/** Append the peaks from a .peaks file into the workspace
* @param outWS :: the workspace in which to place the information
* @param filename :: path to the .peaks file
*/
void LoadIsawPeaks::appendFile( PeaksWorkspace_sptr outWS, std::string filename )
{
// Open the file
std::ifstream in( filename.c_str() );
// Read the header, load the instrument
double T0;
std::string s = readHeader( outWS, in , T0);
// set T0 in the run parameters
API::Run & m_run = outWS->mutableRun();
m_run.addProperty<double>("T0", T0, true);
if( !in.good() || s.length() < 1 )
throw std::runtime_error( "End of Peaks file before peaks" );
if( s.compare( std::string( "0" ) ) != 0 )
throw std::logic_error( "No header for Peak segments" );
readToEndOfLine( in , true );
s = getWord( in , false );
int run, bankNum;
double chi , phi , omega , monCount;
// Build the universal goniometer that will build the rotation matrix.
Mantid::Geometry::Goniometer uniGonio;
uniGonio.makeUniversalGoniometer();
// TODO: Can we find the number of peaks to get better progress reporting?
Progress prog(this, 0.0, 1.0, 100);
while( in.good() )
{
// Read the header if necessary
s = readPeakBlockHeader( s , in , run , bankNum , chi , phi ,
omega , monCount );
// Build the Rotation matrix using phi,chi,omega
uniGonio.setRotationAngle("phi", phi);
uniGonio.setRotationAngle("chi", chi);
uniGonio.setRotationAngle("omega", omega);
//Put goniometer into peaks workspace
outWS->mutableRun().setGoniometer(uniGonio, false);
std::ostringstream oss;
std::string bankString = "bank";
if (outWS->getInstrument()->getName() == "WISH") bankString = "WISHpanel0";
oss << bankString << bankNum;
std::string bankName = oss.str();
int seqNum = -1;
try
{
// Read the peak
Peak peak = readPeak(outWS, s, in, seqNum, bankName);
// Get the calculated goniometer matrix
Matrix<double> gonMat = uniGonio.getR();
peak.setGoniometerMatrix(gonMat);
peak.setRunNumber(run);
peak.setMonitorCount( monCount );
double tof = peak.getTOF();
Kernel::Units::Wavelength wl;
wl.initialize(peak.getL1(), peak.getL2(), peak.getScattering(), 0,
peak.getInitialEnergy(), 0.0);
peak.setWavelength(wl.singleFromTOF( tof));
// Add the peak to workspace
outWS->addPeak(peak);
}
catch (std::runtime_error & e)
{
g_log.warning() << "Error reading peak SEQN " << seqNum << " : " << e.what() << std::endl;
}
prog.report();
}
}
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
}
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
}