void CalculateDIFC::calculate() {
Instrument_const_sptr instrument = m_inputWS->getInstrument();
SpecialWorkspace2D_sptr localWS =
boost::dynamic_pointer_cast<SpecialWorkspace2D>(m_outputWS);
double l1;
Kernel::V3D beamline, samplePos;
double beamline_norm;
instrument->getInstrumentParameters(l1, beamline, beamline_norm, samplePos);
// To get all the detector ID's
detid2det_map allDetectors;
instrument->getDetectors(allDetectors);
// Now go through all
detid2det_map::const_iterator it = allDetectors.begin();
for (; it != allDetectors.end(); ++it) {
Geometry::IDetector_const_sptr det = it->second;
if ((!det->isMasked()) && (!det->isMonitor())) {
const detid_t detID = it->first;
double offset = 0.;
if (m_offsetsWS)
offset = m_offsetsWS->getValue(detID, 0.);
double difc = Geometry::Instrument::calcConversion(
l1, beamline, beamline_norm, samplePos, det, offset);
difc = 1. / difc; // calcConversion gives 1/DIFC
localWS->setValue(detID, difc);
}
}
}
/**
* Make a map of the conversion factors between tof and D-spacing
* for all pixel IDs in a workspace.
*
* @param DFileName name of dspacemap file
* @param offsetsWS :: OffsetsWorkspace with instrument and offsets
*/
void SaveDspacemap::CalculateDspaceFromCal(Mantid::DataObjects::OffsetsWorkspace_sptr offsetsWS,
std::string DFileName)
{
const char * filename = DFileName.c_str();
// Get a pointer to the instrument contained in the workspace
Instrument_const_sptr instrument = offsetsWS->getInstrument();
double l1;
Kernel::V3D beamline,samplePos;
double beamline_norm;
instrument->getInstrumentParameters(l1,beamline,beamline_norm, samplePos);
//To get all the detector ID's
detid2det_map allDetectors;
instrument->getDetectors(allDetectors);
detid2det_map::const_iterator it;
detid_t maxdetID = 0;
for (it = allDetectors.begin(); it != allDetectors.end(); it++)
{
detid_t detectorID = it->first;
if(detectorID > maxdetID) maxdetID = detectorID;
}
detid_t paddetID = detid_t(getProperty("PadDetID"));
if (maxdetID < paddetID)maxdetID = paddetID;
// Now write the POWGEN-style Dspace mapping file
std::ofstream fout(filename, std::ios_base::out|std::ios_base::binary);
Progress prog(this,0.0,1.0,maxdetID);
for (detid_t i = 0; i != maxdetID; i++)
{
//Compute the factor
double factor;
Geometry::IDetector_const_sptr det;
// Find the detector with that detector id
it = allDetectors.find(i);
if (it != allDetectors.end())
{
det = it->second;
factor = Instrument::calcConversion(l1, beamline, beamline_norm, samplePos, det, offsetsWS->getValue(i, 0.0));
//Factor of 10 between ISAW and Mantid
factor *= 0.1 ;
if(factor<0)factor = 0.0;
fout.write( reinterpret_cast<char*>( &factor ), sizeof(double) );
}
else
{
factor = 0;
fout.write( reinterpret_cast<char*>( &factor ), sizeof(double) );
}
//Report progress
prog.report();
}
fout.close();
}
/**
* Make a map of the conversion factors between tof and D-spacing
* for all pixel IDs in a workspace.
*
* @param DFileName :: name of dspacemap file
* @param offsetsWS :: OffsetsWorkspace to be filled.
*/
void LoadDspacemap::CalculateOffsetsFromDSpacemapFile(
const std::string DFileName,
Mantid::DataObjects::OffsetsWorkspace_sptr offsetsWS) {
// Get a pointer to the instrument contained in the workspace
Instrument_const_sptr instrument = offsetsWS->getInstrument();
double l1;
Kernel::V3D beamline, samplePos;
double beamline_norm;
instrument->getInstrumentParameters(l1, beamline, beamline_norm, samplePos);
// To get all the detector ID's
detid2det_map allDetectors;
instrument->getDetectors(allDetectors);
// Read in the POWGEN-style Dspace mapping file
const char *filename = DFileName.c_str();
std::ifstream fin(filename, std::ios_base::in | std::ios_base::binary);
std::vector<double> dspace;
double read;
while (!fin.eof()) {
fin.read(reinterpret_cast<char *>(&read), sizeof read);
// Factor of 10 between ISAW and Mantid
read *= 10.;
dspace.push_back(read);
}
detid2det_map::const_iterator it;
for (it = allDetectors.begin(); it != allDetectors.end(); ++it) {
detid_t detectorID = it->first;
Geometry::IDetector_const_sptr det = it->second;
// Compute the factor
double offset = 0.0;
double factor = Instrument::calcConversion(l1, beamline, beamline_norm,
samplePos, det, offset);
offset = dspace[detectorID] / factor - 1.0;
// Save in the map
try {
offsetsWS->setValue(detectorID, offset);
} catch (std::invalid_argument &) {
}
}
}
/**
* @param offsetsWS
* @param index
* @return The offset adjusted value of DIFC
*/
double calculateDIFC(OffsetsWorkspace_const_sptr offsetsWS, const size_t index) {
Instrument_const_sptr instrument = offsetsWS->getInstrument();
const detid_t detid = getDetID(offsetsWS, index);
const double offset = getOffset(offsetsWS, detid);
double l1;
Kernel::V3D beamline, samplePos;
double beamline_norm;
instrument->getInstrumentParameters(l1, beamline, beamline_norm, samplePos);
Geometry::IDetector_const_sptr detector = instrument->getDetector(detid);
// the factor returned is what is needed to convert TOF->d-spacing
// the table is supposed to be filled with DIFC which goes the other way
const double factor = Instrument::calcConversion(l1, beamline, beamline_norm,
samplePos, detector, offset);
return 1./factor;
}
/** Execute the algorithm.
*/
void SaveIsawPeaks::exec()
{
// Section header
std::string header = "2 SEQN H K L COL ROW CHAN L2 2_THETA AZ WL D IPK INTI SIGI RFLG";
std::string filename = getPropertyValue("Filename");
PeaksWorkspace_sptr ws = getProperty("InputWorkspace");
std::vector<Peak> peaks = ws->getPeaks();
// We must sort the peaks first by run, then bank #, and save the list of workspace indices of it
typedef std::map<int, std::vector<size_t> > bankMap_t;
typedef std::map<int, bankMap_t> runMap_t;
std::set<int> uniqueBanks;
runMap_t runMap;
for (size_t i=0; i < peaks.size(); ++i)
{
Peak & p = peaks[i];
int run = p.getRunNumber();
int bank = 0;
std::string bankName = p.getBankName();
if (bankName.size() <= 4)
{
g_log.information() << "Could not interpret bank number of peak " << i << "(" << bankName << ")\n";
continue;
}
// Take out the "bank" part of the bank name and convert to an int
bankName = bankName.substr(4, bankName.size()-4);
Strings::convert(bankName, bank);
// Save in the map
runMap[run][bank].push_back(i);
// Track unique bank numbers
uniqueBanks.insert(bank);
}
Instrument_const_sptr inst = ws->getInstrument();
if (!inst) throw std::runtime_error("No instrument in PeaksWorkspace. Cannot save peaks file.");
double l1; V3D beamline; double beamline_norm; V3D samplePos;
inst->getInstrumentParameters(l1, beamline, beamline_norm, samplePos);
std::ofstream out;
bool append = getProperty("AppendFile");
if (append)
{
out.open( filename.c_str(), std::ios::app);
}
else
{
out.open( filename.c_str());
out << "Version: 2.0 Facility: SNS " ;
out << " Instrument: " << inst->getName() << " Date: " ;
//TODO: The experiment date might be more useful than the instrument date.
// For now, this allows the proper instrument to be loaded back after saving.
Kernel::DateAndTime expDate = inst->getValidFromDate() + 1.0;
out << expDate.to_ISO8601_string() << std::endl;
out << "6 L1 T0_SHIFT" << std::endl;
out << "7 "<< std::setw( 10 ) ;
out << std::setprecision( 4 ) << std::fixed << ( l1*100 ) ;
out << std::setw( 12 ) << std::setprecision( 3 ) << std::fixed ;
// Time offset of 0.00 for now
out << "0.000" << std::endl;
// ============================== Save .detcal info =========================================
if (true)
{
out << "4 DETNUM NROWS NCOLS WIDTH HEIGHT DEPTH DETD CenterX CenterY CenterZ BaseX BaseY BaseZ UpX UpY UpZ"
<< std::endl;
// Here would save each detector...
std::set<int>::iterator it;
for (it = uniqueBanks.begin(); it != uniqueBanks.end(); it++)
{
// Build up the bank name
int bank = *it;
std::ostringstream mess;
mess << "bank" << bank;
std::string bankName = mess.str();
// Retrieve it
RectangularDetector_const_sptr det = boost::dynamic_pointer_cast<const RectangularDetector>(inst->getComponentByName(bankName));
if (det)
{
// Center of the detector
V3D center = det->getPos();
// Distance to center of detector
double detd = (center - inst->getSample()->getPos()).norm();
// Base unit vector (along the horizontal, X axis)
V3D base = det->getAtXY(det->xpixels()-1,0)->getPos() - det->getAtXY(0,0)->getPos();
base.normalize();
// Up unit vector (along the vertical, Y axis)
V3D up = det->getAtXY(0,det->ypixels()-1)->getPos() - det->getAtXY(0,0)->getPos();
up.normalize();
// Write the line
out << "5 "
<< std::setw(6) << std::right << bank << " "
<< std::setw(6) << std::right << det->xpixels() << " "
<< std::setw(6) << std::right << det->ypixels() << " "
<< std::setw(7) << std::right << std::fixed << std::setprecision(4) << 100.0*det->xsize() << " "
<< std::setw(7) << std::right << std::fixed << std::setprecision(4) << 100.0*det->ysize() << " "
<< " 0.2000 "
<< std::setw(6) << std::right << std::fixed << std::setprecision(2) << 100.0*detd << " "
<< std::setw(9) << std::right << std::fixed << std::setprecision(4) << 100.0*center.X() << " "
<< std::setw(9) << std::right << std::fixed << std::setprecision(4) << 100.0*center.Y() << " "
<< std::setw(9) << std::right << std::fixed << std::setprecision(4) << 100.0*center.Z() << " "
<< std::setw(8) << std::right << std::fixed << std::setprecision(5) << base.X() << " "
<< std::setw(8) << std::right << std::fixed << std::setprecision(5) << base.Y() << " "
<< std::setw(8) << std::right << std::fixed << std::setprecision(5) << base.Z() << " "
<< std::setw(8) << std::right << std::fixed << std::setprecision(5) << up.X() << " "
<< std::setw(8) << std::right << std::fixed << std::setprecision(5) << up.Y() << " "
<< std::setw(8) << std::right << std::fixed << std::setprecision(5) << up.Z() << " "
<< std::endl;
}
}
}
}
// ============================== Save all Peaks =========================================
// Sequence number
int seqNum = 1;
// Go in order of run numbers
runMap_t::iterator runMap_it;
for (runMap_it = runMap.begin(); runMap_it != runMap.end(); runMap_it++)
{
// Start of a new run
int run = runMap_it->first;
bankMap_t & bankMap = runMap_it->second;
bankMap_t::iterator bankMap_it;
for (bankMap_it = bankMap.begin(); bankMap_it != bankMap.end(); bankMap_it++)
{
// Start of a new bank.
int bank = bankMap_it->first;
std::vector<size_t> & ids = bankMap_it->second;
if (ids.size() > 0)
{
// Write the bank header
out << "0 NRUN DETNUM CHI PHI OMEGA MONCNT" << std::endl;
out << "1" << std::setw( 5 ) << run << std::setw( 7 ) <<
std::right << bank;
// Determine goniometer angles by calculating from the goniometer matrix of a peak in the list
Goniometer gon(peaks[ids[0]].getGoniometerMatrix());
std::vector<double> angles = gon.getEulerAngles("yzy");
double phi = angles[2];
double chi = angles[1];
double omega = angles[0];
out << std::setw( 7 ) << std::fixed << std::setprecision( 2 ) << chi << " ";
out << std::setw( 7 ) << std::fixed << std::setprecision( 2 ) << phi << " ";
out << std::setw( 7 ) << std::fixed << std::setprecision( 2 ) << omega << " ";
out << std::setw( 7 ) << (int)( 0 ) << std::endl;
out << header << std::endl;
// Go through each peak at this run / bank
for (size_t i=0; i < ids.size(); i++)
{
size_t wi = ids[i];
Peak & p = peaks[wi];
// Sequence (run) number
out << "3" << std::setw( 7 ) << seqNum;
// HKL is flipped by -1 due to different q convention in ISAW vs mantid.
out << std::setw( 5 ) << Utils::round(-p.getH())
<< std::setw( 5 ) << Utils::round(-p.getK())
<< std::setw( 5 ) << Utils::round(-p.getL());
// Row/column
out << std::setw( 8 ) << std::fixed << std::setprecision( 2 )
<< static_cast<double>(p.getCol()) << " ";
out << std::setw( 8 ) << std::fixed << std::setprecision( 2 )
<< static_cast<double>(p.getRow()) << " ";
out << std::setw( 8 ) << std::fixed << std::setprecision( 0 )
<< p.getTOF() << " ";
out << std::setw( 9 ) << std::fixed << std::setprecision( 3 )
<< (p.getL2()*100.0) << " ";
// This is the scattered beam direction
V3D dir = p.getDetPos() - inst->getSample()->getPos();
double scattering, azimuth;
// Two-theta = polar angle = scattering angle = between +Z vector and the scattered beam
scattering = dir.angle( V3D(0.0, 0.0, 1.0) );
// "Azimuthal" angle: project the beam onto the XY plane, and measure the angle between that and the +X axis (right-handed)
azimuth = atan2( dir.Y(), dir.X() );
out << std::setw( 9 ) << std::fixed << std::setprecision( 5 )
<< scattering << " "; //two-theta scattering
out << std::setw( 9 ) << std::fixed << std::setprecision( 5 )
<< azimuth << " ";
out << std::setw( 10 ) << std::fixed << std::setprecision( 6 )
<< p.getWavelength() << " ";
out << std::setw( 9 ) << std::fixed << std::setprecision( 4 )
<< p.getDSpacing() << " ";
out << std::setw( 8 ) << std::fixed << int(p.getBinCount()) << std::setw( 10 ) << " "
<< std::fixed << std::setprecision( 2 ) << p.getIntensity() << " ";
out << std::setw( 7 ) << std::fixed << std::setprecision( 2 )
<< p.getSigmaIntensity() << " ";
int thisReflag = 310;
out << std::setw( 5 ) << thisReflag;
out << std::endl;
// Count the sequence
seqNum++;
}
}
}
}
out.flush();
out.close();
// //REMOVE:
// std::string line;
// std::ifstream myfile (filename.c_str());
// if (myfile.is_open())
// {
// while ( myfile.good() )
// {
// getline (myfile,line);
// std::cout << line << std::endl;
// }
// myfile.close();
// }
}
/**
* Make a map of the conversion factors between tof and D-spacing
* for all pixel IDs in a workspace.
* map vulcan should contain the module/module and stack/stack offset
*
* @param vulcan :: map between detector ID and vulcan correction factor.
* @param offsetsWS :: OffsetsWorkspace to be filled.
*/
void LoadDspacemap::CalculateOffsetsFromVulcanFactors(
std::map<detid_t, double> &vulcan,
Mantid::DataObjects::OffsetsWorkspace_sptr offsetsWS) {
// Get a pointer to the instrument contained in the workspace
// At this point, instrument VULCAN has been created?
Instrument_const_sptr instrument = offsetsWS->getInstrument();
g_log.notice() << "Name of instrument = " << instrument->getName()
<< std::endl;
g_log.notice() << "Input map (dict): size = " << vulcan.size() << std::endl;
// To get all the detector ID's
detid2det_map allDetectors;
instrument->getDetectors(allDetectors);
detid2det_map::const_iterator it;
int numfinds = 0;
g_log.notice() << "Input number of detectors = " << allDetectors.size()
<< std::endl;
// Get detector information
double l1, beamline_norm;
Kernel::V3D beamline, samplePos;
instrument->getInstrumentParameters(l1, beamline, beamline_norm, samplePos);
/*** A survey of parent detector
std::map<detid_t, bool> parents;
for (it = allDetectors.begin(); it != allDetectors.end(); it++){
int32_t detid = it->first;
// def boost::shared_ptr<const Mantid::Geometry::IDetector>
IDetector_const_sptr;
std::string parentname =
it->second->getParent()->getComponentID()->getName();
g_log.notice() << "Name = " << parentname << std::endl;
// parents.insert(parentid, true);
}
***/
/*** Here some special configuration for VULCAN is hard-coded here!
* Including (1) Super-Parent Information
***/
Kernel::V3D referencePos;
detid_t anydetinrefmodule = 21 * 1250 + 5;
std::map<detid_t, Geometry::IDetector_const_sptr>::iterator det_iter =
allDetectors.find(anydetinrefmodule);
if (det_iter == allDetectors.end()) {
throw std::invalid_argument("Any Detector ID is Instrument's detector");
}
referencePos = det_iter->second->getParent()->getPos();
double refl2 = referencePos.norm();
double halfcosTwoThetaRef =
referencePos.scalar_prod(beamline) / (refl2 * beamline_norm);
double sinThetaRef = sqrt(0.5 - halfcosTwoThetaRef);
double difcRef = sinThetaRef * (l1 + refl2) / CONSTANT;
// Loop over all detectors in instrument to find the offset
for (it = allDetectors.begin(); it != allDetectors.end(); ++it) {
int detectorID = it->first;
Geometry::IDetector_const_sptr det = it->second;
double offset = 0.0;
// Find the vulcan factor;
double vulcan_factor = 0.0;
std::map<detid_t, double>::const_iterator vulcan_iter =
vulcan.find(detectorID);
if (vulcan_iter != vulcan.end()) {
vulcan_factor = vulcan_iter->second;
numfinds++;
}
// g_log.notice() << "Selected Detector with ID = " << detectorID << " ID2
// = " << id2 << std::endl; proved to be same
double intermoduleoffset = 0;
double interstackoffset = 0;
detid_t intermoduleid = detid_t(detectorID / 1250) * 1250 + 1250 - 2;
vulcan_iter = vulcan.find(intermoduleid);
if (vulcan_iter == vulcan.end()) {
g_log.error() << "Cannot find inter-module offset ID = " << intermoduleid
<< std::endl;
} else {
intermoduleoffset = vulcan_iter->second;
}
detid_t interstackid = detid_t(detectorID / 1250) * 1250 + 1250 - 1;
vulcan_iter = vulcan.find(interstackid);
if (vulcan_iter == vulcan.end()) {
g_log.error() << "Cannot find inter-module offset ID = " << intermoduleid
<< std::endl;
} else {
interstackoffset = vulcan_iter->second;
}
/*** This is the previous way to correct upon DIFC[module center pixel]
// The actual factor is 10^(-value_in_the_file)
vulcan_factor = pow(10.0,-vulcan_factor);
// At this point, tof_corrected = vulcan_factor * tof_input
// So this is the offset
offset = vulcan_factor - 1.0;
***/
/*** New approach to correct based on DIFC of each pixel
* Equation: offset = DIFC^(pixel)/DIFC^(parent)*(1+vulcan_offset)-1
* offset should be close to 0
***/
// 1. calculate DIFC
Kernel::V3D detPos;
detPos = det->getPos();
// Now detPos will be set with respect to samplePos
detPos -= samplePos;
double l2 = detPos.norm();
double halfcosTwoTheta =
detPos.scalar_prod(beamline) / (l2 * beamline_norm);
double sinTheta = sqrt(0.5 - halfcosTwoTheta);
double difc_pixel = sinTheta * (l1 + l2) / CONSTANT;
// Kernel::V3D parentPos = det->getParent()->getPos();
// parentPos -= samplePos;
// double l2parent = parentPos.norm();
// double halfcosTwoThetaParent = parentPos.scalar_prod(beamline)/(l2 *
// beamline_norm);
// double sinThetaParent = sqrt(0.5 - halfcosTwoThetaParent);
// double difc_parent = sinThetaParent*(l1+l2parent)/CONSTANT;
/*** Offset Replicate Previous Result
offset = difc_pixel/difc_parent*(pow(10.0, -vulcan_factor))-1.0;
***/
offset =
difc_pixel / difcRef * (pow(10.0, -(vulcan_factor + intermoduleoffset +
interstackoffset))) -
1.0;
// Save in the map
try {
offsetsWS->setValue(detectorID, offset);
if (intermoduleid != 27498 && intermoduleid != 28748 &&
intermoduleid != 29998 && intermoduleid != 33748 &&
intermoduleid != 34998 && intermoduleid != 36248) {
g_log.error() << "Detector ID = " << detectorID
<< " Inter-Module ID = " << intermoduleid << std::endl;
throw std::invalid_argument("Indexing error!");
}
} catch (std::invalid_argument &) {
g_log.notice() << "Misses Detector ID = " << detectorID << std::endl;
}
} // for
g_log.notice() << "Number of matched detectors =" << numfinds << std::endl;
}