From 7c0cc22e47048dbdcfcbf8efb31346f1bdefda2c Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 18 May 2026 13:37:55 +0200
Subject: [PATCH] HDF5: Save per reflection scaling factor

---
 reader/JFJochHDF5Reader.cpp             | 8 +++++++-
 writer/HDF5DataFilePluginReflection.cpp | 5 ++++-
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/reader/JFJochHDF5Reader.cpp b/reader/JFJochHDF5Reader.cpp
index 5b13cce7..67aa3388 100644
--- a/reader/JFJochHDF5Reader.cpp
+++ b/reader/JFJochHDF5Reader.cpp
@@ -149,6 +149,7 @@ bool ReadReflectionsFromGroup(HDF5Object &file,
     auto partiality = file.ReadOptVector<float>(image_group_name + "/partiality");
     auto phi = file.ReadOptVector<float>(image_group_name + "/delta_phi");
     auto zeta = file.ReadOptVector<float>(image_group_name + "/zeta");
+    auto image_scale_corr = file.ReadOptVector<float>(image_group_name + "/image_scale_corr");
 
     if (h.size() != l.size() || h.size() != k.size() || h.size() != d.size()
         || h.size() != predicted_x.size() || h.size() != predicted_y.size()
@@ -170,6 +171,10 @@ bool ReadReflectionsFromGroup(HDF5Object &file,
         if (zeta.size() > i)
             zeta_val = zeta[i];
 
+        float image_scale_corr_val = 1.0f; // Default is 1.0, if we don't know any better
+        if (image_scale_corr.size() > i)
+            image_scale_corr_val = image_scale_corr[i];
+
         Reflection r{
             .h = h.at(i),
             .k = k.at(i),
@@ -183,7 +188,8 @@ bool ReadReflectionsFromGroup(HDF5Object &file,
             .sigma = int_err.at(i),
             .rlp = lp_val,
             .partiality = partiality_val,
-            .zeta = zeta_val
+            .zeta = zeta_val,
+            .image_scale_corr = image_scale_corr_val
         };
         reflections.emplace_back(r);
     }
diff --git a/writer/HDF5DataFilePluginReflection.cpp b/writer/HDF5DataFilePluginReflection.cpp
index 7f8780ef..362b3e6e 100644
--- a/writer/HDF5DataFilePluginReflection.cpp
+++ b/writer/HDF5DataFilePluginReflection.cpp
@@ -16,7 +16,7 @@ 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, zeta;
+    std::vector<float> image, phi, pred_x, pred_y, bkg, partiality, zeta, scale_factor;
 
     h.reserve(msg.reflections.size());
     k.reserve(msg.reflections.size());
@@ -32,6 +32,7 @@ void HDF5DataFilePluginReflection::Write(const DataMessage &msg, uint64_t image_
     image.reserve(msg.reflections.size());
     phi.reserve(msg.reflections.size());
     zeta.reserve(msg.reflections.size());
+    scale_factor.reserve(msg.reflections.size());
 
     for (const auto &refl : msg.reflections) {
         image.emplace_back(refl.image_number);
@@ -48,6 +49,7 @@ void HDF5DataFilePluginReflection::Write(const DataMessage &msg, uint64_t image_
         partiality.emplace_back(refl.partiality);
         phi.emplace_back(refl.delta_phi_deg);
         zeta.emplace_back(refl.zeta);
+        scale_factor.emplace_back(refl.image_scale_corr);
     }
 
     std::string image_group_name = fmt::format("image_{:06d}", image_number);
@@ -67,6 +69,7 @@ void HDF5DataFilePluginReflection::Write(const DataMessage &msg, uint64_t image_
     image_group.SaveVector("lp", lp);
     image_group.SaveVector("partiality", partiality);
     image_group.SaveVector("zeta", zeta);
+    image_group.SaveVector("image_scale_corr", scale_factor);
 }
 
 void HDF5DataFilePluginReflection::WriteFinal(HDF5File &data_file) {