From e70d71912b68afb5fbe4ca0f205234dc8a2e9f5a Mon Sep 17 00:00:00 2001
From: Filip Leonarski <filip.leonarski@psi.ch>
Date: Wed, 13 May 2026 14:36:41 +0200
Subject: [PATCH] Merge: Add partiality limit

---
 common/ScalingSettings.cpp           | 4 +++-
 common/ScalingSettings.h             | 3 +++
 image_analysis/scale_merge/Merge.cpp | 6 ++++++
 image_analysis/scale_merge/Merge.h   | 6 +++---
 4 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/common/ScalingSettings.cpp b/common/ScalingSettings.cpp
index 04f0f8b1..16d5e9de 100644
--- a/common/ScalingSettings.cpp
+++ b/common/ScalingSettings.cpp
@@ -97,4 +97,6 @@ std::optional<double> ScalingSettings::GetRotationWedgeForScaling() const {
     return wedge_for_scaling;
 }
 
-
+double ScalingSettings::GetMinPartiality() const {
+    return min_partiality;
+}
diff --git a/common/ScalingSettings.h b/common/ScalingSettings.h
index 941b6dea..f86c5a2b 100644
--- a/common/ScalingSettings.h
+++ b/common/ScalingSettings.h
@@ -20,6 +20,7 @@ class ScalingSettings {
     bool merge_friedel = true;
     std::optional<double> high_resolution_limit_A;
     std::optional<double> wedge_for_scaling;
+    constexpr static double min_partiality = 0.02;
 public:
     ScalingSettings& SetPartialityModel(PartialityModel mode);
     ScalingSettings& RefineB(bool input);
@@ -46,4 +47,6 @@ public:
 
     [[nodiscard]] std::optional<PartialityModel> GetPartialityModel() const;
     [[nodiscard]] std::optional<double> GetHighResolutionLimit_A() const;
+
+    [[nodiscard]] double GetMinPartiality() const;
 };
diff --git a/image_analysis/scale_merge/Merge.cpp b/image_analysis/scale_merge/Merge.cpp
index 2cad3d64..a54ffdd7 100644
--- a/image_analysis/scale_merge/Merge.cpp
+++ b/image_analysis/scale_merge/Merge.cpp
@@ -15,6 +15,7 @@ std::vector<MergedReflection> MergeAll(const DiffractionExperiment &x, const std
     auto scaling_settings = x.GetScalingSettings();
     HKLKeyGenerator key_generator(scaling_settings.GetMergeFriedel(), x.GetSpaceGroupNumber().value_or(1));
     const std::optional<double> high_resolution_limit = scaling_settings.GetHighResolutionLimit_A();
+    auto min_partiality = scaling_settings.GetMinPartiality();
 
     struct Accum {
         // Keep anomalous + / - together, but separate
@@ -37,6 +38,8 @@ std::vector<MergedReflection> MergeAll(const DiffractionExperiment &x, const std
                 continue;
             if (!AcceptReflection(r, high_resolution_limit))
                 continue;
+            if (r.partiality < min_partiality)
+                continue;
 
             const float I_corr = r.I * r.scaling_correction;
             const float sigma_corr = r.sigma * r.scaling_correction;
@@ -106,6 +109,7 @@ MergeStatistics MergeStats(const DiffractionExperiment &x,
     float d_min = std::numeric_limits<float>::max();
     float d_max = 0.0f;
 
+    auto min_partiality = x.GetScalingSettings().GetMinPartiality();
     auto d_min_limit_A = x.GetScalingSettings().GetHighResolutionLimit_A();
     for (const auto &m: merged) {
         if (!std::isfinite(m.d) || m.d <= 0.0f)
@@ -159,6 +163,8 @@ MergeStatistics MergeStats(const DiffractionExperiment &x,
 
             if (!AcceptReflection(r, d_min_limit_A))
                 continue;
+            if (r.partiality < min_partiality)
+                continue;;
 
             const auto shell = shells.GetShell(r.d);
             if (!shell.has_value())
diff --git a/image_analysis/scale_merge/Merge.h b/image_analysis/scale_merge/Merge.h
index 3ed79f83..a40fb83a 100644
--- a/image_analysis/scale_merge/Merge.h
+++ b/image_analysis/scale_merge/Merge.h
@@ -33,8 +33,8 @@ struct MergeResult {
 };
 
 std::vector<MergedReflection> MergeAll(const DiffractionExperiment &x,
-                                    const std::vector<std::vector<Reflection> > &reflections);
+                                       const std::vector<std::vector<Reflection> > &reflections);
 
 MergeStatistics MergeStats(const DiffractionExperiment &x,
-    const std::vector<MergedReflection> &merged,
-    const std::vector<std::vector<Reflection> > &reflections);
\ No newline at end of file
+                           const std::vector<MergedReflection> &merged,
+                           const std::vector<std::vector<Reflection> > &reflections);