IndexAndRefine: Reorder monoclinic cell

image_analysis/IndexAndRefine.cpp

@@ -83,8 +83,6 @@ IndexAndRefine::IndexingOutcome IndexAndRefine::DetermineLatticeAndSymmetry(Data
         };
         outcome.lattice_candidate = sym_result.conventional;
 
-        if (sym_result.system == gemmi::CrystalSystem::Monoclinic)
-            outcome.lattice_candidate->ReorderMonoclinic();
     }
 
     return outcome;
@@ -128,6 +126,9 @@ void IndexAndRefine::RefineGeometryIfNeeded(DataMessage &msg, IndexAndRefine::In
 
     outcome.lattice_candidate = data.latt;
 
+    if (outcome.symmetry.crystal_system == gemmi::CrystalSystem::Monoclinic)
+        outcome.lattice_candidate->ReorderMonoclinic();
+
     if (outcome.beam_center_updated) {
         msg.beam_corr_x = data.beam_corr_x;
         msg.beam_corr_y = data.beam_corr_y;

image_analysis/RotationIndexer.cpp

@@ -76,8 +76,8 @@ void RotationIndexer::TryIndex() {
     if (!indexer_result.lattice.empty()) {
         // Find lattice type
         search_result_ = LatticeSearch(indexer_result.lattice[0]);
-        // Run refinement
 
+        // Run refinement
         DiffractionExperiment experiment_copy(experiment);
         XtalOptimizerData data{
             .geom = experiment_copy.GetDiffractionGeometry(),
@@ -95,6 +95,8 @@ void RotationIndexer::TryIndex() {
         if (data.crystal_system == gemmi::CrystalSystem::Trigonal)
             data.crystal_system = gemmi::CrystalSystem::Hexagonal;
 
+        if (data.crystal_system == gemmi::CrystalSystem::Monoclinic)
+            data.latt.ReorderMonoclinic();
         if (XtalOptimizer(data, v_sel)) {
             indexed_lattice = data.latt;
             updated_geom_ = data.geom;
@@ -132,6 +134,7 @@ std::optional<RotationIndexerResult> RotationIndexer::ProcessImage(int64_t image
     }
     if (!indexed_lattice)
         return {};
+
     return RotationIndexerResult{
         .lattice = indexed_lattice.value(),
         .search_result = search_result_,