better handling of too high-q peaks

src/ReflectionsInRangeFinder.cpp

@@ -8,9 +8,9 @@ using namespace Eigen;
 
 ReflectionsInRangeFinder::ReflectionsInRangeFinder(const Lattice& lattice)
 {
-    Matrix3f basis = lattice.getBasis();
+    const Matrix3f basis = lattice.getBasis();
 
-    int maxMillerIndex = 100;
+    int maxMillerIndex = 175;
     maxRadius = maxMillerIndex * lattice.getBasisVectorNorms().minCoeff();
     int millerIndicesPerDirection = 2 * maxMillerIndex + 1;
     Matrix3Xf reflections(3, (int)pow(millerIndicesPerDirection, 3));
@@ -33,13 +33,13 @@ ReflectionsInRangeFinder::ReflectionsInRangeFinder(const Lattice& lattice)
     iota(sortIndices.begin(), sortIndices.end(), 0);
     sort(sortIndices.begin(), sortIndices.end(), [&norms](uint32_t i, uint32_t j) { return norms[i] < norms[j]; });
 
-    reflectionsDirections_sorted.resize(3, reflections.cols() - 1);	//leave out  reflection (0,0,0)
+    reflectionsDirections_sorted.resize(3, reflections.cols() - 1); // leave out  reflection (0,0,0)
     norms_sorted.resize(reflections.cols());
     for (int i = 1; i < reflections.cols(); ++i)
     {
         uint32_t sortIndex = sortIndices[i];
         norms_sorted[i] = norms(sortIndex);
-        reflectionsDirections_sorted.col(i-1) = reflections.col(sortIndex) / norms_sorted[i];
+        reflectionsDirections_sorted.col(i - 1) = reflections.col(sortIndex) / norms_sorted[i];
     }
 }
 
@@ -48,17 +48,25 @@ void ReflectionsInRangeFinder::getReflectionsInRanges(EigenSTL::vector_Matrix3Xf
 {
     if (ranges.row(1).maxCoeff() > maxRadius)
     {
-        throw BadInputException("getReflectionsInRanges is called with too large ranges! Limit the maximum resolution of the Bragg peaks!");
+        cerr << "the maximum resolution of Bragg spots exceeds the hardcoded limit of " << maxRadius
+             << "A^-1. These Bragg spots will not be used for indexing, but they will be used for refinement!" << endl;
     }
 
     candidateReflectionsDirections.resize(ranges.cols());
 
     for (int i = 0; i < ranges.cols(); i++)
     {
-        vector<float>::iterator low, up;
-        low = lower_bound(norms_sorted.begin(), norms_sorted.end(), ranges(0, i));
-        up = upper_bound(norms_sorted.begin(), norms_sorted.end(), ranges(1, i));
+        if (ranges(1, i) > maxRadius)
+        {
+            candidateReflectionsDirections[i] = Matrix3Xf(3, 0);
+        }
+        else
+        {
+            vector<float>::iterator low, up;
+            low = lower_bound(norms_sorted.begin(), norms_sorted.end(), ranges(0, i));
+            up = upper_bound(norms_sorted.begin(), norms_sorted.end(), ranges(1, i));
 
-        candidateReflectionsDirections[i] = reflectionsDirections_sorted.block(0, low - norms_sorted.begin(), 3, up - low);
+            candidateReflectionsDirections[i] = reflectionsDirections_sorted.block(0, low - norms_sorted.begin(), 3, up - low);
+        }
     }
 }
\ No newline at end of file

src/Sinogram.cpp

@@ -86,7 +86,7 @@ void Sinogram::computeSinogram(const Eigen::Matrix3Xf& ucsDirections, const Eige
     Matrix<uint32_t, 28, 1> validSinogramPoints_matrix_lin_dilated;
 
     int measuredPeaksCount = ucsDirections.cols();
-	cout << "peak count used for indexing: " << measuredPeaksCount << endl;
+    cout << "peak count used for indexing: " << measuredPeaksCount << endl;
     for (int measuredPeakNumber = 0; measuredPeakNumber < measuredPeaksCount; measuredPeakNumber++)
     {
         if (measuredPeakNumber % 16 == 0)
@@ -97,6 +97,8 @@ void Sinogram::computeSinogram(const Eigen::Matrix3Xf& ucsDirections, const Eige
         Vector3f l = ucsDirections.col(measuredPeakNumber); // rotation axis
 
         Matrix3Xf& candidateReflectionDirections = candidateReflectionsDirections[measuredPeakNumber];
+        if (candidateReflectionDirections.cols() == 0)
+            continue;
 
         fill(sinogram_oneMeasuredPeak.begin(), sinogram_oneMeasuredPeak.end(), 0);
         int candidatePeaksCount = candidateReflectionDirections.cols();
@@ -193,17 +195,19 @@ void Sinogram::computeSinogramParallel(const Eigen::Matrix3Xf& ucsDirections, co
         sinogram_oneMeasuredPeak_matrixMapped(sinogram_oneMeasuredPeak.data(), sinogram_oneMeasuredPeak.size());
 
     int measuredPeaksCount = ucsDirections.cols();
-	cout << "peak count used for indexing: " << measuredPeaksCount << endl;
+    cout << "peak count used for indexing: " << measuredPeaksCount << endl;
     for (int measuredPeakNumber = 0; measuredPeakNumber < measuredPeaksCount; measuredPeakNumber++)
     {
-		if (measuredPeakNumber % 16 == 0)
-		{
-			cout << "computed " << 100 * (float)measuredPeakNumber / measuredPeaksCount << "%" << endl;
-		}
+        if (measuredPeakNumber % 16 == 0)
+        {
+            cout << "computed " << 100 * (float)measuredPeakNumber / measuredPeaksCount << "%" << endl;
+        }
 
         Vector3f l = ucsDirections.col(measuredPeakNumber); // rotation axis
 
         Matrix3Xf& candidateReflectionDirections = candidateReflectionsDirections[measuredPeakNumber];
+        if (candidateReflectionDirections.cols() == 0)
+            continue;
 
         fill(sinogram_oneMeasuredPeak.begin(), sinogram_oneMeasuredPeak.end(), 0);
 
@@ -241,15 +245,17 @@ void Sinogram::computeSinogramParallel2(const Eigen::Matrix3Xf& ucsDirections, c
     cout << "peak count used for indexing: " << measuredPeaksCount << endl;
     for (int measuredPeakNumber = 0; measuredPeakNumber < measuredPeaksCount; measuredPeakNumber++)
     {
-		if (measuredPeakNumber % 16 == 0)
-		{
-			cout << "computed " << 100 * (float)measuredPeakNumber / measuredPeaksCount << "%" << endl;
-		}
+        if (measuredPeakNumber % 16 == 0)
+        {
+            cout << "computed " << 100 * (float)measuredPeakNumber / measuredPeaksCount << "%" << endl;
+        }
 
 
         Vector3f l = ucsDirections.col(measuredPeakNumber); // rotation axis
 
         Matrix3Xf& candidateReflectionDirections = candidateReflectionsDirections[measuredPeakNumber];
+        if (candidateReflectionDirections.cols() == 0)
+            continue;
 
         fill(sinogram_oneMeasuredPeak.begin(), sinogram_oneMeasuredPeak.end(), 0);