From f3e8379a554b7b84d70776e4a5d1fdd4e2748592 Mon Sep 17 00:00:00 2001
From: Filip Leonarski <filip.leonarski@psi.ch>
Date: Tue, 17 Feb 2026 13:08:59 +0100
Subject: [PATCH] jfjoch_process: Write amplitudes at the end into hkl file in
 addition to mmCIF file (to be improved later)

---
 tools/jfjoch_process.cpp | 39 +++++++++++++++++++++------------------
 1 file changed, 21 insertions(+), 18 deletions(-)

diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index f6725a5e..0f3e1090 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -179,6 +179,7 @@ int main(int argc, char **argv) {
     experiment.Mode(DetectorMode::Standard); // Ensure full image analysis
     experiment.PixelSigned(true);
     experiment.OverwriteExistingFiles(true);
+    experiment.PolarizationFactor(0.99); // Unpolarized beam
 
     // Configure Indexing
     IndexingSettings indexing_settings;
@@ -446,21 +447,7 @@ int main(int argc, char **argv) {
                         scale_time, scale_result->gof2,
                         scale_result->merged.size(), scale_result->image_ids.size());
 
-            // Write scaled.hkl  (h  k  l  I  sigma)
-            {
-                const std::string hkl_path = output_prefix + "_scaled.hkl";
-                std::ofstream hkl_file(hkl_path);
-                if (!hkl_file) {
-                    logger.Error("Cannot open {} for writing", hkl_path);
-                } else {
-                    for (const auto &r: scale_result->merged) {
-                        hkl_file << r.h << " " << r.k << " " << r.l << " "
-                                << r.I << " " << r.sigma << "\n";
-                    }
-                    hkl_file.close();
-                    logger.Info("Wrote {} reflections to {}", scale_result->merged.size(), hkl_path);
-                }
-            }
+
 
             // Write image.dat  (image_id  mosaicity_deg  K)
             {
@@ -486,13 +473,29 @@ int main(int argc, char **argv) {
                 fw_opts.acentric = true; // typical for MX
                 fw_opts.num_shells = 20;
 
-                auto fw = FrenchWilson(scale_result->merged, fw_opts); {
+                auto fw = FrenchWilson(scale_result->merged, fw_opts);
+                {
+                    {
+                        // Write scaled.hkl  (h  k  l  I  sigma)
+                        const std::string hkl_path = output_prefix + "_amplitudes.hkl";
+                        std::ofstream hkl_file(hkl_path);
+                        if (!hkl_file) {
+                            logger.Error("Cannot open {} for writing", hkl_path);
+                        } else {
+                            for (const auto &r: fw) {
+                                hkl_file << r.h << " " << r.k << " " << r.l << " "
+                                        << r.F << " " << r.sigmaF << " "
+                                        << r.I << " " << r.sigmaI
+                                        << "\n";
+                            }
+                            hkl_file.close();
+                            logger.Info("Wrote {} reflections to {}", scale_result->merged.size(), hkl_path);
+                        }
+                    }
                     MmcifMetadata cif_meta;
 
                     // Unit cell — from rotation indexing result or experiment setting
                     if (rotation_indexer_ret.has_value()) {
-                        logger.Info("Bla {:f} {:f}", rotation_indexer_ret->lattice.GetUnitCell().a,
-                                    rotation_indexer_ret->lattice.GetUnitCell().b);
                         cif_meta.unit_cell = rotation_indexer_ret->lattice.GetUnitCell();
                     } else if (experiment.GetUnitCell().has_value()) {
                         cif_meta.unit_cell = experiment.GetUnitCell().value();