perf: checking why 5 samples work slower

moving to do codecov, correcting a missing semicolon

Author: MRKonrad

lib/OxCalculatorT1Molli.hxx

@@ -192,6 +192,9 @@ namespace Ox {
 
         MeasureType T1 = (B/A-1)*T1star;
 
+        if (fabs(T1) < std::numeric_limits<MeasureType>::min())
+            return 1; // EXIT_FAILURE
+
         MeasureType dydA = 0;
         MeasureType dydB = 0;
         MeasureType dydT1 = 0;

lib/OxFitterLevenbergMarquardtVnl.h

@@ -123,8 +123,7 @@ namespace Ox {
                     if (this->_UseGradient) {
                         _FunctionsAdaptedToVnl = new FunctionsAdaptedToVnlType(nDims, nSamples, vnl_least_squares_function::use_gradient);
                     } else {
-                        _FunctionsAdaptedToVnl = new FunctionsAdaptedToVnlType(nDims, nSamples,
-                                                                               vnl_least_squares_function::no_gradient);
+                        _FunctionsAdaptedToVnl = new FunctionsAdaptedToVnlType(nDims, nSamples, vnl_least_squares_function::no_gradient);
                     }
 
                     _FunctionsAdaptedToVnl->setFunctionsT1(this->_FunctionsT1);

lib/OxFunctionsT1AdapterVnlLeastSquares.h

@@ -46,15 +46,17 @@ namespace Ox {
         /**
          * constructor
          */
-        FunctionsT1AdapterVnlLeastSquares(int nDims, int nSamples, UseGradient UseGradientVariable) : vnl_least_squares_function (nDims, nSamples, UseGradientVariable){
+        FunctionsT1AdapterVnlLeastSquares(int nDims, int nSamples, UseGradient UseGradientVariable)
+                : vnl_least_squares_function (nDims, nSamples, UseGradientVariable){
             _FunctionsT1 = 0; // nullpointer
         };
 
         /**
          * copy constructor
          * @param old
          */
-        FunctionsT1AdapterVnlLeastSquares(const FunctionsT1AdapterVnlLeastSquares &old) : vnl_least_squares_function(old){
+        FunctionsT1AdapterVnlLeastSquares(const FunctionsT1AdapterVnlLeastSquares &old)
+                : vnl_least_squares_function(old){
             _FunctionsT1 = old._FunctionsT1;
         }
 

tests/OxCalculatorT1Molli_test.cpp

@@ -4,6 +4,7 @@
  * \date 2018/08/01
  */
 
+#include <OxFitterLevenbergMarquardtVnl.h>
 #include "gtest/gtest.h"
 #include "OxTestData.h"
 
@@ -16,6 +17,10 @@
 #include "OxStartPointCalculatorDefault3Dims.h"
 #include "OxCalculatorT1Molli.h"
 
+#ifdef USE_ITK
+#include "itkTimeProbe.h"
+#endif
+
 //TODO: make sure correctSDs are accually correct
 
 #ifdef USE_VNL
@@ -268,3 +273,63 @@ TEST(OxCalculatorT1Molli, correctSDs) {
 }
 
 #endif
+
+////TODO: no difference between 5 samples and 7 samples here.
+//#ifdef USE_ITK
+//
+//TEST(OxCalculatorT1Molli, samples5) {
+//
+//    typedef double TYPE;
+//    int nRepetitions = 10000;
+//
+//    char filePath5 [] = "testData/blood_5samples.yaml";
+//    Ox::TestData<TYPE> testData5(filePath5);
+//    int nSamples5 = testData5.getNSamples();
+//
+//    char filePath7 [] = "testData/blood.yaml";
+//    Ox::TestData<TYPE> testData7(filePath7);
+//    int nSamples7 = testData7.getNSamples();
+//
+//    // init the necessary objects
+//    Ox::FunctionsT1Basic<TYPE> functionsObject;
+//    Ox::FitterLevenbergMarquardtVnl<TYPE> fitterAmoebaVnl;
+//    Ox::SignCalculatorRealImag<TYPE> signCalculator;
+//    Ox::StartPointCalculatorDefault3Dims<TYPE> startPointCalculator;
+//    Ox::CalculatorT1Molli<TYPE> calculatorT1Molli;
+//
+//    // configure
+//    calculatorT1Molli.setFunctionsT1(&functionsObject);
+//    calculatorT1Molli.setFitter(&fitterAmoebaVnl);
+//    calculatorT1Molli.setSignCalculator(&signCalculator);
+//    calculatorT1Molli.setStartPointCalculator(&startPointCalculator);
+//
+//    // set the data
+//    calculatorT1Molli.setNSamples(nSamples5);
+//    calculatorT1Molli.setInvTimes(testData5.getInvTimesPtr());
+//    calculatorT1Molli.setSigPha(testData5.getSignalPhaPtr());
+//    calculatorT1Molli.setSigMag(testData5.getSignalMagPtr());
+//
+//    printf("\n");
+//    itk::TimeProbe clock;
+//    clock.Start();
+//    for (int i = 0; i < nRepetitions; i++)
+//        calculatorT1Molli.calculate();
+//    clock.Stop();
+//    printf("Calculation5 time: %.12fs.\n", clock.GetTotal());
+//
+//    // set the data
+//    calculatorT1Molli.setNSamples(nSamples7);
+//    calculatorT1Molli.setInvTimes(testData7.getInvTimesPtr());
+//    calculatorT1Molli.setSigPha(testData7.getSignalPhaPtr());
+//    calculatorT1Molli.setSigMag(testData7.getSignalMagPtr());
+//
+//    clock.Reset();
+//    clock.Start();
+//    for (int i = 0; i < nRepetitions; i++)
+//        calculatorT1Molli.calculate();
+//    clock.Stop();
+//    printf("Calculation7 time: %.12fs.\n", clock.GetTotal());
+//
+//}
+//
+//#endif