v1.0.0-rc.148 (#58)

This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144.

* jfjoch_broker: Improve azimuthal integration (add <I^2> calculation)
* jfjoch_broker: Fixes around indexing, aiming to handle multi-lattice crystals (work in progress, it is not fully integrated)
* jfjoch_writer: Save mean(I), stddev(I), and count(I) for each azimuthal bin

Reviewed-on: #58

frame_serialize/CBORStream2Deserializer.cpp

@@ -446,6 +446,8 @@ namespace {
                 s.ice_ring = GetCBORBool(map_value);
             else if (key == "indexed")
                 s.indexed = GetCBORBool(map_value);
+            else if (key == "latt")
+                s.lattice = GetCBORInt(map_value);
             else if (key == "h")
                 s.h = GetCBORInt(map_value);
             else if (key == "k")
@@ -711,12 +713,29 @@ namespace {
                 message.spot_count_ice_rings = GetCBORUInt(value);
             else if (key == "az_int_profile")
                 GetCBORFloatArray(value, message.az_int_profile);
+            else if (key == "az_int_profile_std")
+                GetCBORFloatArray(value, message.az_int_profile_std);
+            else if (key == "az_int_profile_count")
+                GetCBORUInt64Array(value, message.az_int_profile_count);
             else if (key == "indexing_result")
                 message.indexing_result = GetCBORBool(value);
+            else if (key == "indexing_lattice_count")
+                message.indexing_lattice_count = GetCBORInt(value);
             else if (key == "indexing_lattice") {
                 std::vector<float> tmp;
                 GetCBORFloatArray(value, tmp);
                 message.indexing_lattice = CrystalLattice(tmp);
+            } else if (key == "indexing_extra_lattices") {
+                size_t array_len = GetCBORArrayLen(value);
+                CborValue array_value;
+                cborErr(cbor_value_enter_container(&value, &array_value));
+                for (size_t i = 0; i < array_len; i++) {
+                    std::vector<float> tmp;
+                    GetCBORFloatArray(array_value, tmp);
+                    if (tmp.size() == 9)
+                        message.indexing_extra_lattices.emplace_back(tmp);
+                }
+                cborErr(cbor_value_leave_container(&value, &array_value));
             } else if (key == "indexing_time")
                 message.indexing_time_s = GetCBORFloat(value);
             else if (key == "spot_finding_time")
@@ -1020,6 +1039,14 @@ namespace {
         cborErr(cbor_value_leave_container(&value, &map_value));
     }
 
+    void ProcessAzintMapElement(StartMessage &message, CborValue &value) {
+        CompressedImage image = GetCBORMultidimTypedArray(value);
+        if (image.GetMode() == CompressedImageMode::Uint16)
+            JFJochDecompress(message.az_int_map, image.GetCompressionAlgorithm(),
+                         image.GetCompressed(), image.GetCompressedSize(),
+                         image.GetWidth() * image.GetHeight());
+    }
+
     std::optional<FileWriterFormat> ProcessHDF5Format(int input) {
         auto tmp = static_cast<FileWriterFormat>(input);
         switch (tmp) {
@@ -1181,6 +1208,8 @@ namespace {
                 message.run_number = GetCBORUInt(value);
             else if (key == "pixel_mask")
                 ProcessPixelMaskElement(message, value);
+            else if (key == "az_int_map")
+                ProcessAzintMapElement(message, value);
             else if (key == "channels")
                 GetCBORStringArray(value, message.channels);
             else if (key == "detector_translation")
@@ -1207,6 +1236,8 @@ namespace {
                 message.unit_cell = ProcessUnitCellElement(value);
             else if (key == "max_spot_count")
                 message.max_spot_count = GetCBORUInt(value);
+            else if (key == "max_extra_lattices")
+                message.max_extra_lattices = GetCBORUInt(value);
             else if (key == "threshold_energy")
                 message.threshold_energy = ProcessThresholdEnergy(value);
             else if (key == "image_dtype") {
@@ -1338,6 +1369,8 @@ namespace {
                 message.bkg_estimate = GetCBORFloat(value);
             else if (key == "indexing_rate")
                 message.indexing_rate = GetCBORFloat(value);
+            else if (key == "indexed_lattice_count")
+               GetCBORInt32Array(value, message.indexed_lattice_count);
             else if (key == "data_collection_efficiency_image")
                 GetCBORFloatArray(value, message.data_collection_efficiency);
             else if (key == "spot_count")
@@ -1390,7 +1423,18 @@ namespace {
                 message.rotation_lattice = CrystalLattice(tmp);
             } else if (key == "rotation_lattice_type")
                 message.rotation_lattice_type = GetCBORLatticeMessage(value);
-            else
+            else if (key == "rotation_extra_lattices") {
+                size_t array_len = GetCBORArrayLen(value);
+                CborValue array_value;
+                cborErr(cbor_value_enter_container(&value, &array_value));
+                for (size_t i = 0; i < array_len; i++) {
+                    std::vector<float> tmp;
+                    GetCBORFloatArray(array_value, tmp);
+                    if (tmp.size() == 9)
+                        message.rotation_extra_lattices.emplace_back(tmp);
+                }
+                cborErr(cbor_value_leave_container(&value, &array_value));
+            } else
                 cbor_value_advance(&value);
             return true;
         } catch (const JFJochException &e) {