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Indexing improvements

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This commit is contained in:
leonarski_f
2024-04-20 13:41:41 +02:00
parent 876457e9c0
commit 4e8c3a88a7
56 changed files with 742 additions and 187 deletions
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51
image_analysis/IndexerWrapper.cpp
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@@ -1,6 +1,7 @@
// Copyright (2019-2023) Paul Scherrer Institute
// Copyright (2019-2024) Paul Scherrer Institute
#include "IndexerWrapper.h"
#define MAX_SPOT_COUNT_INDEXING 50
void IndexerWrapper::Setup(const UnitCell &cell) {
#ifdef JFJOCH_USE_CUDA
@@ -8,16 +9,18 @@ void IndexerWrapper::Setup(const UnitCell &cell) {
#endif
}
std::vector<IndexingResult> IndexerWrapper::Run(const std::vector<Coord> &coord) {
std::vector<IndexingResult> IndexerWrapper::Run(const std::vector<Coord> &coord, float indexing_threshold) {
#ifdef JFJOCH_USE_CUDA
std::vector<IndexingResult> ret;
if (coord.size() <= min_spots)
return ret;
size_t nspots = std::min<size_t>(MAX_SPOT_COUNT, coord.size());
assert(coord.size() < MAX_SPOT_COUNT);
for (int i = 0; i < nspots; i++) {
size_t nspots = std::min<size_t>(MAX_SPOT_COUNT_INDEXING, coord.size());
for (int i = 0; i < coord.size(); i++) {
indexer.spotX(i) = coord[i].x;
indexer.spotY(i) = coord[i].y;
indexer.spotZ(i) = coord[i].z;
@@ -26,28 +29,40 @@ std::vector<IndexingResult> IndexerWrapper::Run(const std::vector<Coord> &coord)
// Index
indexer.index(1, nspots);
fast_feedback::refine::indexer_ifssr<float>::refine(indexer.spotM().topRows(coord.size()),
indexer.oCellM(),
indexer.oScoreV(),
fast_feedback::refine::config_ifssr<float>{});
// Find cell most similar to the current one
for (unsigned i=0u; i<cpers.max_output_cells; i++)
indexer.oScore(i) += fast_feedback::refine::cell_similarity(indexer.oCell(i), indexer.iCell(0), 0.02f);
// Get best cell
auto id = fast_feedback::refine::best_cell(indexer.oScoreV());
// get indexed spots
using M3x = Eigen::MatrixX3<float>;
M3x resid = indexer.Spots() * indexer.oCell(id).transpose();
const M3x miller = round(resid.array());
resid -= miller;
auto arr = resid.rowwise().norm().array() < threshold;
auto indexed_spot_count = arr.count();
bool indexed = fast_feedback::refine::is_viable_cell(indexer.oCell(id), indexer.Spots(), indexing_threshold, 9);
// Check if result is viable
if (indexed_spot_count > min_spots) {
if (indexed) {
auto cell = indexer.oCell(id).colwise().reverse();
fast_feedback::refine::make_right_handed(cell);
// get indexed spots
using M3x = Eigen::MatrixX3<float>;
M3x resid = indexer.spotM().topRows(coord.size()) * cell.transpose();
const M3x miller = round(resid.array());
const M3x predicted = miller * cell.transpose().inverse();
IndexingResult result;
result.l = CrystalLattice(indexer.oCell(id));
result.l = CrystalLattice(cell);
result.indexed_spots.resize(coord.size());
for (int i = 0; i < arr.size(); i++)
result.indexed_spots[i] = arr[i];
result.predicted_spots.resize(coord.size());
result.indexed_spots_count = indexed_spot_count;
for (int i = 0; i < coord.size(); i++)
result.predicted_spots[i] = Coord(predicted.coeff(i, 0),
predicted.coeff(i, 1),
predicted.coeff(i, 2));
ret.emplace_back(result);
}