refactoring + finer multi seed refinement

include/PinkIndexer.h

@@ -53,6 +53,7 @@ class PinkIndexer
   private:
     void reducePeakCount(Eigen::Matrix3Xf& ucsDirections, Eigen::Array2Xf& ucsBorderNorms, Eigen::RowVectorXf& intensities,
                          const Eigen::Matrix2Xf& detectorPeaks_m);
+    void refine(Lattice& indexedLattice, const Eigen::Matrix3Xf& ucsDirections, const Eigen::Array2Xf& ucsBorderNorms);
 
     float getAngleResolution();
     int getConsideredPeaksCount();

include/Refinement.h

@@ -16,6 +16,8 @@ class Refinement
     int getFittedPeaksCount(Lattice& lattice, const Eigen::Matrix3Xf& ucsDirections, const Eigen::Matrix2Xf& ucsBorderNorms);
     int getFittedPeaks(Lattice& lattice, Eigen::Array<bool, Eigen::Dynamic, 1>& fittedPeaks, const Eigen::Matrix3Xf& ucsDirections,
                        const Eigen::Matrix2Xf& ucsBorderNorms);
+    double getMeanDefect(const Eigen::Matrix3f& basis, const Eigen::Matrix3Xf& ucsDirections, const Eigen::Matrix2Xf& ucsBorderNorms,
+                         bool significantChangesToPreviousCall = true);
 
     void setTolerance(float tolerance)
     {
@@ -29,8 +31,6 @@ class Refinement
   private:
     void getDefects(Eigen::ArrayXf& defects, const Eigen::Matrix3f& basis, const Eigen::Matrix3Xf& ucsDirections, const Eigen::Matrix2Xf& ucsBorderNorms,
                     bool significantChangesToPreviousCall = true);
-    double getMeanDefect(const Eigen::Matrix3f& basis, const Eigen::Matrix3Xf& ucsDirections, const Eigen::Matrix2Xf& ucsBorderNorms,
-                         bool significantChangesToPreviousCall = true);
 
     float tolerance;
 

src/PinkIndexer.cpp

@@ -64,6 +64,17 @@ int PinkIndexer::indexPattern(Lattice& indexedLattice, Eigen::Array<bool, Eigen:
     Matrix3f bestBasis = bestRotation * sampleLattice.getBasis();
     indexedLattice = Lattice(bestBasis);
 
+    refine(indexedLattice, ucsDirections, ucsBorderNorms);
+
+    indexedLattice.minimize();
+
+    return refinement.getFittedPeaks(indexedLattice, fittedPeaks, ucsDirections, ucsBorderNorms);
+
+    // sinogram.saveToFile("C:\\DesyFiles\\workspaces\\VisualStudio_workspace\\pinkIndexer\\workfolder\\sinogram");
+}
+
+void PinkIndexer::refine(Lattice& indexedLattice, const Matrix3Xf& ucsDirections, const Array2Xf& ucsBorderNorms)
+{
     switch (refinementType)
     {
         case RefinementType::none:
@@ -92,6 +103,7 @@ int PinkIndexer::indexPattern(Lattice& indexedLattice, Eigen::Array<bool, Eigen:
         {
 #define REFINEMENT_TRIES 250
             int fittedNodesCount[REFINEMENT_TRIES];
+            double fittedNodesMeanDefects[REFINEMENT_TRIES];
             Lattice fittedLattices[REFINEMENT_TRIES];
 
             float maxRelativeDeviation = 0.012;
@@ -111,16 +123,18 @@ int PinkIndexer::indexPattern(Lattice& indexedLattice, Eigen::Array<bool, Eigen:
                 refinement.setTolerance(finalRefinementTolerance);
                 refinement.refineVariableLattice(fittedLattices[i], ucsDirections, ucsBorderNorms);
 
-                fittedNodesCount[i] = refinement.getFittedPeaks(fittedLattices[i], fittedPeaks, ucsDirections, ucsBorderNorms);
+                fittedNodesCount[i] = refinement.getFittedPeaksCount(fittedLattices[i], ucsDirections, ucsBorderNorms);
+                fittedNodesMeanDefects[i] = refinement.getMeanDefect(fittedLattices[i].getBasis(), ucsDirections, ucsBorderNorms);
             }
 
-            Lattice bestLattice = indexedLattice;
-            int maxFittedNodesCount = refinement.getFittedPeaks(indexedLattice, fittedPeaks, ucsDirections, ucsBorderNorms);
+            int maxFittedNodesCount = refinement.getFittedPeaksCount(indexedLattice, ucsDirections, ucsBorderNorms);
+            double minFittedNodesMeanDefect = refinement.getMeanDefect(indexedLattice.getBasis(), ucsDirections, ucsBorderNorms);
             for (int i = 0; i < REFINEMENT_TRIES; ++i)
             {
-                if (fittedNodesCount[i] > maxFittedNodesCount)
+                if (fittedNodesCount[i] > maxFittedNodesCount || (fittedNodesCount[i] == maxFittedNodesCount && fittedNodesMeanDefects[i] < minFittedNodesMeanDefect))
                 {
                     maxFittedNodesCount = fittedNodesCount[i];
+                    minFittedNodesMeanDefect = fittedNodesMeanDefects[i];
                     indexedLattice = fittedLattices[i];
                 }
             }
@@ -129,22 +143,6 @@ int PinkIndexer::indexPattern(Lattice& indexedLattice, Eigen::Array<bool, Eigen:
         default:
             break;
     }
-
-    indexedLattice.minimize();
-
-    return refinement.getFittedPeaks(indexedLattice, fittedPeaks, ucsDirections, ucsBorderNorms);
-
-    // int fittedPeaksCount = refinement.getFittedPeaksCount(indexedLattice, ucsDirections, ucsBorderNorms);
-    // if ((fittedPeaksCount >= 20 && fittedPeaksCount >= detectorPeaks_m.cols() * 0.3) || fittedPeaksCount >= detectorPeaks_m.cols() * 0.5)
-    //{
-    //    return true;
-    //}
-    // else
-    //{
-    //    return false;
-    //}
-
-    // sinogram.saveToFile("C:\\DesyFiles\\workspaces\\VisualStudio_workspace\\pinkIndexer\\workfolder\\sinogram");
 }
 
 void PinkIndexer::reducePeakCount(Matrix3Xf& ucsDirections, Array2Xf& ucsBorderNorms, RowVectorXf& intensities, const Eigen::Matrix2Xf& detectorPeaks_m)