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IndexAndRefine: Use mosaicity from indexing for scaling

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This commit is contained in:
leonarski_f
2026-02-20 13:18:16 +01:00
parent 203eefca66
commit c33366f3d6
3 changed files with 18 additions and 16 deletions
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9
image_analysis/IndexAndRefine.cpp
View File

@@ -18,6 +18,7 @@ IndexAndRefine::IndexAndRefine(const DiffractionExperiment &x, IndexerThreadPool
if (indexer && x.IsRotationIndexing())
rotation_indexer = std::make_unique<RotationIndexer>(x, *indexer);
reflections.resize(x.GetImageNum());
mosaicity.resize(x.GetImageNum(), NAN);
}
IndexAndRefine::IndexingOutcome IndexAndRefine::DetermineLatticeAndSymmetry(DataMessage &msg) {
@@ -167,8 +168,10 @@ void IndexAndRefine::QuickPredictAndIntegrate(DataMessage &msg,
if (experiment.GetGoniometer().has_value()) {
wedge_deg = experiment.GetGoniometer()->GetWedge_deg() / 2.0;
if (msg.mosaicity_deg)
if (msg.mosaicity_deg) {
mos_deg = msg.mosaicity_deg.value();
mosaicity[msg.number] = mos_deg;
}
}
const BraggPredictionSettings settings_prediction{
@@ -255,8 +258,10 @@ std::optional<ScaleMergeResult> IndexAndRefine::ScaleRotationData(const ScaleMer
ScaleMergeOptions options = opts;
// If the experiment provides a wedge, propagate it
if (experiment.GetGoniometer().has_value())
if (experiment.GetGoniometer().has_value()) {
options.wedge_deg = experiment.GetGoniometer()->GetWedge_deg();
options.mosaicity_init_deg_vec = mosaicity;
}
// If caller left space_group unset, try to pick it from the indexed lattice
if (!options.space_group.has_value()) {

1
image_analysis/IndexAndRefine.h
View File

@@ -46,6 +46,7 @@ class IndexAndRefine {
mutable std::mutex reflections_mutex;
std::vector<std::vector<Reflection>> reflections;
std::vector<double> mosaicity;
IndexingOutcome DetermineLatticeAndSymmetry(DataMessage &msg);
void RefineGeometryIfNeeded(DataMessage &msg, IndexingOutcome &outcome);

24
image_analysis/scale_merge/ScaleAndMerge.cpp
View File

@@ -214,8 +214,6 @@ ScaleMergeResult ScaleAndMergeReflectionsCeres(const std::vector<std::vector<Ref
size_t n_image_slots = observations.size() / opt.image_cluster + (observations.size() % opt.image_cluster > 0 ? 1 : 0);
std::vector<double> g(n_image_slots, 1.0);
std::vector<double> mosaicity(n_image_slots, opt.mosaicity_init_deg);
std::vector<uint8_t> image_slot_used(n_image_slots, 0);
for (int i = 0; i < observations.size(); i++) {
@@ -262,17 +260,20 @@ ScaleMergeResult ScaleAndMergeReflectionsCeres(const std::vector<std::vector<Ref
}
}
const int nhkl = static_cast<int>(hklToSlot.size());
std::vector<double> Itrue(nhkl, 0.0);
std::vector<double> g(n_image_slots, 1.0);
std::vector<double> mosaicity(n_image_slots, opt.mosaicity_init_deg);
for (int i = 0; i < n_image_slots; i++) {
if (!image_slot_used[i]) {
mosaicity[i] = NAN;
g[i] = NAN;
} else if (opt.mosaicity_init_deg_vec.size() > i && std::isfinite(opt.mosaicity_init_deg_vec[i])) {
mosaicity[i] = opt.mosaicity_init_deg_vec[i];
}
}
const int nhkl = static_cast<int>(hklToSlot.size());
std::vector<double> Itrue(nhkl, 0.0);
// Initialize Itrue from per-HKL median of observed intensities
{
std::vector<std::vector<double> > per_hkl_I(nhkl);
@@ -305,6 +306,7 @@ ScaleMergeResult ScaleAndMergeReflectionsCeres(const std::vector<std::vector<Ref
&Itrue[o.hkl_slot]);
is_valid_hkl_slot[o.hkl_slot] = true;
}
for (int i = 0; i < g.size(); ++i) {
if (image_slot_used[i]) {
auto *cost = new ceres::AutoDiffCostFunction<ScaleRegularizationResidual, 1, 1>(
@@ -320,10 +322,7 @@ ScaleMergeResult ScaleAndMergeReflectionsCeres(const std::vector<std::vector<Ref
auto *cost = new ceres::AutoDiffCostFunction<SmoothnessRegularizationResidual, 1, 1, 1, 1>(
new SmoothnessRegularizationResidual(0.05));
problem.AddResidualBlock(cost, nullptr,
&g[i],
&g[i + 1],
&g[i + 2]);
problem.AddResidualBlock(cost, nullptr, &g[i], &g[i + 1], &g[i + 2]);
}
}
}
@@ -334,10 +333,7 @@ ScaleMergeResult ScaleAndMergeReflectionsCeres(const std::vector<std::vector<Ref
auto *cost = new ceres::AutoDiffCostFunction<SmoothnessRegularizationResidual, 1, 1, 1, 1>(
new SmoothnessRegularizationResidual(0.05));
problem.AddResidualBlock(cost, nullptr,
&mosaicity[i],
&mosaicity[i + 1],
&mosaicity[i + 2]);
problem.AddResidualBlock(cost, nullptr, &mosaicity[i], &mosaicity[i + 1], &mosaicity[i + 2]);
}
}
}