added stage of fixed refinement for center refinement

include/PinkIndexer.h

@@ -41,7 +41,7 @@ class PinkIndexer
         firstFixedThenVariableLatticeParameters,
         firstFixedThenVariableLatticeParametersMultiSeedLengths,
         firstFixedThenVariableLatticeParametersMultiSeed,
-        variableLatticeParametersCenterAdjustmentMultiSeed
+        firstFixedThenVariableLatticeParametersCenterAdjustmentMultiSeed
     };
 
     PinkIndexer(const ExperimentSettings& experimentSettings, ConsideredPeaksCount consideredPeaksCount, AngleResolution angleResolution,

include/adaptions/crystfel/PinkIndexer.h

@@ -38,7 +38,7 @@ typedef enum
     REFINEMENT_TYPE_variableLatticeParameters = 2,
     REFINEMENT_TYPE_firstFixedThenVariableLatticeParameters = 3,
     REFINEMENT_TYPE_firstFixedThenVariableLatticeParametersMultiSeed = 4,
-    REFINEMENT_TYPE_variableLatticeParametersCenterAdjustmentMultiSeed = 5,
+    REFINEMENT_TYPE_firstFixedThenVariableLatticeParametersCenterAdjustmentMultiSeed = 5,
     REFINEMENT_TYPE_lastEnum
 } refinementType_t;
 

src/PinkIndexer.cpp

@@ -144,7 +144,7 @@ void PinkIndexer::refine(Lattice& indexedLattice, Vector2f& centerShift, const M
             }
         }
         break;
-        case RefinementType::variableLatticeParametersCenterAdjustmentMultiSeed:
+        case RefinementType::firstFixedThenVariableLatticeParametersCenterAdjustmentMultiSeed:
         {
             constexpr int refinementTries = 750;
             int fittedNodesCount[refinementTries];
@@ -164,6 +164,10 @@ void PinkIndexer::refine(Lattice& indexedLattice, Vector2f& centerShift, const M
                 fittedLattices[i] = Lattice(currentBasis);
                 centerShifts[i] = Vector2f::Random() * 80e-6;
 
+				refinement.setTolerance(min(finalRefinementTolerance * 2.5, 0.12));
+                refinement.refineFixedLattice(fittedLattices[i], ucsDirections, ucsBorderNorms);
+                refinement.setTolerance(min(finalRefinementTolerance * 1.8, 0.10));
+                refinement.refineVariableLatticeWithCenter(fittedLattices[i], centerShifts[i], detectorPeaks_m);
                 refinement.setTolerance(finalRefinementTolerance);
                 refinement.refineVariableLatticeWithCenter(fittedLattices[i], centerShifts[i], detectorPeaks_m);
 

src/adaptions/crystfel/PinkIndexer.cpp

@@ -73,8 +73,8 @@ extern "C" PinkIndexer* PinkIndexer_new(ExperimentSettings* experimentSettings,
         case REFINEMENT_TYPE_firstFixedThenVariableLatticeParametersMultiSeed:
             refinementType_enumClass = PinkIndexer::RefinementType::firstFixedThenVariableLatticeParametersMultiSeed;
             break;
-        case REFINEMENT_TYPE_variableLatticeParametersCenterAdjustmentMultiSeed:
-            refinementType_enumClass = PinkIndexer::RefinementType::variableLatticeParametersCenterAdjustmentMultiSeed;
+        case REFINEMENT_TYPE_firstFixedThenVariableLatticeParametersCenterAdjustmentMultiSeed:
+            refinementType_enumClass = PinkIndexer::RefinementType::firstFixedThenVariableLatticeParametersCenterAdjustmentMultiSeed;
             break;
 
         default: