IndexAndRefine: Fixes

image_analysis/IndexAndRefine.cpp

@@ -18,11 +18,10 @@ IndexAndRefine::IndexAndRefine(const DiffractionExperiment &x, IndexerThreadPool
       geom_(x.GetDiffractionGeometry()),
       updated_geom_(geom_),
       indexer_(indexer) {
-
     auto axis = x.GetGoniometer();
 
     if (indexer && axis && x.GetIndexingSettings().GetRotationIndexing()) {
-        float angle_norm_deg = std::fabs(axis_->GetIncrement_deg());
+        float angle_norm_deg = std::fabs(axis->GetIncrement_deg());
         if (angle_norm_deg > 1e-6) {
             axis_ = axis;
             if (x.GetImageNum() > min_images_for_indexing) {
@@ -108,9 +107,9 @@ void IndexAndRefine::TryIndexRotationData() {
 }
 
 void IndexAndRefine::ProcessImage(DataMessage &msg,
-                                   const SpotFindingSettings &spot_finding_settings,
-                                   const CompressedImage &image,
-                                   BraggPrediction &prediction) {
+                                  const SpotFindingSettings &spot_finding_settings,
+                                  const CompressedImage &image,
+                                  BraggPrediction &prediction) {
     if (!indexer_)
         return;
 
@@ -267,11 +266,12 @@ std::optional<RotationIndexerResult> IndexAndRefine::Finalize(bool retry) {
 
         if (!indexed_lattice || retry)
             TryIndexRotationData();
-        return RotationIndexerResult{
-            .lattice = indexed_lattice.value(),
-            .search_result = search_result_,
-            .geom = geom_
-        };
+        if (indexed_lattice)
+            return RotationIndexerResult{
+                .lattice = indexed_lattice.value(),
+                .search_result = search_result_,
+                .geom = geom_
+            };
     }
     return {};
 }

image_analysis/IndexAndRefine.h

@@ -48,8 +48,8 @@ class IndexAndRefine {
 
     IndexerThreadPool *indexer_;
 
-    int64_t image_stride;
-    int64_t first_image_to_try_indexing;
+    int64_t image_stride = 1;
+    int64_t first_image_to_try_indexing = INT64_MAX;
 
     void TryIndexRotationData();
 public:

tools/jfjoch_indexing_test.cpp

@@ -24,7 +24,7 @@ int main(int argc, char** argv) {
     IndexingSettings indexing_settings;
     indexing_settings.Algorithm(IndexingAlgorithmEnum::FFT);
     indexing_settings.RotationIndexing(true);
-
+    indexing_settings.GeomRefinementAlgorithm(GeomRefinementAlgorithmEnum::BeamCenter);
     DiffractionExperiment experiment(reader.GetDataset()->experiment);
     experiment.ImportIndexingSettings(indexing_settings);
     experiment.SetUnitCell({});

viewer/JFJochImageReadingWorker.cpp

@@ -101,8 +101,9 @@ void JFJochImageReadingWorker::LoadImage(int64_t image_number, int64_t summation
 void JFJochImageReadingWorker::UpdateAzint_i(const JFJochReaderDataset *dataset) {
     if (dataset) {
         azint_mapping = std::make_unique<AzimuthalIntegration>(curr_experiment, dataset->pixel_mask);
+        index_and_refine = std::make_unique<IndexAndRefine>(curr_experiment, indexing.get());
         image_analysis = std::make_unique<MXAnalysisWithoutFPGA>(curr_experiment, *azint_mapping, dataset->pixel_mask,
-            indexing.get());
+            *index_and_refine.get());
     }
 }
 

viewer/JFJochImageReadingWorker.h

@@ -52,6 +52,7 @@ private:
     std::shared_ptr<JFJochReaderImage> current_image_ptr;
     std::unique_ptr<AzimuthalIntegration> azint_mapping;
     std::unique_ptr<MXAnalysisWithoutFPGA> image_analysis;
+    std::unique_ptr<IndexAndRefine> index_and_refine;
 
     std::unique_ptr<ROIElement> roi;