UpdateReflectionResolution: Separate file + clear bug

image_analysis/CMakeLists.txt

@@ -32,7 +32,9 @@ ADD_LIBRARY(JFJochImageAnalysis STATIC
         WriteMmcif.cpp
         WriteMmcif.h
         LoadFCalcFromMtz.cpp
-        LoadFCalcFromMtz.h)
+        LoadFCalcFromMtz.h
+        UpdateReflectionResolution.cpp
+        UpdateReflectionResolution.h)
 
 FIND_PACKAGE(Eigen3 3.4 REQUIRED NO_MODULE)  # provides Eigen3::Eigen
 

image_analysis/UpdateReflectionResolution.cpp

@@ -0,0 +1,23 @@
+// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include "UpdateReflectionResolution.h"
+#include "../common/CrystalLattice.h"
+
+void UpdateReflectionResolution(const UnitCell &cell, std::vector<std::vector<Reflection> > &reflections) {
+    CrystalLattice latt(cell);
+    const auto astar = latt.Astar();
+    const auto bstar = latt.Bstar();
+    const auto cstar = latt.Cstar();
+
+    for (auto &image: reflections) {
+        for (auto &r: image) {
+            Coord q = r.h * astar + r.k * bstar + r.l * cstar;
+            auto qlen = q.Length();
+            if (qlen > 1e-6)
+                r.d = 1/qlen;
+            else
+                r.d = NAN;
+        }
+    }
+}

image_analysis/UpdateReflectionResolution.h

@@ -0,0 +1,8 @@
+// SPDX-FileCopyrightText: 2025 Filip Leonarski, Paul Scherrer Institute <filip.leonarski@psi.ch>
+// SPDX-License-Identifier: GPL-3.0-only
+
+#include <vector>
+#include "../common/Reflection.h"
+#include "../common/UnitCell.h"
+
+void UpdateReflectionResolution(const UnitCell &cell, std::vector<std::vector<Reflection> > &reflections);

image_analysis/scale_merge/ScaleOnTheFly.cpp

@@ -355,21 +355,3 @@ ScalingResult ScaleOnTheFly::Scale(std::vector<std::vector<Reflection> > &reflec
 
     return result;
 }
-
-void UpdateReflectionResolution(const UnitCell &cell, std::vector<std::vector<Reflection> > &reflections) {
-    CrystalLattice latt(cell);
-    const auto astar = latt.Astar();
-    const auto bstar = latt.Bstar();
-    const auto cstar = latt.Cstar();
-
-    for (auto &image: reflections) {
-        for (auto &r: image) {
-            Coord q = r.h * astar + r.k * bstar + r.l * cstar;
-            auto qlen = q.Length();
-            if (qlen > 1e6)
-                r.d = 1/qlen;
-            else
-                r.d = NAN;
-        }
-    }
-}

image_analysis/scale_merge/ScaleOnTheFly.h

@@ -22,8 +22,6 @@ struct ScaleOnTheFlyResult {
     bool succesful = false;
 };
 
-void UpdateReflectionResolution(const UnitCell &cell, std::vector<std::vector<Reflection> > &reflections);
-
 class ScaleOnTheFly {
     constexpr static size_t MIN_REFLECTIONS = 20;
 

tools/jfjoch_process.cpp

@@ -29,6 +29,7 @@
 #include "../image_analysis/scale_merge/Merge.h"
 #include "../image_analysis/scale_merge/SearchSpaceGroup.h"
 #include "../image_analysis/WriteMmcif.h"
+#include "../image_analysis/UpdateReflectionResolution.h"
 
 void print_usage(Logger &logger) {
     logger.Info("Usage ./jfjoch_analysis {<options>} <input.h5>");
@@ -616,7 +617,7 @@ int main(int argc, char **argv) {
         auto rejected_uc = CalcMergeMaskUnitCell(experiment, *consensus_cell, indexer.GetUnitCells(), merging_mask_uc);
         if (rejected_uc > 0)
             logger.Info("Rejected {} images for merging due to unit cell being too far from consensus", rejected_uc);
-        UpdateReflectionResolution(consensus_cell.value(), indexer.GetReflections());
+        // UpdateReflectionResolution(consensus_cell.value(), indexer.GetReflections());
         logger.Info("Reflection resolution updated based on consensus unit cell");
     } else
         logger.Info("Consensus unit cell not found - calculation tool {:.2f} ms", consensus_duration * 1e3);

tools/jfjoch_scale.cpp

@@ -29,6 +29,7 @@
 #include "../image_analysis/scale_merge/Merge.h"
 #include "../image_analysis/scale_merge/SearchSpaceGroup.h"
 #include "../image_analysis/WriteMmcif.h"
+#include "../image_analysis/UpdateReflectionResolution.h"
 
 void print_usage(Logger &logger) {
     logger.Info("Usage ./jfjoch_analysis {<options>} <input.h5>");