From d555042dc6d1c16d01e220762ca5e034a43836af Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Mon, 18 May 2026 13:38:23 +0200
Subject: [PATCH] jfjoch_scale: Seems to work (though unstable)

---
 tools/jfjoch_scale.cpp | 73 +++++++++++++++++++++++++-----------------
 1 file changed, 43 insertions(+), 30 deletions(-)

diff --git a/tools/jfjoch_scale.cpp b/tools/jfjoch_scale.cpp
index 11f6df07..d9f22bf8 100644
--- a/tools/jfjoch_scale.cpp
+++ b/tools/jfjoch_scale.cpp
@@ -242,6 +242,20 @@ int main(int argc, char **argv) {
 
     logger.Info("Running scaling (mosaicity refinement) ...");
     auto reflections = reader.ReadReflections(start_image, end_image);
+    size_t nimages = 0;
+    size_t nrefl = 0;
+    for (auto& image : reflections) {
+        if (!image.empty()) {
+            nimages++;
+            nrefl += image.size();
+
+            for (auto &r: image) {
+                r.image_scale_corr = 1.0; // restart these numbers, since we don't know any better
+            }
+        }
+    }
+
+    logger.Info("Read {} reflections from {} images", nrefl, nimages);
 
     if (experiment.GetUnitCell()) {
         UpdateReflectionResolution(experiment.GetUnitCell().value(), reflections);
@@ -325,39 +339,38 @@ int main(int argc, char **argv) {
             }
         }
         logger.Info("");
+    }
 
+    // Print resolution-shell statistics table
+    merge_stats.Print(logger);
 
-        // Print resolution-shell statistics table
-        merge_stats.Print(logger);
-
-        {
-            const std::string hkl_path = output_prefix + "_intensities.hkl";
-            std::ofstream hkl_file(hkl_path);
-            if (!hkl_file) {
-                logger.Error("Cannot open {} for writing", hkl_path);
-            } else {
-                for (const auto &r: merge_result) {
-                    hkl_file << r.h << " " << r.k << " " << r.l << " "
-                            << r.I << " " << r.sigma
-                            << "\n";
-                }
-                hkl_file.close();
-                logger.Info("Wrote {} reflections to {}", merge_result.size(), hkl_path);
+    {
+        const std::string hkl_path = output_prefix + "_intensities.hkl";
+        std::ofstream hkl_file(hkl_path);
+        if (!hkl_file) {
+            logger.Error("Cannot open {} for writing", hkl_path);
+        } else {
+            for (const auto &r: merge_result) {
+                hkl_file << r.h << " " << r.k << " " << r.l << " "
+                        << r.I << " " << r.sigma
+                        << "\n";
             }
-        }
-
-        try {
-            const std::string cif_path = output_prefix + "_intensities.cif";
-
-            MmcifMetadata cif_meta;
-
-            cif_meta.Fill(experiment);
-            cif_meta.data_block_name = output_prefix;
-
-            WriteMmcifReflections(cif_path, merge_result, cif_meta);
-            logger.Info("Wrote mmCIF reflections to {}", cif_path);
-        } catch (const std::exception &e) {
-            logger.Error("Failed to write mmCIF: {}", e.what());
+            hkl_file.close();
+            logger.Info("Wrote {} reflections to {}", merge_result.size(), hkl_path);
         }
     }
+
+    try {
+        const std::string cif_path = output_prefix + "_intensities.cif";
+
+        MmcifMetadata cif_meta;
+
+        cif_meta.Fill(experiment);
+        cif_meta.data_block_name = output_prefix;
+
+        WriteMmcifReflections(cif_path, merge_result, cif_meta);
+        logger.Info("Wrote mmCIF reflections to {}", cif_path);
+    } catch (const std::exception &e) {
+        logger.Error("Failed to write mmCIF: {}", e.what());
+    }
 }