added openmp for multi seed refinement

CMakeLists.txt

@@ -13,6 +13,7 @@ if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
 endif()
  
 find_package(Eigen3 3.3.4 NO_MODULE)
+find_package(OpenMP)
 
 include_directories(include)
 
@@ -41,12 +42,16 @@ set(SOURCES_test src/main.cpp
 				 src/tests.cpp
 )
  
-if(PINKINDEXER_BUILD_EXECUTABLE)
+ if(PINKINDEXER_BUILD_EXECUTABLE)
 	add_executable(pinkIndexer ${SOURCES} ${SOURCES_test})
 else(PINKINDEXER_BUILD_EXECUTABLE)
 	add_library(pinkIndexer SHARED ${SOURCES})
 endif(PINKINDEXER_BUILD_EXECUTABLE)
 
+if(OpenMP_CXX_FOUND)
+	target_link_libraries(pinkIndexer PUBLIC OpenMP::OpenMP_CXX)
+endif(OpenMP_CXX_FOUND)
+
 if(EIGEN3_FOUND)
     target_link_libraries (pinkIndexer PUBLIC Eigen3::Eigen)
 else()

src/PinkIndexer.cpp

@@ -63,7 +63,6 @@ int PinkIndexer::indexPattern(Lattice& indexedLattice, Eigen::Array<bool, Eigen:
 
     Matrix3f bestBasis = bestRotation * sampleLattice.getBasis();
     indexedLattice = Lattice(bestBasis);
-    // indexedLattice.minimize();
 
     switch (refinementType)
     {
@@ -91,37 +90,48 @@ int PinkIndexer::indexPattern(Lattice& indexedLattice, Eigen::Array<bool, Eigen:
             break;
         case RefinementType::firstFixedThenVariableLatticeParametersMultiSeed:
         {
-            Lattice bestLattice = indexedLattice;
-            int maxFittedNodesCount = refinement.getFittedPeaks(indexedLattice, fittedPeaks, ucsDirections, ucsBorderNorms);
+#define REFINEMENT_TRIES 250
+            int fittedNodesCount[REFINEMENT_TRIES];
+            Lattice fittedLattices[REFINEMENT_TRIES];
 
-            float maxRelativeDeviation = 0.01;
+            float maxRelativeDeviation = 0.012;
             Array<float, 1, 3> columnDeviationNorms = indexedLattice.getBasis().colwise().norm() * maxRelativeDeviation;
-            for (uint32_t i = 0; i < 16; ++i)
+#pragma omp parallel for
+            for (int i = 0; i < REFINEMENT_TRIES; ++i)
             {
-                Matrix3f currentBasis = indexedLattice.getBasis() + (Array33f::Random().rowwise() * columnDeviationNorms ).matrix();
-                Lattice currentLattice(currentBasis);
+                Refinement refinement(finalRefinementTolerance);
+
+                Matrix3f currentBasis = indexedLattice.getBasis() + (Array33f::Random().rowwise() * columnDeviationNorms).matrix();
+                fittedLattices[i] = Lattice(currentBasis);
 
                 refinement.setTolerance(min(finalRefinementTolerance * 2.5, 0.12));
-                refinement.refineFixedLattice(currentLattice, ucsDirections, ucsBorderNorms);
+                refinement.refineFixedLattice(fittedLattices[i], ucsDirections, ucsBorderNorms);
                 refinement.setTolerance(min(finalRefinementTolerance * 1.8, 0.10));
-                refinement.refineVariableLattice(currentLattice, ucsDirections, ucsBorderNorms);
+                refinement.refineVariableLattice(fittedLattices[i], ucsDirections, ucsBorderNorms);
                 refinement.setTolerance(finalRefinementTolerance);
-                refinement.refineVariableLattice(currentLattice, ucsDirections, ucsBorderNorms);
+                refinement.refineVariableLattice(fittedLattices[i], ucsDirections, ucsBorderNorms);
+
+                fittedNodesCount[i] = refinement.getFittedPeaks(fittedLattices[i], fittedPeaks, ucsDirections, ucsBorderNorms);
+            }
 
-                int fittedNodesCount = refinement.getFittedPeaks(currentLattice, fittedPeaks, ucsDirections, ucsBorderNorms);
-                if (fittedNodesCount > maxFittedNodesCount)
+            Lattice bestLattice = indexedLattice;
+            int maxFittedNodesCount = refinement.getFittedPeaks(indexedLattice, fittedPeaks, ucsDirections, ucsBorderNorms);
+            for (int i = 0; i < REFINEMENT_TRIES; ++i)
+            {
+                if (fittedNodesCount[i] > maxFittedNodesCount)
                 {
-                    maxFittedNodesCount = fittedNodesCount;
-                    bestLattice = currentLattice;
+                    maxFittedNodesCount = fittedNodesCount[i];
+                    indexedLattice = fittedLattices[i];
                 }
             }
-            indexedLattice = bestLattice;
         }
         break;
         default:
             break;
     }
 
+    indexedLattice.minimize();
+
     return refinement.getFittedPeaks(indexedLattice, fittedPeaks, ucsDirections, ucsBorderNorms);
 
     // int fittedPeaksCount = refinement.getFittedPeaksCount(indexedLattice, ucsDirections, ucsBorderNorms);