void PeaksWorkspace::saveNexus(::NeXus::File * file) const
{
//Number of Peaks
const size_t np(peaks.size());
// Column vectors for peaks table
std::vector<int> detectorID(np);
std::vector<double> H(np);
std::vector<double> K(np);
std::vector<double> L(np);
std::vector<double> intensity(np);
std::vector<double> sigmaIntensity(np);
std::vector<double> binCount(np);
std::vector<double> initialEnergy(np);
std::vector<double> finalEnergy(np);
std::vector<double> waveLength(np);
std::vector<double> scattering(np);
std::vector<double> dSpacing(np);
std::vector<double> TOF(np);
std::vector<int> runNumber(np);
std::vector<double> goniometerMatrix(9 * np);
// Populate column vectors from Peak Workspace
for (size_t i = 0; i < np; i++)
{
Peak p = peaks[i];
detectorID[i] = p.getDetectorID();
H[i] = p.getH();
K[i] = p.getK();
L[i] = p.getL();
intensity[i] = p.getIntensity();
sigmaIntensity[i] = p.getSigmaIntensity();
binCount[i] = p.getBinCount();
initialEnergy[i] = p.getInitialEnergy();
finalEnergy[i] = p.getFinalEnergy();
waveLength[i] = p.getWavelength();
scattering[i] = p.getScattering();
dSpacing[i] = p.getDSpacing();
TOF[i] = p.getTOF();
runNumber[i] = p.getRunNumber();
{
Matrix<double> gm = p.getGoniometerMatrix();
goniometerMatrix[9 * i] = gm[0][0];
goniometerMatrix[9 * i + 1] = gm[1][0];
goniometerMatrix[9 * i + 2] = gm[2][0];
goniometerMatrix[9 * i + 3] = gm[0][1];
goniometerMatrix[9 * i + 4] = gm[1][1];
goniometerMatrix[9 * i + 5] = gm[2][1];
goniometerMatrix[9 * i + 6] = gm[0][2];
goniometerMatrix[9 * i + 7] = gm[1][2];
goniometerMatrix[9 * i + 8] = gm[1][2];
}
// etc.
}
// Start Peaks Workspace in Nexus File
std::string specifyInteger = "An integer";
std::string specifyDouble = "A double";
file->makeGroup("peaks_workspace", "NXentry", true); // For when peaksWorkspace can be loaded
// Detectors column
file->writeData("column_1", detectorID);
file->openData("column_1");
file->putAttr("name", "Dectector ID");
file->putAttr("interpret_as", specifyInteger);
file->putAttr("units", "Not known");
file->closeData();
// H column
file->writeData("column_2", H);
file->openData("column_2");
file->putAttr("name", "H");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// K column
file->writeData("column_3", K);
file->openData("column_3");
file->putAttr("name", "K");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// L column
file->writeData("column_4", L);
file->openData("column_4");
file->putAttr("name", "L");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Intensity column
file->writeData("column_5", intensity);
file->openData("column_5");
file->putAttr("name", "Intensity");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Sigma Intensity column
file->writeData("column_6", sigmaIntensity);
file->openData("column_6");
file->putAttr("name", "Sigma Intensity");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Bin Count column
file->writeData("column_7", binCount);
file->openData("column_7");
file->putAttr("name", "Bin Count");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Initial Energy column
file->writeData("column_8", initialEnergy);
file->openData("column_8");
file->putAttr("name", "Initial Energy");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Final Energy column
file->writeData("column_9", finalEnergy);
file->openData("column_9");
file->putAttr("name", "Final Energy");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Wave Length Column
file->writeData("column_10", waveLength);
file->openData("column_10");
file->putAttr("name", "Wave Length");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Scattering Column
file->writeData("column_11", scattering);
file->openData("column_11");
file->putAttr("name", "Scattering");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// D Spacing Column
file->writeData("column_12", dSpacing);
file->openData("column_12");
file->putAttr("name", "D Spacing");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// TOF Column
file->writeData("column_13", TOF);
file->openData("column_13");
file->putAttr("name", "TOF");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
//Run Number column
file->writeData("column_14", runNumber);
file->openData("column_14");
file->putAttr("name", "Run Number");
file->putAttr("interpret_as", specifyInteger);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Goniometer Matrix Column
std::vector<int> array_dims;
array_dims.push_back(static_cast<int>(peaks.size()));
array_dims.push_back(9);
file->writeData("column_15", goniometerMatrix, array_dims);
file->openData("column_15");
file->putAttr("name", "Goniometer Matrix");
file->putAttr("interpret_as", "A matrix of 3x3 doubles");
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// QLab & QSample are calculated and do not need to be saved
file->closeGroup(); // end of peaks workpace
}
/**
* Calculates the h,k, and l offsets from an integer for (some of )the peaks,
*given the parameter values.
*
* @param out For each peak there are 3 consecutive elements in this array. The
*first is for the h offset from an
* integer, the second is the k offset and the 3rd is the l offset
* @param xValues xValues give the index in the PeaksWorkspace for the peak.
*For each peak considered there are
* three consecutive entries all with the same index
* @param nData The size of the xValues and out arrays
*/
void PeakHKLErrors::function1D(double *out, const double *xValues,
const size_t nData) const {
PeaksWorkspace_sptr Peaks =
AnalysisDataService::Instance().retrieveWS<PeaksWorkspace>(
PeakWorkspaceName);
boost::shared_ptr<Geometry::Instrument> instNew = getNewInstrument(Peaks);
if (!Peaks)
throw std::invalid_argument("Peaks not stored under the name " +
PeakWorkspaceName);
std::map<int, Mantid::Kernel::Matrix<double>> RunNum2GonMatrixMap;
getRun2MatMap(Peaks, OptRuns, RunNum2GonMatrixMap);
const DblMatrix &UBx = Peaks->sample().getOrientedLattice().getUB();
DblMatrix UBinv(UBx);
UBinv.Invert();
UBinv /= (2 * M_PI);
double GonRotx = getParameter("GonRotx");
double GonRoty = getParameter("GonRoty");
double GonRotz = getParameter("GonRotz");
Matrix<double> GonRot = RotationMatrixAboutRegAxis(GonRotx, 'x') *
RotationMatrixAboutRegAxis(GonRoty, 'y') *
RotationMatrixAboutRegAxis(GonRotz, 'z');
double ChiSqTot = 0.0;
for (size_t i = 0; i < nData; i += 3) {
int peakNum = boost::math::iround(xValues[i]);
IPeak &peak_old = Peaks->getPeak(peakNum);
int runNum = peak_old.getRunNumber();
std::string runNumStr = std::to_string(runNum);
Peak peak = createNewPeak(peak_old, instNew, 0, peak_old.getL1());
size_t N = OptRuns.find("/" + runNumStr + "/");
if (N < OptRuns.size()) {
peak.setGoniometerMatrix(GonRot * RunNum2GonMatrixMap[runNum]);
} else {
peak.setGoniometerMatrix(GonRot * peak.getGoniometerMatrix());
}
V3D sampOffsets(getParameter("SampleXOffset"),
getParameter("SampleYOffset"),
getParameter("SampleZOffset"));
peak.setSamplePos(peak.getSamplePos() + sampOffsets);
V3D hkl = UBinv * peak.getQSampleFrame();
for (int k = 0; k < 3; k++) {
double d1 = hkl[k] - floor(hkl[k]);
if (d1 > .5)
d1 = d1 - 1;
if (d1 < -.5)
d1 = d1 + 1;
out[i + k] = d1;
ChiSqTot += d1 * d1;
}
}
g_log.debug() << "------------------------Function---------------------------"
"--------------------\n";
for (size_t p = 0; p < nParams(); p++) {
g_log.debug() << parameterName(p) << "(" << getParameter(p) << "),";
if ((p + 1) % 6 == 0)
g_log.debug() << '\n';
}
g_log.debug() << '\n';
g_log.debug() << "Off constraints=";
for (size_t p = 0; p < nParams(); p++) {
IConstraint *constr = getConstraint(p);
if (constr)
if ((constr->check() > 0))
g_log.debug() << "(" << parameterName(p) << "=" << constr->check()
<< ");";
}
g_log.debug() << '\n';
g_log.debug() << " Chi**2 = " << ChiSqTot << " nData = " << nData
<< '\n';
}
void PeakHKLErrors::functionDeriv1D(Jacobian *out, const double *xValues,
const size_t nData) {
PeaksWorkspace_sptr Peaks =
AnalysisDataService::Instance().retrieveWS<PeaksWorkspace>(
PeakWorkspaceName);
boost::shared_ptr<Geometry::Instrument> instNew = getNewInstrument(Peaks);
const DblMatrix &UB = Peaks->sample().getOrientedLattice().getUB();
DblMatrix UBinv(UB);
UBinv.Invert();
UBinv /= 2 * M_PI;
double GonRotx = getParameter("GonRotx");
double GonRoty = getParameter("GonRoty");
double GonRotz = getParameter("GonRotz");
Matrix<double> InvGonRotxMat = RotationMatrixAboutRegAxis(GonRotx, 'x');
Matrix<double> InvGonRotyMat = RotationMatrixAboutRegAxis(GonRoty, 'y');
Matrix<double> InvGonRotzMat = RotationMatrixAboutRegAxis(GonRotz, 'z');
Matrix<double> GonRot = InvGonRotxMat * InvGonRotyMat * InvGonRotzMat;
InvGonRotxMat.Invert();
InvGonRotyMat.Invert();
InvGonRotzMat.Invert();
std::map<int, Kernel::Matrix<double>> RunNums2GonMatrix;
getRun2MatMap(Peaks, OptRuns, RunNums2GonMatrix);
g_log.debug()
<< "----------------------------Derivative------------------------\n";
V3D samplePosition = instNew->getSample()->getPos();
IPeak &ppeak = Peaks->getPeak(0);
double L0 = ppeak.getL1();
double velocity = (L0 + ppeak.getL2()) / ppeak.getTOF();
double K =
2 * M_PI / ppeak.getWavelength() / velocity; // 2pi/lambda = K* velocity
V3D beamDir = instNew->getBeamDirection();
size_t paramNums[] = {parameterIndex(std::string("SampleXOffset")),
parameterIndex(std::string("SampleYOffset")),
parameterIndex(std::string("SampleZOffset"))};
for (size_t i = 0; i < nData; i += 3) {
int peakNum = boost::math::iround(xValues[i]);
IPeak &peak_old = Peaks->getPeak(peakNum);
Peak peak = createNewPeak(peak_old, instNew, 0, peak_old.getL1());
int runNum = peak_old.getRunNumber();
std::string runNumStr = std::to_string(runNum);
for (int kk = 0; kk < static_cast<int>(nParams()); kk++) {
out->set(i, kk, 0.0);
out->set(i + 1, kk, 0.0);
out->set(i + 2, kk, 0.0);
}
double chi, phi, omega;
size_t chiParamNum, phiParamNum, omegaParamNum;
size_t N = OptRuns.find("/" + runNumStr);
if (N < OptRuns.size()) {
chi = getParameter("chi" + (runNumStr));
phi = getParameter("phi" + (runNumStr));
omega = getParameter("omega" + (runNumStr));
peak.setGoniometerMatrix(GonRot * RunNums2GonMatrix[runNum]);
chiParamNum = parameterIndex("chi" + (runNumStr));
phiParamNum = parameterIndex("phi" + (runNumStr));
omegaParamNum = parameterIndex("omega" + (runNumStr));
} else {
Geometry::Goniometer Gon(peak.getGoniometerMatrix());
std::vector<double> phichiOmega = Gon.getEulerAngles("YZY");
chi = phichiOmega[1];
phi = phichiOmega[2];
omega = phichiOmega[0];
// peak.setGoniometerMatrix( GonRot*Gon.getR());
chiParamNum = phiParamNum = omegaParamNum = nParams() + 10;
peak.setGoniometerMatrix(GonRot * peak.getGoniometerMatrix());
}
V3D sampOffsets(getParameter("SampleXOffset"),
getParameter("SampleYOffset"),
getParameter("SampleZOffset"));
peak.setSamplePos(peak.getSamplePos() + sampOffsets);
// NOTE:Use getQLabFrame except for below.
// For parameters the getGoniometerMatrix should remove GonRot, for derivs
// wrt GonRot*, wrt chi*,phi*,etc.
// Deriv wrt chi phi and omega
if (phiParamNum < nParams()) {
Matrix<double> chiMatrix = RotationMatrixAboutRegAxis(chi, 'z');
Matrix<double> phiMatrix = RotationMatrixAboutRegAxis(phi, 'y');
Matrix<double> omegaMatrix = RotationMatrixAboutRegAxis(omega, 'y');
Matrix<double> dchiMatrix = DerivRotationMatrixAboutRegAxis(chi, 'z');
Matrix<double> dphiMatrix = DerivRotationMatrixAboutRegAxis(phi, 'y');
Matrix<double> domegaMatrix = DerivRotationMatrixAboutRegAxis(omega, 'y');
Matrix<double> InvG = omegaMatrix * chiMatrix * phiMatrix;
InvG.Invert();
// Calculate Derivatives wrt chi(phi,omega) in degrees
Matrix<double> R = omegaMatrix * chiMatrix * dphiMatrix;
Matrix<double> InvR = InvG * R * InvG * -1;
V3D lab = peak.getQLabFrame();
V3D Dhkl0 = UBinv * InvR * lab;
R = omegaMatrix * dchiMatrix * phiMatrix;
InvR = InvG * R * InvG * -1;
V3D Dhkl1 = UBinv * InvR * peak.getQLabFrame();
R = domegaMatrix * chiMatrix * phiMatrix;
InvR = InvG * R * InvG * -1;
V3D Dhkl2 =
UBinv * InvR * peak.getQLabFrame(); // R.transpose should be R inverse
out->set(i, chiParamNum, Dhkl1[0]);
out->set(i + 1, chiParamNum, Dhkl1[1]);
out->set(i + 2, chiParamNum, Dhkl1[2]);
out->set(i, phiParamNum, Dhkl0[0]);
out->set(i + 1, phiParamNum, Dhkl0[1]);
out->set(i + 2, phiParamNum, Dhkl0[2]);
out->set(i, omegaParamNum, Dhkl2[0]);
out->set(i + 1, omegaParamNum, Dhkl2[1]);
out->set(i + 2, omegaParamNum, Dhkl2[2]);
} // if optimize for chi phi and omega on this peak
//------------------------Goniometer Rotation Derivatives
//-----------------------
Matrix<double> InvGonRot(GonRot);
InvGonRot.Invert();
Matrix<double> InvGon = InvGonRot * peak.getGoniometerMatrix();
InvGon.Invert();
V3D DGonx = (UBinv * InvGon * InvGonRotzMat * InvGonRotyMat *
DerivRotationMatrixAboutRegAxis(
-GonRotx, 'x') * // - gives inverse of GonRot
peak.getQLabFrame()) *
-1;
V3D DGony = (UBinv * InvGon * InvGonRotzMat *
DerivRotationMatrixAboutRegAxis(-GonRoty, 'y') *
InvGonRotxMat * peak.getQLabFrame()) *
-1;
V3D DGonz =
(UBinv * InvGon * DerivRotationMatrixAboutRegAxis(-GonRotz, 'z') *
InvGonRotyMat * InvGonRotxMat * peak.getQLabFrame()) *
-1;
size_t paramnum = parameterIndex("GonRotx");
out->set(i, paramnum, DGonx[0]);
out->set(i + 1, paramnum, DGonx[1]);
out->set(i + 2, paramnum, DGonx[2]);
out->set(i, parameterIndex("GonRoty"), DGony[0]);
out->set(i + 1, parameterIndex("GonRoty"), DGony[1]);
out->set(i + 2, parameterIndex("GonRoty"), DGony[2]);
out->set(i, parameterIndex("GonRotz"), DGonz[0]);
out->set(i + 1, parameterIndex("GonRotz"), DGonz[1]);
out->set(i + 2, parameterIndex("GonRotz"), DGonz[2]);
//-------------------- Sample Orientation derivatives
//----------------------------------
// Qlab = -KV + k|V|*beamdir
// D = pos-sampPos
//|V|= vmag=(L0 + D )/tof
// t1= tof - L0/|V| {time from sample to pixel}
// V = D/t1
V3D D = peak.getDetPos() - samplePosition;
double vmag = (L0 + D.norm()) / peak.getTOF();
double t1 = peak.getTOF() - L0 / vmag;
// Derivs wrt sample x, y, z
// Ddsx =( - 1, 0, 0), d|D|^2/dsx -> 2|D|d|D|/dsx =d(tranp(D)* D)/dsx =2
// Ddsx* tranp(D)
//|D| also called Dmag
V3D Dmagdsxsysz(D);
Dmagdsxsysz *= (-1 / D.norm());
V3D vmagdsxsysz = Dmagdsxsysz / peak.getTOF();
V3D t1dsxsysz = vmagdsxsysz * (L0 / vmag / vmag);
Matrix<double> Gon = peak.getGoniometerMatrix();
Gon.Invert();
// x=0 is deriv wrt SampleXoffset, x=1 is deriv wrt SampleYoffset, etc.
for (int x = 0; x < 3; x++) {
V3D pp;
pp[x] = 1;
V3D dQlab1 = pp / -t1 - D * (t1dsxsysz[x] / t1 / t1);
V3D dQlab2 = beamDir * vmagdsxsysz[x];
V3D dQlab = dQlab2 - dQlab1;
dQlab *= K;
V3D dQSamp = Gon * dQlab;
V3D dhkl = UBinv * dQSamp;
out->set(i, paramNums[x], dhkl[0]);
out->set(i + 1, paramNums[x], dhkl[1]);
out->set(i + 2, paramNums[x], dhkl[2]);
}
}
}
void PeaksWorkspace::saveNexus(::NeXus::File *file) const {
// Number of Peaks
const size_t np(peaks.size());
// Column vectors for peaks table
std::vector<int> detectorID(np);
std::vector<double> H(np);
std::vector<double> K(np);
std::vector<double> L(np);
std::vector<double> intensity(np);
std::vector<double> sigmaIntensity(np);
std::vector<double> binCount(np);
std::vector<double> initialEnergy(np);
std::vector<double> finalEnergy(np);
std::vector<double> waveLength(np);
std::vector<double> scattering(np);
std::vector<double> dSpacing(np);
std::vector<double> TOF(np);
std::vector<int> runNumber(np);
std::vector<double> goniometerMatrix(9 * np);
std::vector<std::string> shapes(np);
// Populate column vectors from Peak Workspace
size_t maxShapeJSONLength = 0;
for (size_t i = 0; i < np; i++) {
Peak p = peaks[i];
detectorID[i] = p.getDetectorID();
H[i] = p.getH();
K[i] = p.getK();
L[i] = p.getL();
intensity[i] = p.getIntensity();
sigmaIntensity[i] = p.getSigmaIntensity();
binCount[i] = p.getBinCount();
initialEnergy[i] = p.getInitialEnergy();
finalEnergy[i] = p.getFinalEnergy();
waveLength[i] = p.getWavelength();
scattering[i] = p.getScattering();
dSpacing[i] = p.getDSpacing();
TOF[i] = p.getTOF();
runNumber[i] = p.getRunNumber();
{
Matrix<double> gm = p.getGoniometerMatrix();
goniometerMatrix[9 * i] = gm[0][0];
goniometerMatrix[9 * i + 1] = gm[1][0];
goniometerMatrix[9 * i + 2] = gm[2][0];
goniometerMatrix[9 * i + 3] = gm[0][1];
goniometerMatrix[9 * i + 4] = gm[1][1];
goniometerMatrix[9 * i + 5] = gm[2][1];
goniometerMatrix[9 * i + 6] = gm[0][2];
goniometerMatrix[9 * i + 7] = gm[1][2];
goniometerMatrix[9 * i + 8] = gm[2][2];
}
const std::string shapeJSON = p.getPeakShape().toJSON();
shapes[i] = shapeJSON;
if (shapeJSON.size() > maxShapeJSONLength) {
maxShapeJSONLength = shapeJSON.size();
}
}
// Start Peaks Workspace in Nexus File
const std::string specifyInteger = "An integer";
const std::string specifyDouble = "A double";
const std::string specifyString = "A string";
file->makeGroup("peaks_workspace", "NXentry",
true); // For when peaksWorkspace can be loaded
// Coordinate system
file->writeData("coordinate_system", static_cast<uint32_t>(m_coordSystem));
// Write out the Qconvention
// ki-kf for Inelastic convention; kf-ki for Crystallography convention
std::string m_QConvention = this->getConvention();
file->putAttr("QConvention", m_QConvention);
// Detectors column
file->writeData("column_1", detectorID);
file->openData("column_1");
file->putAttr("name", "Detector ID");
file->putAttr("interpret_as", specifyInteger);
file->putAttr("units", "Not known");
file->closeData();
// H column
file->writeData("column_2", H);
file->openData("column_2");
file->putAttr("name", "H");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// K column
file->writeData("column_3", K);
file->openData("column_3");
file->putAttr("name", "K");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// L column
file->writeData("column_4", L);
file->openData("column_4");
file->putAttr("name", "L");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Intensity column
file->writeData("column_5", intensity);
file->openData("column_5");
file->putAttr("name", "Intensity");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Sigma Intensity column
file->writeData("column_6", sigmaIntensity);
file->openData("column_6");
file->putAttr("name", "Sigma Intensity");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Bin Count column
file->writeData("column_7", binCount);
file->openData("column_7");
file->putAttr("name", "Bin Count");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Initial Energy column
file->writeData("column_8", initialEnergy);
file->openData("column_8");
file->putAttr("name", "Initial Energy");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Final Energy column
file->writeData("column_9", finalEnergy);
file->openData("column_9");
file->putAttr("name", "Final Energy");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Wave Length Column
file->writeData("column_10", waveLength);
file->openData("column_10");
file->putAttr("name", "Wave Length");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Scattering Column
file->writeData("column_11", scattering);
file->openData("column_11");
file->putAttr("name", "Scattering");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// D Spacing Column
file->writeData("column_12", dSpacing);
file->openData("column_12");
file->putAttr("name", "D Spacing");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// TOF Column
file->writeData("column_13", TOF);
file->openData("column_13");
file->putAttr("name", "TOF");
file->putAttr("interpret_as", specifyDouble);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Run Number column
file->writeData("column_14", runNumber);
file->openData("column_14");
file->putAttr("name", "Run Number");
file->putAttr("interpret_as", specifyInteger);
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Goniometer Matrix Column
std::vector<int> array_dims;
array_dims.push_back(static_cast<int>(peaks.size()));
array_dims.push_back(9);
file->writeData("column_15", goniometerMatrix, array_dims);
file->openData("column_15");
file->putAttr("name", "Goniometer Matrix");
file->putAttr("interpret_as", "A matrix of 3x3 doubles");
file->putAttr("units", "Not known"); // Units may need changing when known
file->closeData();
// Shape
std::vector<int64_t> dims;
dims.push_back(np);
dims.push_back(static_cast<int>(maxShapeJSONLength));
const std::string name = "column_16";
file->makeData(name, NeXus::CHAR, dims, false);
file->openData(name);
auto toNexus = new char[maxShapeJSONLength * np];
for (size_t ii = 0; ii < np; ii++) {
std::string rowStr = shapes[ii];
for (size_t ic = 0; ic < rowStr.size(); ic++)
toNexus[ii * maxShapeJSONLength + ic] = rowStr[ic];
for (size_t ic = rowStr.size();
ic < static_cast<size_t>(maxShapeJSONLength); ic++)
toNexus[ii * maxShapeJSONLength + ic] = ' ';
}
file->putData((void *)(toNexus));
delete[] toNexus;
file->putAttr("units", "Not known"); // Units may need changing when known
file->putAttr("name", "Shape");
file->putAttr("interpret_as", specifyString);
file->closeData();
// QLab & QSample are calculated and do not need to be saved
file->closeGroup(); // end of peaks workpace
}