v1.0.0-rc.148 (#58)

This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144.

* jfjoch_broker: Improve azimuthal integration (add <I^2> calculation)
* jfjoch_broker: Fixes around indexing, aiming to handle multi-lattice crystals (work in progress, it is not fully integrated)
* jfjoch_writer: Save mean(I), stddev(I), and count(I) for each azimuthal bin

Reviewed-on: #58

image_analysis/IndexAndRefine.cpp

@@ -8,6 +8,7 @@
 #include "geom_refinement/XtalOptimizer.h"
 #include "indexing/AnalyzeIndexing.h"
 #include "indexing/FFTIndexer.h"
+#include "indexing/MultiLatticeSearch.h"
 #include "lattice_search/LatticeSearch.h"
 #include "scale_merge/ScaleOnTheFly.h"
 
@@ -56,7 +57,12 @@ IndexAndRefine::IndexingOutcome IndexAndRefine::DetermineLatticeAndSymmetryRotat
         auto gon = result->axis;
         if (gon) {
             const float angle_deg = gon->GetAngle_deg(msg.number) + gon->GetWedge_deg() / 2.0f;
-            outcome.lattice_candidate = result->lattice.Multiply(gon->GetTransformationAngle(-angle_deg));
+            const auto rot_to_image = gon->GetTransformationAngle(-angle_deg);
+            outcome.lattice_candidate = result->lattice.Multiply(rot_to_image);
+
+            outcome.extra_lattice_candidates.reserve(result->extra_lattices.size());
+            for (const auto &el : result->extra_lattices)
+                outcome.extra_lattice_candidates.push_back(el.Multiply(rot_to_image));
         }
 
         outcome.experiment.BeamX_pxl(result->geom.GetBeamX_pxl())
@@ -113,6 +119,22 @@ IndexAndRefine::IndexingOutcome IndexAndRefine::DetermineLatticeAndSymmetry(Data
                 };
                 outcome.lattice_candidate = sym_result.conventional;
             }
+
+            // Multi-lattice search for stills: store rotations that map the reference
+            // lattice to each accepted extra lattice. Candidates are materialized later
+            // in RefineGeometryIfNeeded so they're rooted in the refined (and, for
+            // monoclinic, reordered) main lattice.
+            if (indexer_result.lattice.size() > 1) {
+                auto ml_latt = MultiLatticeSearch(indexer_result.lattice);
+                for (auto &ml : ml_latt) {
+                    if (outcome.extra_lattice_rotations.size() >= experiment.GetIndexingSettings().GetMaxExtraLattices())
+                        break;
+                    outcome.extra_lattice_rotations.push_back(ml.rotation_vector);
+                    RotMatrix rot(ml.rotation_vector.Length(), ml.rotation_vector.Normalize());
+                    outcome.extra_lattice_candidates.push_back(outcome.lattice_candidate->Multiply(rot));
+                }
+            }
+
         }
     }
 
@@ -166,6 +188,39 @@ void IndexAndRefine::RefineGeometryIfNeeded(DataMessage &msg, IndexAndRefine::In
     if (outcome.symmetry.crystal_system == gemmi::CrystalSystem::Monoclinic)
         outcome.lattice_candidate->ReorderMonoclinic();
 
+    // Rebuild extra-lattice candidates from the refined (and possibly reordered) main
+    // lattice so they share its cell and obtuse-beta convention.
+    if (!outcome.extra_lattice_rotations.empty()) {
+        outcome.extra_lattice_candidates.clear();
+        outcome.extra_lattice_candidates.reserve(outcome.extra_lattice_rotations.size());
+        for (const auto &rv : outcome.extra_lattice_rotations) {
+            RotMatrix rot(rv.Length(), rv.Normalize());
+            outcome.extra_lattice_candidates.push_back(outcome.lattice_candidate->Multiply(rot));
+        }
+    }
+
+    // Quick orientation-only refinement of extra lattices (stills path).
+    // Cell, beam center, detector geometry are taken from the first lattice.
+    if (!experiment.IsRotationIndexing() && !outcome.extra_lattice_candidates.empty()) {
+        for (auto &el : outcome.extra_lattice_candidates) {
+            XtalOptimizerData data_extra{
+                .geom = data.geom,
+                .latt = el,
+                .crystal_system = data.crystal_system,
+                .min_spots = experiment.GetIndexingSettings().GetViableCellMinSpots(),
+                .refine_beam_center = false,
+                .refine_distance_mm = false,
+                .refine_detector_angles = false,
+                .refine_unit_cell = false,
+                .refine_rotation_axis = false,
+                .index_ice_rings = experiment.GetIndexingSettings().GetIndexIceRings(),
+                .max_time = 0.02
+            };
+            XtalOptimizerRotationOnly(data_extra, msg.spots, 0.1);
+            el = data_extra.latt;
+        }
+    }
+
     if (outcome.beam_center_updated) {
         msg.beam_corr_x = data.beam_corr_x;
         msg.beam_corr_y = data.beam_corr_y;
@@ -296,7 +351,7 @@ void IndexAndRefine::ProcessImage(DataMessage &msg,
     if (!outcome.lattice_candidate.has_value())
         return;
 
-    if (!AnalyzeIndexing(msg, outcome.experiment, *outcome.lattice_candidate))
+    if (!AnalyzeIndexing(msg, outcome.experiment, *outcome.lattice_candidate, outcome.extra_lattice_candidates))
         return;
 
     {
@@ -433,3 +488,8 @@ std::vector<IntegrationOutcome> &IndexAndRefine::GetIntegrationOutcome() {
 const std::vector<IntegrationOutcome> &IndexAndRefine::GetIntegrationOutcome() const {
     return integration_outcome;
 }
+
+void IndexAndRefine::ForceRotationIndexerLattice(const CrystalLattice &lattice) {
+    if (rotation_indexer)
+        rotation_indexer->ForceLattice(lattice);
+}