From 02ecf5c32e93fb803495d0ae916acdb3e1e964fd Mon Sep 17 00:00:00 2001
From: leonarski_f <filip.leonarski@psi.ch>
Date: Fri, 5 Jun 2026 11:36:23 +0200
Subject: [PATCH] MultiLatticeSearch: Explore all valid sign flips when
 comparing with reference cell

---
 common/CrystalLattice.cpp                     |  9 ++-
 common/CrystalLattice.h                       |  1 +
 .../indexing/MultiLatticeSearch.cpp           | 68 +++++++++++++------
 tests/MultiLatticeSearchTest.cpp              | 15 ++++
 4 files changed, 73 insertions(+), 20 deletions(-)

diff --git a/common/CrystalLattice.cpp b/common/CrystalLattice.cpp
index 0172b8fa..17dbca65 100644
--- a/common/CrystalLattice.cpp
+++ b/common/CrystalLattice.cpp
@@ -80,9 +80,16 @@ void CrystalLattice::Sort() {
         std::swap(vec[0], vec[1]);
 }
 
+void CrystalLattice::FlipSign(size_t i1) {
+    if (i1 >= 3)
+        throw JFJochException(JFJochExceptionCategory::InputParameterInvalid,
+            "index out of range (0..2)");
+    vec[i1] *= -1;
+}
+
 void CrystalLattice::FixHandedness() {
     if (CalcVolume() < 0)
-        vec[2] *= -1;
+        FlipSign(2);
 }
 
 
diff --git a/common/CrystalLattice.h b/common/CrystalLattice.h
index 5f4e6519..cb18b179 100644
--- a/common/CrystalLattice.h
+++ b/common/CrystalLattice.h
@@ -39,6 +39,7 @@ public:
     void Regularize(const gemmi::CrystalSystem &input);
     [[nodiscard]] std::vector<float> GetUBMatrix() const;
     CrystalLattice NiggliReduce() const;
+    void FlipSign(size_t i1);
 };
 
 inline std::ostream &operator<<( std::ostream &output, const CrystalLattice &in ) {
diff --git a/image_analysis/indexing/MultiLatticeSearch.cpp b/image_analysis/indexing/MultiLatticeSearch.cpp
index c799d9ab..11d0cf55 100644
--- a/image_analysis/indexing/MultiLatticeSearch.cpp
+++ b/image_analysis/indexing/MultiLatticeSearch.cpp
@@ -35,6 +35,30 @@ namespace {
     }
 }
 
+CrystalLattice Transform(const CrystalLattice &in_latt, int i) {
+    CrystalLattice latt = in_latt;
+    switch (i) {
+        case 0:
+            break;
+        case 1:
+            latt.FlipSign(0);
+            latt.FlipSign(1);
+            break;
+        case 2:
+            latt.FlipSign(0);
+            latt.FlipSign(2);
+            break;
+        case 3:
+            latt.FlipSign(1);
+            latt.FlipSign(2);
+            break;
+        default:
+            break;
+    }
+
+    return latt;
+}
+
 std::vector<MultiLatticeSearchResult> MultiLatticeSearch(const std::vector<CrystalLattice> &lattices,
                                                          float dist_tolerance,
                                                          float angle_tolerance_deg) {
@@ -48,29 +72,35 @@ std::vector<MultiLatticeSearchResult> MultiLatticeSearch(const std::vector<Cryst
     ret.push_back({reference, reference, Coord(0, 0, 0)});
 
     for (size_t i = 1; i < lattices.size(); i++) {
-        const CrystalLattice &latt = lattices[i];
+        bool found = false;
+        for (int flip = 0; flip < 4; flip++) {
+            if (found)
+                continue;
+            const CrystalLattice latt = Transform(lattices[i], flip);
 
-        if (!latt.GetUnitCell().is_close(ref_cell, dist_tolerance, angle_tolerance_deg))
-            continue;
+            if (!latt.GetUnitCell().is_close(ref_cell, dist_tolerance, angle_tolerance_deg))
+                continue;
 
-        const Eigen::Matrix3d R = RotationRefToTarget(reference, latt);
+            const Eigen::Matrix3d R = RotationRefToTarget(reference, latt);
 
-        const Eigen::AngleAxisd aa(R);
-        const Eigen::Vector3d rod = aa.angle() * aa.axis();
-        const Coord rotation_vector(static_cast<float>(rod.x()),
-                                    static_cast<float>(rod.y()),
-                                    static_cast<float>(rod.z()));
+            const Eigen::AngleAxisd aa(R);
+            const Eigen::Vector3d rod = aa.angle() * aa.axis();
+            const Coord rotation_vector(static_cast<float>(rod.x()),
+                                        static_cast<float>(rod.y()),
+                                        static_cast<float>(rod.z()));
 
-        // output_lattice = R * reference, built straight from the Eigen matrix
-        // so it is exactly a proper rotation of the reference (full double precision).
-        const Eigen::Matrix3d out = R * LatticeMatrix(reference);
-        ret.push_back({
-            latt,
-            CrystalLattice(Coord(out(0, 0), out(1, 0), out(2, 0)),
-                           Coord(out(0, 1), out(1, 1), out(2, 1)),
-                           Coord(out(0, 2), out(1, 2), out(2, 2))),
-            rotation_vector
-        });
+            // output_lattice = R * reference, built straight from the Eigen matrix
+            // so it is exactly a proper rotation of the reference (full double precision).
+            const Eigen::Matrix3d out = R * LatticeMatrix(reference);
+            ret.push_back({
+                latt,
+                CrystalLattice(Coord(out(0, 0), out(1, 0), out(2, 0)),
+                               Coord(out(0, 1), out(1, 1), out(2, 1)),
+                               Coord(out(0, 2), out(1, 2), out(2, 2))),
+                rotation_vector
+            });
+            found = true;
+        }
     }
 
     return ret;
diff --git a/tests/MultiLatticeSearchTest.cpp b/tests/MultiLatticeSearchTest.cpp
index b40cc537..6e5df735 100644
--- a/tests/MultiLatticeSearchTest.cpp
+++ b/tests/MultiLatticeSearchTest.cpp
@@ -65,4 +65,19 @@ TEST_CASE("MultiLatticeSearch_SkipsDifferentCell") {
 TEST_CASE("MultiLatticeSearch_Empty") {
     auto result = MultiLatticeSearch({});
     CHECK(result.empty());
+}
+
+TEST_CASE("MultiLatticeSearch_EP") {
+    // Real EP case
+    CrystalLattice cell1(Coord(-13.2, -30.0, -29.6),
+        Coord(70.1, -12.16, -18.6),
+        Coord(7.6, -23.9, 44.8));
+    CrystalLattice cell2(Coord(-13.2, -29.9, -29.5),
+        Coord(-70.1, 12.15, 18.8),
+        Coord(1.8, 45.4, -23.7)
+    );
+
+    auto result = MultiLatticeSearch({cell1, cell2},
+        0.1, 5);
+    REQUIRE(result.size() == 2);
 }
\ No newline at end of file