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Scaling: reference dataset, 3D combine (-P rot3d), R-meas, profile-fit integrator

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Reference dataset (a): LoadReferenceMtz adds column selection + cell/SG/resolution +
a data-vs-reference consistency check; jfjoch_process/jfjoch_scale gain
--reference-column; the viewer gets a Reference section in the MX settings dock
(worker-owned, independent of the loaded dataset) that flows into reprocessing jobs.

3D combine (-P rot3d): Combine3D weight-sums a reflection's per-frame partials into one
counting-limited full before merging (orthogonal ScalingSettings::combine_3d flag, not a
partiality model), with a de-biased Poisson variance. Crystal 2: ISa 1.7->8.4, R-meas
~67%->18.9%, intensities unchanged (CCref held).

Quality metrics (b): R-meas (Diederichs-Karplus) + redundancy columns in MergeStats; ISa
logged. jfjoch fulls 18.9% vs XDS 4.5% (same ASU/run).

Profile-fit integrator (experimental): ProfileIntegrate2D (--integrator gaussian|empirical)
is a reference-free, rot3d-compatible profile-fit extraction (the decomposed PixelRefine
intensity step). Gaussian: R-meas 18.9->14.6%, ISa ->9.5. Anisotropy/per-region add nothing
(the discriminating info is in the discarded rocking direction). See NEXTGEN_INTEGRATOR.md.
--dump-observations exports the unmerged fulls for XDS comparison.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
This commit is contained in:
leonarski_f
2026-06-25 20:43:04 +02:00
co-authored by Claude Opus 4.8
parent 6136f858af
commit e4b3064254
27 changed files with 1222 additions and 54 deletions
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process/JFJochProcess.cpp
+18 -3
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@@ -28,6 +28,7 @@
#include "../image_analysis/image_preprocessing/ImagePreprocessorBuffer.h"
#include "../image_analysis/scale_merge/Merge.h"
#include "../image_analysis/scale_merge/SearchSpaceGroup.h"
#include "../image_analysis/scale_merge/Combine3D.h"
#include "../image_analysis/WriteReflections.h"
namespace {
@@ -387,15 +388,29 @@ ProcessResult JFJochProcess::Run(JFJochProcessObserver *observer) {
}
}
// -P rot3d: weight-sum each reflection's per-frame partials into one full before merging, so
// the error model sees counting statistics (high ISa) instead of rocking-curve slicing scatter.
const bool rot3d = experiment_.GetScalingSettings().GetCombine3D();
std::vector<IntegrationOutcome> combined;
if (rot3d)
combined = CombineRotationObservations(indexer->GetIntegrationOutcome(), experiment_, &logger,
config_.observation_dump_path);
const std::vector<IntegrationOutcome> &merge_input =
rot3d ? combined : indexer->GetIntegrationOutcome();
MergeOnTheFly merge_engine(experiment_);
if (result.consensus_cell.has_value())
merge_engine.ReferenceCell(*result.consensus_cell);
merge_engine.RefineErrorModel(indexer->GetIntegrationOutcome());
for (const auto &outcome: indexer->GetIntegrationOutcome())
merge_engine.RefineErrorModel(merge_input);
if (merge_engine.ErrorModelActive())
logger.Info("Error model: a={:.3f} b={:.3f} ISa={:.1f}", merge_engine.ErrorModelA(),
merge_engine.ErrorModelB(),
merge_engine.ErrorModelB() > 0 ? 1.0 / merge_engine.ErrorModelB() : 0.0);
for (const auto &outcome: merge_input)
merge_engine.AddImage(outcome);
auto merged_reflections = merge_engine.ExportReflections();
auto merged_statistics = merge_engine.MergeStats(merged_reflections, indexer->GetIntegrationOutcome(),
auto merged_statistics = merge_engine.MergeStats(merged_reflections, merge_input,
config_.reference_data);
logger.Info("Merge complete ({} unique reflections)", merged_reflections.size());