From 957980307f0dc895ac3ecfa9c8f10502e7ab705b Mon Sep 17 00:00:00 2001
From: Filip Leonarski <filip.leonarski@psi.ch>
Date: Tue, 17 Feb 2026 13:18:40 +0100
Subject: [PATCH] jfjoch_process: Add anomalous mode

---
 tools/jfjoch_process.cpp | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/tools/jfjoch_process.cpp b/tools/jfjoch_process.cpp
index 0f3e1090..dc2cc9ab 100644
--- a/tools/jfjoch_process.cpp
+++ b/tools/jfjoch_process.cpp
@@ -43,6 +43,7 @@ void print_usage(Logger &logger) {
     logger.Info("   -M         Scale and merge (refine mosaicity) and write scaled.hkl + image.dat");
     logger.Info("   -L         Use log-scaling residual");
     logger.Info("   -m<txt>    Mosaicity refinement none|fixed|image (default: image)");
+    logger.Info("   -A         Anomalous mode (don't merge Friedel pairs)");
 }
 
 int main(int argc, char **argv) {
@@ -63,6 +64,7 @@ int main(int argc, char **argv) {
     bool use_fft = false;
     bool refine_beam_center = true;
     bool run_scaling = false;
+    bool anomalous_mode = false;
     std::optional<int> space_group_number;
 
     bool log_residual = false;
@@ -77,7 +79,7 @@ int main(int argc, char **argv) {
     }
 
     int opt;
-    while ((opt = getopt(argc, argv, "o:N:s:e:vR::Fxd:S:MLm:")) != -1) {
+    while ((opt = getopt(argc, argv, "o:N:s:e:vR::Fxd:S:MLm:A")) != -1) {
         switch (opt) {
             case 'o':
                 output_prefix = optarg;
@@ -116,6 +118,9 @@ int main(int argc, char **argv) {
             case 'L':
                 log_residual = true;
                 break;
+            case 'A':
+                anomalous_mode = true;
+                break;
             case 'm':
                 if (strcmp(optarg, "none") == 0)
                     mosaicity_refinement_mode = MosaicityRefinementMode::None;
@@ -419,6 +424,8 @@ int main(int argc, char **argv) {
         scale_opts.max_num_iterations = 500;
         scale_opts.max_solver_time_s = 240.0; // generous cutoff for now
         scale_opts.log_scaling_residual = log_residual;
+        scale_opts.merge_friedel = !anomalous_mode;
+
         switch (mosaicity_refinement_mode) {
             case MosaicityRefinementMode::None:
                 scale_opts.refine_mosaicity = false;