) * (Attrib[S_y]) / Attrib[S_1];
// CommonsOK = false;
TotI = Attrib[S_int];
TotN = Attrib[S_1];
// CommonsOK = false;
if (getConstraint(0) == NULL) {
addConstraint((new BoundaryConstraint(this, "Background", 0,
Attrib[S_int] / Attrib[S_1])));
}
double maxIntensity = Attrib[S_int] + 3 * sqrt(Attrib[S_int]);
if (maxIntensity < 100)
maxIntensity = 100;
if (getConstraint(1) == NULL) {
addConstraint(new BoundaryConstraint(this, "Intensity", 0, maxIntensity));
}
double minMeany = MinY * .9 + .1 * MaxY;
double maxMeany = MinY * .1 + .9 * MaxY;
if (getConstraint(3) == NULL) {
addConstraint(new BoundaryConstraint(this, "Mrow", minMeany, maxMeany));
}
double minMeanx = MinX * .9 + .1 * MaxX;
double maxMeanx = MinX * .1 + .9 * MaxX;
if (getConstraint(2) == NULL) {
addConstraint(new BoundaryConstraint(this, "Mcol", minMeanx, maxMeanx));
}
if (CalcVariances && nParams() > 6) {
std::ostringstream ssxx, ssyy, ssxy;
ssyy << std::string("(") << (SIyy) << "+(Mrow-" << (mIy) << ")*(Mrow-"
<< (mIy) << ")*" << Attrib[S_int] << "-Background*" << (Syy)
<< "-Background*(Mrow-" << (my) << ")*(Mrow-" << (my) << ")*"
<< Attrib[S_1] << ")/(" << (Attrib[S_int]) << "-Background*"
<< (Attrib[S_1]) << ")";
if (getTie(IVYY) == NULL) {
tie("SSrow", ssyy.str());
CalcVxx = true;
}
ssxx << std::string("(") << (SIxx) << "+(Mcol-" << (mIx) << ")*(Mcol-"
<< (mIx) << ")*" << Attrib[S_int] << "-Background*" << (Sxx)
<< "-Background*(Mcol-" << (mx) << ")*(Mcol-" << (mx) << ")*"
<< Attrib[S_1] << ")/(" << (Attrib[S_int]) << "-Background*"
<< (Attrib[S_1]) << ")";
if (getTie(IVXX) == NULL) {
tie("SScol", ssxx.str());
CalcVyy = true;
}
ssxy << std::string("(") << (SIxy) << "+(Mcol-" << (mIx) << ")*(Mrow-"
<< (mIy) << ")*" << Attrib[S_int] << "-Background*" << (Sxy)
<< "-Background*(Mcol-" << (mx) << ")*(Mrow-" << (my) << ")*"
<< Attrib[S_1] << ")/(" << (Attrib[S_int]) << "-Background*"
<< (Attrib[S_1]) << ")";
if (getTie(IVXY) == NULL) {
tie("SSrc", ssxy.str());
CalcVxy = true;
}
}
CommonsOK = true;
}
if (LastParams[IVXX] < 0) {
ParamsOK = false;
CommonsOK = false;
} else
for (size_t i = 0; i < nParams() && ParamsOK; i++)
if (getParameter(i) != LastParams[i])
ParamsOK = false;
if (!ParamsOK) {
for (size_t i = 0; i < nParams(); i++)
LastParams[i] = getParameter(i);
}
if (!CommonsOK || !ParamsOK) {
int NCells1;
double Varxx, Varxy, Varyy;
Varxx = Varxy = Varyy = -1;
penalty = initCoeff(D, X, Y, coefNorm, expCoeffx2, expCoeffy2, expCoeffxy,
NCells1, Varxx, Varxy, Varyy);
if (Varx0 < 0 && penalty <= 0) {
Varx0 = Varxx;
Vary0 = Varyy;
}
LastParams[IVXX] = Varxx;
LastParams[IVXY] = Varxy;
LastParams[IVYY] = Varyy;
delete[] expVals;
expVals = new double[NCells];
for (int i = 0; i < NCells; i++) {
double dx = X[i] - LastParams[IXMEAN];
double dy = Y[i] - LastParams[IYMEAN];
expVals[i] = exp(expCoeffx2 * dx * dx + expCoeffxy * dx * dy +
expCoeffy2 * dy * dy);
}
}
return penalty;
}