/**
* Tries to refine the initial cell using the supplied peaks
*
* This method tries to refine the initial unit cell using the indexed peaks
* that are supplied in the PoldiPeakCollection. If there are unindexed peaks,
* the cell will not be refined at all, instead the unmodified initial cell
* is returned.
*
* @param initialCell :: String with the initial unit cell
* @param crystalSystem :: Crystal system name
* @param peakCollection :: Collection of bragg peaks, must be indexed
*
* @return String for refined unit cell
*/
std::string PoldiFitPeaks2D::getRefinedStartingCell(
const std::string &initialCell, const std::string &latticeSystem,
const PoldiPeakCollection_sptr &peakCollection) {
Geometry::UnitCell cell = Geometry::strToUnitCell(initialCell);
ILatticeFunction_sptr latticeFunction =
boost::dynamic_pointer_cast<ILatticeFunction>(
FunctionFactory::Instance().createFunction("LatticeFunction"));
latticeFunction->setLatticeSystem(latticeSystem);
latticeFunction->fix(latticeFunction->parameterIndex("ZeroShift"));
latticeFunction->setUnitCell(cell);
// Remove errors from d-values
PoldiPeakCollection_sptr clone = peakCollection->clone();
for (size_t i = 0; i < clone->peakCount(); ++i) {
PoldiPeak_sptr peak = clone->peak(i);
// If there are unindexed peaks, don't refine, just return the initial cell
if (peak->hkl() == MillerIndices()) {
return initialCell;
}
peak->setD(UncertainValue(peak->d().value()));
}
TableWorkspace_sptr peakTable = clone->asTableWorkspace();
IAlgorithm_sptr fit = createChildAlgorithm("Fit");
fit->setProperty("Function",
boost::static_pointer_cast<IFunction>(latticeFunction));
fit->setProperty("InputWorkspace", peakTable);
fit->setProperty("CostFunction", "Unweighted least squares");
fit->execute();
Geometry::UnitCell refinedCell = latticeFunction->getUnitCell();
return Geometry::unitCellToStr(refinedCell);
}
