Multi lattice search: Small changes (WIP)

common/JFJochMessages.h

@@ -112,9 +112,8 @@ struct DataMessage {
     std::optional<float> bkg_estimate;
 
     std::optional<bool> indexing_result;
-    std::optional<int64_t> indexing_lattice_count;
     std::optional<CrystalLattice> indexing_lattice;
-    std::vector<CrystalLattice> extra_lattices;
+    std::vector<CrystalLattice> indexing_extra_lattices;
     std::optional<UnitCell> indexing_unit_cell;
     std::optional<int64_t> spot_count_indexed;
 
@@ -330,7 +329,7 @@ struct EndMessage {
 
     std::optional<LatticeMessage> rotation_lattice_type;
     std::optional<CrystalLattice> rotation_lattice;
-    std::vector<CrystalLattice> extra_lattices;
+    std::vector<CrystalLattice> rotation_extra_lattices;
     std::optional<UnitCell> unit_cell;
 
     // Vectors with end result:

frame_serialize/CBORStream2Deserializer.cpp

@@ -733,7 +733,7 @@ namespace {
                     std::vector<float> tmp;
                     GetCBORFloatArray(array_value, tmp);
                     if (tmp.size() == 9)
-                        message.extra_lattices.emplace_back(tmp);
+                        message.indexing_extra_lattices.emplace_back(tmp);
                 }
                 cborErr(cbor_value_leave_container(&value, &array_value));
             } else if (key == "indexing_time")
@@ -1429,7 +1429,7 @@ namespace {
                     std::vector<float> tmp;
                     GetCBORFloatArray(array_value, tmp);
                     if (tmp.size() == 9)
-                        message.extra_lattices.emplace_back(tmp);
+                        message.rotation_extra_lattices.emplace_back(tmp);
                 }
                 cborErr(cbor_value_leave_container(&value, &array_value));
             } else

frame_serialize/CBORStream2Serializer.cpp

@@ -722,11 +722,11 @@ void CBORStream2Serializer::SerializeSequenceEnd(const EndMessage& message) {
     CBOR_ENC(mapEncoder, "rotation_lattice_type", message.rotation_lattice_type);
     if (message.rotation_lattice.has_value())
         CBOR_ENC(mapEncoder, "rotation_lattice", message.rotation_lattice->GetVector());
-    if (!message.extra_lattices.empty()) {
+    if (!message.rotation_extra_lattices.empty()) {
         CborEncoder arrayEncoder;
         cborErr(cbor_encode_text_stringz(&mapEncoder, "extra_lattices"));
-        cborErr(cbor_encoder_create_array(&mapEncoder, &arrayEncoder, message.extra_lattices.size()));
-        for (const auto &el : message.extra_lattices)
+        cborErr(cbor_encoder_create_array(&mapEncoder, &arrayEncoder, message.rotation_extra_lattices.size()));
+        for (const auto &el : message.rotation_extra_lattices)
             CBOR_ENC_FLOAT_ARRAY_NOKEY(arrayEncoder, el.GetVector());
         cborErr(cbor_encoder_close_container(&mapEncoder, &arrayEncoder));
     }
@@ -781,11 +781,11 @@ void CBORStream2Serializer::SerializeImageInternal(CborEncoder &mapEncoder, cons
     CBOR_ENC(mapEncoder, "indexing_lattice_count", message.indexing_lattice_count);
     if (message.indexing_lattice)
         CBOR_ENC(mapEncoder, "indexing_lattice", message.indexing_lattice->GetVector());
-    if (!message.extra_lattices.empty()) {
+    if (!message.indexing_extra_lattices.empty()) {
         CborEncoder arrayEncoder;
         cborErr(cbor_encode_text_stringz(&mapEncoder, "extra_lattices"));
-        cborErr(cbor_encoder_create_array(&mapEncoder, &arrayEncoder, message.extra_lattices.size()));
-        for (const auto &el : message.extra_lattices)
+        cborErr(cbor_encoder_create_array(&mapEncoder, &arrayEncoder, message.indexing_extra_lattices.size()));
+        for (const auto &el : message.indexing_extra_lattices)
             CBOR_ENC_FLOAT_ARRAY_NOKEY(arrayEncoder, el.GetVector());
         cborErr(cbor_encoder_close_container(&mapEncoder, &arrayEncoder));
     }

image_analysis/indexing/AnalyzeIndexing.cpp

@@ -369,8 +369,8 @@ bool AnalyzeIndexing(DataMessage &message,
             // Spots already assigned to the main lattice (lattice == 0) are never
             // overwritten. Each extra lattice gets index 1, 2, 3, ...
             const size_t n_extra = std::min<size_t>(extra_lattices.size(), experiment.GetIndexingSettings().GetMaxExtraLattices());
-            message.extra_lattices.clear();
-            message.extra_lattices.reserve(n_extra);
+            message.indexing_extra_lattices.clear();
+            message.indexing_extra_lattices.reserve(n_extra);
 
             for (size_t li = 0; li < n_extra; li++) {
                 const CrystalLattice &el = extra_lattices[li];
@@ -414,10 +414,10 @@ bool AnalyzeIndexing(DataMessage &message,
                     }
                 }
 
-                message.extra_lattices.push_back(el);
+                message.indexing_extra_lattices.push_back(el);
             }
 
-            message.indexing_lattice_count = static_cast<int64_t>(1 + message.extra_lattices.size());
+            message.indexing_lattice_count = static_cast<int64_t>(1 + message.indexing_extra_lattices.size());
             outcome = true;
         }
     }

receiver/JFJochReceiver.cpp

@@ -172,7 +172,7 @@ void JFJochReceiver::SendEndMessage() {
             .niggli_class = rotation_indexer_ret->search_result.niggli_class,
             .crystal_system = rotation_indexer_ret->search_result.system
         };
-        message.extra_lattices = rotation_indexer_ret->extra_lattices;
+        message.rotation_extra_lattices = rotation_indexer_ret->extra_lattices;
         rotation_indexing_lattice = rotation_indexer_ret->lattice;
     }
     message.unit_cell = indexer.GetConsensusUnitCell();

receiver/JFJochReceiverPlots.cpp

@@ -168,7 +168,7 @@ void JFJochReceiverPlots::Add(const DataMessage &msg, const AzimuthalIntegration
         indexing_uc_gamma.AddElement(msg.number, msg.indexing_unit_cell->gamma);
     }
 
-    indexing_lattice_count.AddElement(msg.number, msg.indexing_lattice_count);
+    indexing_lattice_count.AddElement(msg.number, msg.indexing_extra_lattices.size());
     beam_center_x.AddElement(msg.number, msg.beam_corr_x);
     beam_center_y.AddElement(msg.number, msg.beam_corr_y);
 

writer/HDF5DataFilePluginMX.cpp

@@ -177,8 +177,8 @@ void HDF5DataFilePluginMX::Write(const DataMessage &msg, uint64_t image_number)
 
         for (size_t li = 0; li < max_extra_lattices; li++) {
             const size_t base = (image_number * max_extra_lattices + li) * 9;
-            if (li < msg.extra_lattices.size()) {
-                auto tmp = msg.extra_lattices[li].GetVector();
+            if (li < msg.indexing_extra_lattices.size()) {
+                auto tmp = msg.indexing_extra_lattices[li].GetVector();
                 for (int i = 0; i < 9; i++)
                     extra_lattices[base + i] = tmp[i];
             } else {