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#include "MantidCrystal/IndexPeaks.h"
#include "MantidDataObjects/PeaksWorkspace.h"
#include "MantidGeometry/Crystal/IndexingUtils.h"
#include "MantidGeometry/Crystal/OrientedLattice.h"
#include "MantidKernel/BoundedValidator.h"
#include "MantidAPI/Sample.h"
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namespace Crystal {
// Register the algorithm into the AlgorithmFactory
DECLARE_ALGORITHM(IndexPeaks)
using namespace Mantid::Kernel;
using namespace Mantid::API;
using namespace Mantid::DataObjects;
using namespace Mantid::Geometry;
/** Initialize the algorithm's properties.
*/
void IndexPeaks::init() {
this->declareProperty(make_unique<WorkspaceProperty<PeaksWorkspace>>(
"PeaksWorkspace", "", Direction::InOut),
"Input Peaks Workspace");
auto mustBePositive = boost::make_shared<BoundedValidator<double>>();
mustBePositive->setLower(0.0);
this->declareProperty(
make_unique<PropertyWithValue<double>>("Tolerance", 0.15, mustBePositive,
Direction::Input),
"Indexing Tolerance (0.15)");
this->declareProperty("RoundHKLs", true,
"Round H, K and L values to integers");
this->declareProperty("CommonUBForAll", false,
"Index all orientations with a common UB");
this->declareProperty(
make_unique<PropertyWithValue<double>>("ToleranceForSatellite", 0.1,
mustBePositive, Direction::Input),
"Satellite Indexing Tolerance (0.1)");
this->declareProperty(
make_unique<PropertyWithValue<int>>("NumIndexed", 0, Direction::Output),
"Gets set with the number of indexed peaks.");
this->declareProperty(make_unique<PropertyWithValue<double>>(
"AverageError", 0.0, Direction::Output),
"Gets set with the average HKL indexing error.");
this->declareProperty(make_unique<PropertyWithValue<int>>("TotalNumIndexed", 0, Direction::Output),
"Gets set with the number of Total indexed peaks.");
this->declareProperty(make_unique<PropertyWithValue<int>>("MainNumIndexed", 0, Direction::Output),
"Gets set with the number of indexed main peaks.");
this->declareProperty(make_unique<PropertyWithValue<int>>("SateNumIndexed", 0, Direction::Output),
"Gets set with the number of indexed main peaks.");
this->declareProperty(make_unique<PropertyWithValue<double>>("MainError", 0.0, Direction::Output),
"Gets set with the average HKL indexing error of Main Peaks.");
this->declareProperty(make_unique<PropertyWithValue<double>>("SatelliteError", 0.0, Direction::Output),
"Gets set with the average HKL indexing error of Satellite Peaks.");
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/** Execute the algorithm.
*/
void IndexPeaks::exec() {
PeaksWorkspace_sptr ws = this->getProperty("PeaksWorkspace");
if (!ws)
{
throw std::runtime_error("Could not read the peaks workspace");
}
OrientedLattice o_lattice = ws->mutableSample().getOrientedLattice();
const Matrix<double> &UB = o_lattice.getUB();
if (!IndexingUtils::CheckUB(UB))
{
throw std::runtime_error(
"ERROR: The stored UB is not a valid orientation matrix");
}
bool round_hkls = this->getProperty("RoundHKLs");
bool commonUB = this->getProperty("CommonUBForAll");
std::vector<Peak> &peaks = ws->getPeaks();
size_t n_peaks = ws->getNumberPeaks();
int total_indexed = 0;
int total_main = 0;
int total_sate = 0;
double average_error;
double average_main_error;
double average_sate_error;
double tolerance = this->getProperty("Tolerance");
if (commonUB)
{
std::vector<V3D> miller_indices;
std::vector<V3D> q_vectors;
q_vectors.reserve(n_peaks);
for (size_t i = 0; i < n_peaks; i++) {
q_vectors.push_back(peaks[i].getQSampleFrame());
}
total_indexed = IndexingUtils::CalculateMillerIndices(
UB, q_vectors, tolerance, miller_indices, average_error);
for (size_t i = 0; i < n_peaks; i++)
{
peaks[i].setHKL(miller_indices[i]);
peaks[i].setIntHKL(V3D(round(miller_indices[i][0]),round(miller_indices[i][1]),round(miller_indices[i][2])));
peaks[i].setIntMNP(V3D(0,0,0));
}
}
else
{
double total_error = 0;
double total_main_error = 0;
double total_sate_error = 0;
double satetolerance = this->getProperty("ToleranceForSatellite");
// get list of run numbers in this peaks workspace
std::vector<int> run_numbers;
for (size_t i = 0; i < n_peaks; i++)
{
int run = peaks[i].getRunNumber();
bool found = false;
size_t k = 0;
while (k < run_numbers.size() && !found)
{
if (run == run_numbers[k])
found = true;
else
k++;
}
if (!found)
run_numbers.push_back(run);
}
// index the peaks for each run separately, using a UB matrix optimized for
// that run
for (size_t run_index = 0; run_index < run_numbers.size(); run_index++) {
std::vector<V3D> miller_indices;
std::vector<V3D> q_vectors;
int run = run_numbers[run_index];
for (size_t i = 0; i < n_peaks; i++) {
if (peaks[i].getRunNumber() == run)
q_vectors.push_back(peaks[i].getQSampleFrame());
}
Matrix<double> tempUB(UB);
int num_indexed = 0;
int original_indexed = 0;
double original_error = 0;
original_indexed = IndexingUtils::CalculateMillerIndices(
tempUB, q_vectors, tolerance, miller_indices, original_error);
IndexingUtils::RoundHKLs(miller_indices); // HKLs must be rounded for
// Optimize_UB to work
num_indexed = original_indexed;
average_error = original_error;
bool done = false;
if (num_indexed < 3) // can't optimize without at least 3
{ // peaks
done = true;
}
int iteration = 0;
while (iteration < 4 && !done) // try repeatedly optimizing 4 times
{ // which is usually sufficient
try {
IndexingUtils::Optimize_UB(tempUB, miller_indices, q_vectors);
} catch (...) // If there is any problem, such as too few
{ // independent peaks, just use the original UB
tempUB = UB;
done = true;
}
num_indexed = IndexingUtils::CalculateMillerIndices(
tempUB, q_vectors, tolerance, miller_indices, average_error);
IndexingUtils::RoundHKLs(miller_indices); // HKLs must be rounded for
// Optimize_UB to work
if (num_indexed < original_indexed) // just use the original UB
{
num_indexed = original_indexed;
average_error = original_error;
done = true;
}
iteration++;
}
g_log.notice() << "Maximum Order: " << o_lattice.getMaxOrder() << '\n';
if (!round_hkls && o_lattice.getMaxOrder() == 0) // If data not modulated, recalculate fractional HKL
{
num_indexed = IndexingUtils::CalculateMillerIndices(
tempUB, q_vectors, tolerance, miller_indices, average_error);
total_indexed += num_indexed;
total_error += average_error * num_indexed;
// tell the user how many were indexed in each run
if (run_numbers.size() > 1)
{
g_log.notice() << "Run " << run << ": indexed " << num_indexed
<< " Peaks out of " << q_vectors.size()
<< " with tolerance of " << tolerance << '\n';
g_log.notice() << "Average error in h,k,l for indexed peaks = "
<< average_error << '\n';
}
size_t miller_index_counter = 0;
for (size_t i = 0; i < n_peaks; i++)
{
if (peaks[i].getRunNumber() == run)
{
peaks[i].setHKL(miller_indices[miller_index_counter]);
peaks[i].setIntHKL(V3D(round(miller_indices[miller_index_counter][0]),round(miller_indices[miller_index_counter][1]),round(miller_indices[miller_index_counter][2])));
peaks[i].setIntMNP(V3D(0,0,0));
miller_index_counter++;
}
}
}
else
{
int ModDim = 0;
int main_indexed = 0;
int sate_indexed = 0;
double main_error = 0;
double sate_error = 0;
int maxOrder = o_lattice.getMaxOrder();
bool CT = o_lattice.getCrossTerm();
V3D offsets1 = o_lattice.getModVec(1);
V3D offsets2 = o_lattice.getModVec(2);
V3D offsets3 = o_lattice.getModVec(3);
if (offsets1 == V3D(0,0,0))
throw std::runtime_error("Invalid Modulation Vector");
else if (offsets2 == V3D(0,0,0))
ModDim = 1;
else if (offsets3 == V3D(0,0,0))
ModDim = 2;
else
ModDim = 3;
IndexingUtils::CalculateMillerIndices(tempUB, q_vectors, 1.0, miller_indices, average_error);
// Index satellite peaks
size_t miller_index_counter = 0;
for (size_t i = 0; i < n_peaks; i++)
{
if (peaks[i].getRunNumber() == run)
{
peaks[i].setHKL(miller_indices[miller_index_counter]);
miller_index_counter++;
V3D hkl;
hkl[0] = peaks[i].getH();
hkl[1] = peaks[i].getK();
hkl[2] = peaks[i].getL();
double h_error;
double k_error;
double l_error;
if (IndexingUtils::ValidIndex(hkl, tolerance))
{
peaks[i].setIntHKL(hkl);
peaks[i].setIntMNP(V3D(0, 0, 0));
main_indexed++;
h_error = fabs(round(hkl[0]) - hkl[0]);
k_error = fabs(round(hkl[1]) - hkl[1]);
l_error = fabs(round(hkl[2]) - hkl[2]);
main_error += h_error + k_error + l_error;
}
else if (!CT)
{
if (ModDim > 0)
{
for (int order = -maxOrder; order <= maxOrder; order++) {
if (order == 0)
continue; // exclude order 0
V3D hkl1(hkl);
hkl1[0] -= order * offsets1[0];
hkl1[1] -= order * offsets1[1];
hkl1[2] -= order * offsets1[2];
if (IndexingUtils::ValidIndex(hkl1, satetolerance)) {
peaks[i].setIntHKL(hkl1);
peaks[i].setIntMNP(V3D(order, 0, 0));
sate_indexed++;
h_error = fabs(round(hkl1[0]) - hkl1[0]);
k_error = fabs(round(hkl1[1]) - hkl1[1]);
l_error = fabs(round(hkl1[2]) - hkl1[2]);
sate_error += h_error + k_error + l_error;
}
}
}
if (ModDim > 1)
{
for (int order = -maxOrder; order <= maxOrder; order++) {
if (order == 0)
continue; // exclude order 0
V3D hkl1(hkl);
hkl1[0] -= order * offsets2[0];
hkl1[1] -= order * offsets2[1];
hkl1[2] -= order * offsets2[2];
if (IndexingUtils::ValidIndex(hkl1, satetolerance)) {
peaks[i].setIntHKL(hkl1);
peaks[i].setIntMNP(V3D(0, order, 0));
sate_indexed++;
h_error = fabs(round(hkl1[0]) - hkl1[0]);
k_error = fabs(round(hkl1[1]) - hkl1[1]);
l_error = fabs(round(hkl1[2]) - hkl1[2]);
sate_error += h_error + k_error + l_error;
}
}
}
if (ModDim > 2)
{
for (int order = -maxOrder; order <= maxOrder; order++) {
if (order == 0)
continue; // exclude order 0
V3D hkl1(hkl);
hkl1[0] -= order * offsets3[0];
hkl1[1] -= order * offsets3[1];
hkl1[2] -= order * offsets3[2];
if (IndexingUtils::ValidIndex(hkl1, satetolerance)) {
peaks[i].setIntHKL(hkl1);
peaks[i].setIntMNP(V3D(0, 0, order));
sate_indexed++;
h_error = fabs(round(hkl1[0]) - hkl1[0]);
k_error = fabs(round(hkl1[1]) - hkl1[1]);
l_error = fabs(round(hkl1[2]) - hkl1[2]);
sate_error += h_error + k_error + l_error;
}
}
}
}
else
{
if (ModDim == 1)
{
for (int order = -maxOrder; order <= maxOrder; order++) {
if (order == 0)
continue; // exclude order 0
V3D hkl1(hkl);
hkl1[0] -= order * offsets1[0];
hkl1[1] -= order * offsets1[1];
hkl1[2] -= order * offsets1[2];
if (IndexingUtils::ValidIndex(hkl1, satetolerance)) {
peaks[i].setIntHKL(hkl1);
peaks[i].setIntMNP(V3D(order, 0, 0));
sate_indexed++;
h_error = fabs(round(hkl1[0]) - hkl1[0]);
k_error = fabs(round(hkl1[1]) - hkl1[1]);
l_error = fabs(round(hkl1[2]) - hkl1[2]);
sate_error += h_error + k_error + l_error;
}
}
}
if (ModDim == 2)
{
for (int m = -maxOrder; m <= maxOrder; m++)
for (int n = -maxOrder; m <= maxOrder; n++)
{
if (m==0 && n==0)
continue; // exclude 0,0
V3D hkl1(hkl);
hkl1[0] -= m * offsets1[0] + n * offsets2[0];
hkl1[1] -= m * offsets1[1] + n * offsets2[1];
hkl1[2] -= m * offsets1[2] + n * offsets2[2];
if (IndexingUtils::ValidIndex(hkl1, satetolerance))
{
peaks[i].setIntHKL(hkl1);
peaks[i].setIntMNP(V3D(m, n, 0));
sate_indexed++;
h_error = fabs(round(hkl1[0]) - hkl1[0]);
k_error = fabs(round(hkl1[1]) - hkl1[1]);
l_error = fabs(round(hkl1[2]) - hkl1[2]);
sate_error += h_error + k_error + l_error;
}
}
}
if (ModDim == 3)
{
for (int m = -maxOrder; m <= maxOrder; m++)
for (int n = -maxOrder; m <= maxOrder; n++)
for (int p = -maxOrder; m <= maxOrder; p++)
{
if (m==0 && n==0 && p==0)
continue; // exclude 0,0,0
V3D hkl1(hkl);
hkl1[0] -= m * offsets1[0] + n * offsets2[0] + p * offsets3[0];
hkl1[1] -= m * offsets1[1] + n * offsets2[1] + p * offsets3[1];
hkl1[2] -= m * offsets1[2] + n * offsets2[2] + p * offsets3[2];
if (IndexingUtils::ValidIndex(hkl1, satetolerance))
{
peaks[i].setIntHKL(hkl1);
peaks[i].setIntMNP(V3D(m, n, p));
sate_indexed++;
h_error = fabs(round(hkl1[0]) - hkl1[0]);
k_error = fabs(round(hkl1[1]) - hkl1[1]);
l_error = fabs(round(hkl1[2]) - hkl1[2]);
sate_error += h_error + k_error + l_error;
}
}
}
}
}
}
num_indexed = main_indexed + sate_indexed;
total_main += main_indexed;
total_sate += sate_indexed;
total_main_error += main_error/3;
total_sate_error += sate_error/3;
total_indexed += main_indexed + sate_indexed;
total_error += main_error/3 + sate_error/3;
if (run_numbers.size() > 1)
{
g_log.notice() << "Run " << run << ": indexed " << num_indexed
<< " Peaks out of " << q_vectors.size() << '\n';
g_log.notice() << "of which, " << main_indexed << " Main Bragg Peaks are indexed with tolerance of " << tolerance << ", " << sate_indexed << " Satellite Peaks are indexed with tolerance of " << satetolerance << '\n';
// g_log.notice() << "Average error in h,k,l for indexed main peaks = "
// << main_error << '\n';
// g_log.notice() << "Average error in h,k,l for indexed satellite peaks = "
// << sate_error << '\n';
}
}
}
if (total_indexed > 0)
average_error = total_error / total_indexed;
else
average_error = 0;
if (total_main > 0)
average_main_error = total_main_error / total_main;
else
average_main_error = 0;
if (total_sate > 0)
average_sate_error = total_sate_error / total_sate;
else
average_sate_error = 0;
}
if (o_lattice.getMaxOrder() == 0 || commonUB)
{
// tell the user how many were indexed overall and the overall average error
g_log.notice() << "ALL Runs: indexed " << total_indexed << " Peaks out of "
<< n_peaks << " with tolerance of " << tolerance << '\n';
g_log.notice() << "Average error in h,k,l for indexed peaks = "
<< average_error << '\n';
// Save output properties
this->setProperty("NumIndexed", total_indexed);
this->setProperty("AverageError", average_error);
// Show the lattice parameters
g_log.notice() << o_lattice << "\n";
}
else
{
g_log.notice() << "ALL Runs: indexed " << total_indexed << " Peaks out of "
<< n_peaks << " with tolerance of " << tolerance << '\n';
g_log.notice() << "Out of " << total_indexed << " Indexed Peaks "
<< total_main << " are Main Bragg Peaks, and "
<< total_sate << " are satellite peaks " << '\n';
g_log.notice() << "Average error in h,k,l for indexed peaks = "
<< average_error << '\n';
g_log.notice() << "Average error in h,k,l for indexed main peaks = "
<< average_main_error << '\n';
g_log.notice() << "Average error in h,k,l for indexed satellite peaks = "
<< average_sate_error << '\n';
// Save output properties
setProperty("TotalNumIndexed", total_indexed);
setProperty("MainNumIndexed", total_main);
setProperty("SateNumIndexed", total_sate);
setProperty("MainError", average_main_error);
setProperty("SatelliteError", average_sate_error);
// Show the lattice parameters
g_log.notice() << o_lattice << "\n";
}
} // namespace Mantid
} // namespace Crystal