From b44b0a56fbaa15d154db5ca1f2fb243199530b99 Mon Sep 17 00:00:00 2001
From: Filip Leonarski <filip.leonarski@psi.ch>
Date: Fri, 29 May 2026 12:01:58 +0200
Subject: [PATCH] RotationIndexer: For fixed space group, set explicitly
 lattice type and centering for refinement

---
 image_analysis/RotationIndexer.cpp | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/image_analysis/RotationIndexer.cpp b/image_analysis/RotationIndexer.cpp
index cd7a04ea..8ed00d83 100644
--- a/image_analysis/RotationIndexer.cpp
+++ b/image_analysis/RotationIndexer.cpp
@@ -73,9 +73,19 @@ void RotationIndexer::TryIndex() {
     }
 
     auto indexer_result = indexer_.Run(experiment, coords_sel);
-    if (!indexer_result.lattice.empty()) {
-        // Find lattice type
-        search_result_ = LatticeSearch(indexer_result.lattice[0]);
+    if (!indexer_result.lattice.empty() && indexer_result.lattice[0].CalcVolume() > 1.0) {
+        auto sg = experiment.GetGemmiSpaceGroup();
+        if (sg) {
+            search_result_ = LatticeSearchResult{
+                .niggli_class = 0, // Since Niggli class was not searched for, we don't know which one
+                .conventional = indexer_result.lattice[0], // If lattice provided, it is for now primitive == conventional
+                .system = sg->crystal_system(),
+                .centering = sg->centring_type(),
+            };
+        } else {
+            // Find lattice type based on cell
+            search_result_ = LatticeSearch(indexer_result.lattice[0]);
+        }
 
         // Run refinement
         DiffractionExperiment experiment_copy(experiment);
@@ -97,6 +107,7 @@ void RotationIndexer::TryIndex() {
 
         if (data.crystal_system == gemmi::CrystalSystem::Monoclinic)
             data.latt.ReorderMonoclinic();
+
         if (XtalOptimizer(data, v_sel)) {
             indexed_lattice = data.latt;
             updated_geom_ = data.geom;