ScaleAndMerge: clean-up (no log residual, no fixed mosaicity, return per-image values)

image_analysis/IndexAndRefine.cpp

@@ -17,6 +17,7 @@ IndexAndRefine::IndexAndRefine(const DiffractionExperiment &x, IndexerThreadPool
       indexer_(indexer) {
     if (indexer && x.IsRotationIndexing())
         rotation_indexer = std::make_unique<RotationIndexer>(x, *indexer);
+    reflections.resize(x.GetImageNum());
 }
 
 IndexAndRefine::IndexingOutcome IndexAndRefine::DetermineLatticeAndSymmetry(DataMessage &msg) {
@@ -198,16 +199,15 @@ void IndexAndRefine::QuickPredictAndIntegrate(DataMessage &msg,
                   [](const Reflection& a, const Reflection& b) { return a.d < b.d; });
     }
 
+    {
+        std::unique_lock ul(reflections_mutex);
+        reflections[msg.number] = refl_ret; // Image is not processed twice, so thread-safe in principle, but better safe than sorry :)
+    }
+
     msg.reflections = std::move(refl_ret);
 
     CalcISigma(msg);
     CalcWilsonBFactor(msg);
-
-    // Append reflections to the class-wide reflections buffer (thread-safe)
-    {
-        std::unique_lock ul(reflections_mutex);
-        reflections.insert(reflections.end(), msg.reflections.begin(), msg.reflections.end());
-    }
 }
 
 void IndexAndRefine::ProcessImage(DataMessage &msg,
@@ -242,15 +242,13 @@ std::optional<RotationIndexerResult> IndexAndRefine::Finalize() {
 }
 
 std::optional<ScaleMergeResult> IndexAndRefine::ScaleRotationData(const ScaleMergeOptions &opts) const {
-    std::vector<Reflection> snapshot;
-    {
-        std::unique_lock ul(reflections_mutex);
-        snapshot = reflections;          // cheap copy under lock
-    }
+    size_t nrefl = 0;
+    for (const auto &i: reflections)
+        nrefl += i.size();
 
     // Need a reasonable number of reflections to make refinement meaningful
     constexpr size_t kMinReflections = 20;
-    if (snapshot.size() < kMinReflections)
+    if (nrefl < kMinReflections)
         return std::nullopt;
 
     // Build options focused on mosaicity refinement but allow caller override
@@ -267,5 +265,5 @@ std::optional<ScaleMergeResult> IndexAndRefine::ScaleRotationData(const ScaleMer
             options.space_group = *sg;
     }
 
-    return ScaleAndMergeReflectionsCeres(snapshot, options);
-}
+    return ScaleAndMergeReflectionsCeres(reflections, options);
+}