renaming variables to match naming scheme in publication

src/Sinogram.cpp

@@ -77,8 +77,8 @@ namespace pinkIndexer
         EigenSTL::vector_Matrix3Xf candidateReflectionsDirections;	//unit vectors to all candidate reflections
         reflectionsInRangeFinder.getReflectionsInRanges(candidateReflectionsDirections, ucsBorderNorms);	//get candidate reflections
 
-        Matrix3Xf n(3, anglesCount);	//resulting rotation axes
-        Array<float, 1, Eigen::Dynamic> gammah(anglesCount); // gamma half - resulting rotation angle (around n)
+        Matrix3Xf e(3, anglesCount);	//resulting rotation axes
+        Array<float, 1, Eigen::Dynamic> thetah(anglesCount); // theta half - resulting rotation angle (around e)
         Matrix<uint32_t, 3, Eigen::Dynamic> validSinogramPoints_matrix(3, anglesCount);		// coordinates (3D) of sampled curve in sinogram
         Matrix<uint32_t, 1, Eigen::Dynamic> validSinogramPoints_matrix_lin(1, anglesCount);	//linear indices (1D) of validSinogramPoints_matrix
 
@@ -93,7 +93,7 @@ namespace pinkIndexer
                 cout << "computed " << 100 * (float)measuredPeakNumber / measuredPeaksCount << "%" << endl;
             }
 
-            Vector3f l = ucsDirections.col(measuredPeakNumber); // rotation axis
+            Vector3f q = ucsDirections.col(measuredPeakNumber); 
 
             Matrix3Xf& candidateReflectionDirections = candidateReflectionsDirections[measuredPeakNumber];
             if (candidateReflectionDirections.cols() == 0)
@@ -103,15 +103,15 @@ namespace pinkIndexer
             int candidatePeaksCount = candidateReflectionDirections.cols();
             for (int candidatePeakNumber = 0; candidatePeakNumber < candidatePeaksCount; candidatePeakNumber++)	//calculation of curves for each candidate peak
             {
-                const auto& candidateReflectionDirection = candidateReflectionDirections.col(candidatePeakNumber);
+                const auto& h = candidateReflectionDirections.col(candidatePeakNumber);
 
-                Vector3f m = (candidateReflectionDirection + l).normalized();
+                Vector3f m = (h + q).normalized();
 
-                gammah = acos(sinah * (-l.dot(m)));
-                n = (m * cosah.matrix() + l.cross(m) * sinah.matrix()).array().rowwise() / sin(gammah);
+                thetah = acos(sinah * (-q.dot(m)));
+                e = (m * cosah.matrix() + q.cross(m) * sinah.matrix()).array().rowwise() / sin(thetah);
 
-                Matrix3Xf& validSinogramPoints = n; // memory reuse
-                validSinogramPoints = (n.array().rowwise() * atan(gammah / 2)).matrix();
+                Matrix3Xf& validSinogramPoints = e; // memory reuse
+                validSinogramPoints = (e.array().rowwise() * atan(thetah / 2)).matrix();
 
                 validSinogramPoints_matrix = ((validSinogramPoints * realToMatrixScaling).array() + realToMatrixOffset).matrix().cast<uint32_t>();
                 validSinogramPoints_matrix_lin = validSinogramPoints_matrix.row(0) + strides * validSinogramPoints_matrix.bottomRows(2);
@@ -134,10 +134,10 @@ namespace pinkIndexer
         }
     }
 
-    void Sinogram::computePartOfSinogramOnePeak(Matrix3Xf* candidateReflectionDirections, Vector3f* l, int threadCount, int threadNumber)
+    void Sinogram::computePartOfSinogramOnePeak(Matrix3Xf* candidateReflectionDirections, Vector3f* q, int threadCount, int threadNumber)
     {
-        Matrix3Xf n(3, anglesCount);
-        Array<float, 1, Eigen::Dynamic> gammah(anglesCount); // gamma half
+        Matrix3Xf e(3, anglesCount);
+        Array<float, 1, Eigen::Dynamic> thetah(anglesCount);	//theta half
         Matrix<uint32_t, 3, Eigen::Dynamic> validSinogramPoints_matrix(3, anglesCount);
         Matrix<uint32_t, 1, Eigen::Dynamic> validSinogramPoints_matrix_lin(1, anglesCount);
 
@@ -149,20 +149,20 @@ namespace pinkIndexer
         int candidatePeaksCount = candidateReflectionDirections->cols();
         for (int candidatePeakNumber = threadNumber; candidatePeakNumber < candidatePeaksCount; candidatePeakNumber += threadCount)
         {
-            const auto& candidateReflectionDirection = candidateReflectionDirections->col(candidatePeakNumber);
+            const auto& h = candidateReflectionDirections->col(candidatePeakNumber);
 
-            Vector3f m = (candidateReflectionDirection + *l).normalized();
+            Vector3f m = (h + *q).normalized();
 
-            temp2 = sinah * (-l->dot(m));
-            gammah = acos(temp2);
+            temp2 = sinah * (-q->dot(m));
+            thetah = acos(temp2);
             temp1.noalias() = m * cosah.matrix();
-            temp1.noalias() += l->cross(m) * sinah.matrix();
-            n = temp1.array().rowwise() * rsqrt(1 - temp2.square());
-            // gammah = acos(sinah * (-l->dot(m)));
-            // n = (m * cosah.matrix() + l->cross(m) * sinah.matrix()).array().rowwise() / sin(gammah);
+            temp1.noalias() += q->cross(m) * sinah.matrix();
+            e = temp1.array().rowwise() * rsqrt(1 - temp2.square());
+            // thetah = acos(sinah * (-q->dot(m)));
+            // e = (m * cosah.matrix() + q->cross(m) * sinah.matrix()).array().rowwise() / sin(thetah);
 
-            Matrix3Xf& validSinogramPoints = n; // memory reuse
-            validSinogramPoints = (n.array().rowwise() * atan(gammah / 2)).matrix();
+            Matrix3Xf& validSinogramPoints = e; // memory reuse
+            validSinogramPoints = (e.array().rowwise() * atan(thetah / 2)).matrix();
 
             validSinogramPoints_matrix = ((validSinogramPoints * realToMatrixScaling).array() + realToMatrixOffset).matrix().cast<uint32_t>();
             validSinogramPoints_matrix_lin = validSinogramPoints_matrix.row(0);
@@ -201,7 +201,7 @@ namespace pinkIndexer
                 cout << "computed " << 100 * (float)measuredPeakNumber / measuredPeaksCount << "%" << endl;
             }
 
-            Vector3f l = ucsDirections.col(measuredPeakNumber); // rotation axis
+            Vector3f q = ucsDirections.col(measuredPeakNumber); // rotation axis
 
             Matrix3Xf& candidateReflectionDirections = candidateReflectionsDirections[measuredPeakNumber];
             if (candidateReflectionDirections.cols() == 0)
@@ -211,7 +211,7 @@ namespace pinkIndexer
 
             for (int threadNumber = 0; threadNumber < slaveThreadCount; threadNumber++)
             {
-                threads.push_back(thread(&Sinogram::computePartOfSinogramOnePeak, this, &candidateReflectionDirections, &l, slaveThreadCount, threadNumber));
+                threads.push_back(thread(&Sinogram::computePartOfSinogramOnePeak, this, &candidateReflectionDirections, &q, slaveThreadCount, threadNumber));
             }
             for (int threadNumber = 0; threadNumber < slaveThreadCount; threadNumber++)
             {
@@ -247,7 +247,7 @@ namespace pinkIndexer
                 cout << "computed " << 100 * (float)measuredPeakNumber / measuredPeaksCount << "%" << endl;
             }
 
-            Vector3f l = ucsDirections.col(measuredPeakNumber); // rotation axis
+            Vector3f q = ucsDirections.col(measuredPeakNumber); 
 
             Matrix3Xf& candidateReflectionDirections = candidateReflectionsDirections[measuredPeakNumber];
             if (candidateReflectionDirections.cols() == 0)
@@ -257,7 +257,7 @@ namespace pinkIndexer
 
             for (int threadNumber = 0; threadNumber < slaveThreadCount; threadNumber++)
             {
-                threads.push_back(thread(&Sinogram::computePartOfSinogramOnePeak, this, &candidateReflectionDirections, &l, slaveThreadCount, threadNumber));
+                threads.push_back(thread(&Sinogram::computePartOfSinogramOnePeak, this, &candidateReflectionDirections, &q, slaveThreadCount, threadNumber));
             }
 
             if (measuredPeakNumber > 0)