bool FindUBUsingIndexedPeaks::isPeakIndexed(Peak &peak) {
V3D hkl(peak.getIntHKL()); // ##### KEEP
V3D mnp(peak.getIntMNP());
return (IndexingUtils::ValidIndex(hkl, 1.0) ||
IndexingUtils::ValidIndex(mnp, 1.0));
}
/** Execute the algorithm.
*/
void FindUBUsingIndexedPeaks::exec()
{
PeaksWorkspace_sptr ws;
ws = boost::dynamic_pointer_cast<PeaksWorkspace>(
AnalysisDataService::Instance().retrieve(this->getProperty("PeaksWorkspace")) );
if (!ws)
{
throw std::runtime_error("Could not read the peaks workspace");
}
std::vector<Peak> peaks = ws->getPeaks();
size_t n_peaks = ws->getNumberPeaks();
std::vector<V3D> q_vectors;
std::vector<V3D> hkl_vectors;
q_vectors.reserve( n_peaks );
hkl_vectors.reserve( n_peaks );
size_t indexed_count = 0;
for ( size_t i = 0; i < n_peaks; i++ )
{
V3D hkl( peaks[i].getH(), peaks[i].getK(), peaks[i].getL() ); // ##### KEEP
if ( IndexingUtils::ValidIndex( hkl, 1.0 ) ) // use tolerance == 1 to
// just check for (0,0,0)
{
q_vectors.push_back( peaks[i].getQSampleFrame() );
V3D miller_ind( round(hkl[0]), round(hkl[1]), round(hkl[2]) );
hkl_vectors.push_back( V3D(miller_ind) );
indexed_count++;
}
}
if ( indexed_count < 3 )
{
throw std::runtime_error(
"At least three linearly independent indexed peaks are needed.");
}
Matrix<double> UB(3,3,false);
double error = IndexingUtils::Optimize_UB( UB, hkl_vectors, q_vectors );
std::cout << "Error = " << error << std::endl;
std::cout << "UB = " << UB << std::endl;
if ( ! IndexingUtils::CheckUB( UB ) ) // UB not found correctly
{
g_log.notice( std::string(
"Found Invalid UB...peaks used might not be linearly independent") );
g_log.notice( std::string(
"UB NOT SAVED.") );
}
else // tell user how many would be indexed
{ // from the full list of peaks, and
q_vectors.clear(); // save the UB in the sample
q_vectors.reserve( n_peaks );
for ( size_t i = 0; i < n_peaks; i++ )
{
q_vectors.push_back( peaks[i].getQSampleFrame() );
}
double tolerance = 0.1;
int num_indexed = IndexingUtils::NumberIndexed(UB, q_vectors, tolerance);
char logInfo[200];
sprintf( logInfo,
std::string("New UB will index %1d Peaks out of %1d with tolerance %5.3f").c_str(),
num_indexed, n_peaks, tolerance);
g_log.notice( std::string(logInfo) );
OrientedLattice o_lattice;
o_lattice.setUB( UB );
double calc_a = o_lattice.a();
double calc_b = o_lattice.b();
double calc_c = o_lattice.c();
double calc_alpha = o_lattice.alpha();
double calc_beta = o_lattice.beta();
double calc_gamma = o_lattice.gamma();
// Show the modified lattice parameters
sprintf( logInfo,
std::string("Lattice Parameters: %8.3f %8.3f %8.3f %8.3f %8.3f %8.3f").c_str(),
calc_a, calc_b, calc_c, calc_alpha, calc_beta, calc_gamma);
g_log.notice( std::string(logInfo) );
ws->mutableSample().setOrientedLattice( new OrientedLattice(o_lattice) );
}
}