General function to write reflections in multiple formats (need to better integrate into jfjoch_scale and jfjoch_process)

tools/jfjoch_process.cpp

@@ -28,7 +28,7 @@
 #include "../image_analysis/LoadFCalcFromMtz.h"
 #include "../image_analysis/scale_merge/Merge.h"
 #include "../image_analysis/scale_merge/SearchSpaceGroup.h"
-#include "../image_analysis/WriteMmcif.h"
+#include "../image_analysis/WriteReflections.h"
 #include "../image_analysis/UpdateReflectionResolution.h"
 
 void print_usage(Logger &logger) {
@@ -719,39 +719,8 @@ int main(int argc, char **argv) {
 
         merged_statistics.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: merged_reflections) {
-                    hkl_file << r.h << " " << r.k << " " << r.l << " "
-                            << r.I << " " << r.sigma
-                            << "\n";
-                }
-                hkl_file.close();
-                logger.Info("Wrote {} reflections to {}", merged_reflections.size(), hkl_path);
-            }
-        }
-
-        try {
-            const std::string cif_path = output_prefix + "_intensities.cif";
-
-            MmcifMetadata cif_meta;
-
-            cif_meta.Fill(experiment);
-
-            if (rotation_indexer_ret.has_value())
-                cif_meta.unit_cell = rotation_indexer_ret->lattice.GetUnitCell();
-            cif_meta.data_block_name = output_prefix;
-
-            WriteMmcifReflections(cif_path, merged_reflections, cif_meta);
-            logger.Info("Wrote mmCIF reflections to {}", cif_path);
-        } catch (const std::exception &e) {
-            logger.Error("Failed to write mmCIF: {}", e.what());
-        }
-
+        if (consensus_cell && !output_prefix.empty())
+            WriteReflections(merged_reflections, *consensus_cell, experiment, output_prefix);
     }
 
     // Write End Message