Documentation (with Oleksandr)

src/PinkIndexer.cpp

@@ -118,12 +118,12 @@ namespace pinkIndexer
                 break;
             case RefinementType::firstFixedThenVariableLatticeParametersMultiSeed:
             {
-                constexpr int refinementTries = 1000;
+                constexpr int refinementTries = 1000;  //TODO: increase if better refinement needed
                 int fittedNodesCount[refinementTries];
                 double fittedNodesMeanDefects[refinementTries];
                 Lattice fittedLattices[refinementTries];
 
-                float maxRelativeDeviation = 0.0125;
+                float maxRelativeDeviation = 0.0125;	//TODO: Parameter??
                 Array<float, 1, 3> columnDeviationNorms = indexedLattice.getBasis().colwise().norm() * maxRelativeDeviation;
 
 #ifdef OPENMP_AVAILABLE
@@ -164,7 +164,7 @@ namespace pinkIndexer
                     //    (fittedNodesCount[i] == maxFittedNodesCount && fittedNodesMeanDefects[i] < minFittedNodesMeanDefect))
                     if (fittedNodesCount[i] / maxFittedNodesCount > 1.2 ||
                         ((fittedNodesCount[i] > maxFittedNodesCount || fittedNodesMeanDefects[i] < minFittedNodesMeanDefect) &&
-                         (fittedNodesCount[i] / maxFittedNodesCount - 1) * 3 > (minFittedNodesMeanDefect / fittedNodesMeanDefects[i] - 1)))
+                         (fittedNodesCount[i] / maxFittedNodesCount - 1) * 3 > (minFittedNodesMeanDefect / fittedNodesMeanDefects[i] - 1)))  //TODO: can be optimized
                     {
                         maxFittedNodesCount = fittedNodesCount[i];
                         minFittedNodesMeanDefect = fittedNodesMeanDefects[i];
@@ -175,7 +175,7 @@ namespace pinkIndexer
             break;
             case RefinementType::firstFixedThenVariableLatticeParametersCenterAdjustmentMultiSeed:
             {
-                constexpr int refinementTries = 2000;
+                constexpr int refinementTries = 2000;		//TODO: increase if better refinement needed
                 int fittedNodesCount[refinementTries];
                 double fittedNodesMeanDefects[refinementTries];
                 Lattice fittedLattices[refinementTries];
@@ -203,7 +203,7 @@ namespace pinkIndexer
                         currentBasis = indexedLattice.getBasis();
                     }
                     fittedLattices[i] = Lattice(currentBasis);
-                    centerShifts[i] = Vector2f::Random() * 80e-6;
+                    centerShifts[i] = Vector2f::Random() * 80e-6;  //TODO: hardcoded JUNGFRAU pixel size. Can be improved (maybe parameter??)
 
                     refinement.setTolerance(min(finalRefinementTolerance * 2.5, 0.12));
                     refinement.refineFixedLattice(fittedLattices[i], ucsDirections, ucsBorderNorms);

src/Refinement.cpp

@@ -32,7 +32,7 @@ namespace pinkIndexer
     void Refinement::refineVariableLattice(Lattice& lattice, const Matrix3Xf& ucsDirections, const Array2Xf& ucsBorderNorms)
     {
         Matrix3f basis = lattice.getBasis();
-        float delta = 1e-8;
+        float delta = 1e-8; //for numerical differentiation, in A^-1
 
         float stepSize = lattice.getBasisVectorNorms().maxCoeff() * 0.002;
         float minStepSize = lattice.getBasisVectorNorms().minCoeff() * 0.00001;
@@ -43,7 +43,7 @@ namespace pinkIndexer
         {
             // cout << meanDefects[i] << endl;
 
-            Array33f gradient;
+            Array33f gradient; //gradient for change of each basis matrix element
             Matrix3f offsetBasis = basis;
             offsetBasis(0, 0) += delta;
             gradient(0, 0) = getMeanDefect(offsetBasis, ucsDirections, ucsBorderNorms, false) - meanDefects[i];