Reflection: Save zeta

common/Reflection.h

@@ -25,6 +25,7 @@ struct Reflection {
     bool observed = false;
     float S_x, S_y, S_z;
     float partiality;
+    float zeta;
 };
 
 #endif //JFJOCH_REFLECTION_H

frame_serialize/CBORStream2Deserializer.cpp

@@ -471,6 +471,8 @@ namespace {
                 r.dist_ewald = GetCBORFloat(map_value);
             else if (key == "partiality")
                 r.partiality = GetCBORFloat(map_value);
+            else if (key == "zeta")
+                r.zeta = GetCBORFloat(map_value);
             else
                 cbor_value_advance(&map_value);
         }

frame_serialize/CBORStream2Serializer.cpp

@@ -246,6 +246,7 @@ inline void CBOR_ENC(CborEncoder &encoder, const Reflection& r) {
     CBOR_ENC(mapEncoder, "rp", r.dist_ewald);
     CBOR_ENC(mapEncoder, "rlp", r.rlp);
     CBOR_ENC(mapEncoder, "partiality", r.partiality);
+    CBOR_ENC(mapEncoder, "zeta", r.zeta);
 
     cborErr(cbor_encoder_close_container(&encoder, &mapEncoder));
 }

image_analysis/bragg_prediction/BraggPrediction.cpp

@@ -96,6 +96,7 @@ int BraggPrediction::Calc(const DiffractionExperiment &experiment, const Crystal
                         .h = h,
                         .k = k,
                         .l = l,
+                        .delta_phi = NAN,
                         .predicted_x = x,
                         .predicted_y = y,
                         .d = d,
@@ -103,7 +104,9 @@ int BraggPrediction::Calc(const DiffractionExperiment &experiment, const Crystal
                         .rlp = 1.0,
                         .S_x = S_x,
                         .S_y = S_y,
-                        .S_z = S_z
+                        .S_z = S_z,
+                        .partiality = 1.0,
+                        .zeta = NAN
                     };
                     ++i;
                 }

image_analysis/bragg_prediction/BraggPredictionGPU.cu

@@ -77,6 +77,7 @@ namespace {
         out.h = h;
         out.k = k;
         out.l = l;
+        out.delta_phi = NAN;
         out.predicted_x = x;
         out.predicted_y = y;
         out.d = 1.0f / sqrtf(recip_sq);
@@ -85,6 +86,8 @@ namespace {
         out.S_y = Sy;
         out.S_z = Sz;
         out.rlp = 1.0f;
+        out.partiality = 1.0f;
+        out.zeta = NAN;
         return true;
     }
 

image_analysis/bragg_prediction/BraggPredictionRot.cpp

@@ -144,7 +144,8 @@ int BraggPredictionRot::Calc(const DiffractionExperiment &experiment, const Crys
                         .S_x = S.x,
                         .S_y = S.y,
                         .S_z = S.z,
-                        .partiality = partiality
+                        .partiality = partiality,
+                        .zeta = zeta_abs
                     };
                     i++;
                 }

image_analysis/bragg_prediction/BraggPredictionRotGPU.cu

@@ -160,6 +160,7 @@ namespace {
             out[count].S_y = Sy;
             out[count].S_z = Sz;
             out[count].partiality = partiality;
+            out[count].zeta = zeta_abs;
             count++;
         }
         return count;

reader/JFJochHDF5Reader.cpp

@@ -683,6 +683,8 @@ bool JFJochHDF5Reader::LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset
         auto lp = source_file->ReadOptVector<float>(image_group_name + "/lp");
         auto partiality = source_file->ReadOptVector<float>(image_group_name + "/partiality");
         auto phi = source_file->ReadOptVector<float>(image_group_name + "/delta_phi");
+        auto zeta = source_file->ReadOptVector<float>(image_group_name + "/zeta");
+
         if (h.size() != l.size() || h.size() != k.size() || h.size() != d.size()
             || h.size() != predicted_x.size() || h.size() != predicted_y.size()
             || h.size() != int_sum.size() || h.size() != int_err.size() || h.size() != bkg.size())
@@ -699,6 +701,9 @@ bool JFJochHDF5Reader::LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset
             float delta_phi_val = NAN;
             if (phi.size() > i)
                 delta_phi_val = phi[i];
+            float zeta_val = NAN;
+            if (zeta.size() > i)
+                zeta_val = zeta[i];
 
             Reflection r{
                 .h = h.at(i),
@@ -712,7 +717,8 @@ bool JFJochHDF5Reader::LoadImage_i(std::shared_ptr<JFJochReaderDataset> &dataset
                 .bkg = bkg.at(i),
                 .sigma = int_err.at(i),
                 .rlp = lp_val,
-                .partiality = partiality_val
+                .partiality = partiality_val,
+                .zeta = zeta_val
             };
             message.reflections.emplace_back(r);
         }

writer/HDF5DataFilePluginReflection.cpp

@@ -17,7 +17,7 @@ void HDF5DataFilePluginReflection::Write(const DataMessage &msg, uint64_t image_
 
     std::vector<int32_t> h, k, l;
     std::vector<float> I, sigma, d, lp;
-    std::vector<float> image, phi, pred_x, pred_y, bkg, partiality;
+    std::vector<float> image, phi, pred_x, pred_y, bkg, partiality, zeta;
 
     for (const auto &refl : msg.reflections) {
         image.emplace_back(refl.image_number);
@@ -33,6 +33,7 @@ void HDF5DataFilePluginReflection::Write(const DataMessage &msg, uint64_t image_
         lp.emplace_back(1.0/refl.rlp);
         partiality.emplace_back(refl.partiality);
         phi.emplace_back(refl.delta_phi);
+        zeta.emplace_back(refl.zeta);
     }
 
     std::string image_group_name = fmt::format("image_{:06d}", image_number);
@@ -51,6 +52,7 @@ void HDF5DataFilePluginReflection::Write(const DataMessage &msg, uint64_t image_
     image_group.SaveVector("observed_frame", image);
     image_group.SaveVector("lp", lp);
     image_group.SaveVector("partiality", partiality);
+    image_group.SaveVector("zeta", zeta);
 }
 
 void HDF5DataFilePluginReflection::WriteFinal(HDF5File &data_file) {