Refactoring in FitObjects

Core/Algorithms/inc/FitElement.h

@@ -17,6 +17,7 @@
 #define FITELEMENT_H
 
 #include "WinDllMacros.h"
+#include <cstddef>
 
 //! @class FitElement
 //! @ingroup fitting_internal
@@ -27,10 +28,12 @@ class BA_CORE_API_ FitElement
 {
 public:
     FitElement();
-    FitElement(double simul_value, double real_value);
+    FitElement(size_t index, double simul_value, double real_value);
     FitElement(const FitElement &other);
     FitElement &operator=(const FitElement &other);
 
+    size_t getIndex() const;
+
     double getSimulValue() const;
 
     double getRealValue() const;
@@ -45,7 +48,7 @@ public:
 
 private:
     void swapContent(FitElement &other);
-
+    size_t m_index;
     double m_simul_value;
     double m_real_value;
     double m_weight;
@@ -54,6 +57,11 @@ private:
 };
 
 
+inline size_t FitElement::getIndex() const
+{
+    return m_index;
+}
+
 inline double FitElement::getSimulValue() const
 {
     return m_simul_value;

Core/Algorithms/src/FitElement.cpp

@@ -17,7 +17,8 @@
 #include <algorithm>
 
 FitElement::FitElement()
-    : m_simul_value(0.0)
+    : m_index(0)
+    , m_simul_value(0.0)
     , m_real_value(0.0)
     , m_weight(1.0)
     , m_squared_difference(0.0)
@@ -25,8 +26,9 @@ FitElement::FitElement()
 {
 }
 
-FitElement::FitElement(double simul_value, double real_value)
-    : m_simul_value(simul_value)
+FitElement::FitElement(size_t index, double simul_value, double real_value)
+    : m_index(index)
+    , m_simul_value(simul_value)
     , m_real_value(real_value)
     , m_weight(1.0)
     , m_squared_difference(0.0)
@@ -36,7 +38,8 @@ FitElement::FitElement(double simul_value, double real_value)
 
 
 FitElement::FitElement(const FitElement &other)
-    : m_simul_value(other.m_simul_value)
+    : m_index(other.m_index)
+    , m_simul_value(other.m_simul_value)
     , m_real_value(other.m_real_value)
     , m_weight(other.m_weight)
     , m_squared_difference(other.m_squared_difference)
@@ -57,6 +60,7 @@ FitElement &FitElement::operator=(const FitElement &other)
 
 void FitElement::swapContent(FitElement &other)
 {
+    std::swap(this->m_index, other.m_index);
     std::swap(this->m_simul_value, other.m_simul_value);
     std::swap(this->m_real_value, other.m_real_value);
     std::swap(this->m_weight, other.m_weight);

Examples/python/fitting/ex05_FitWithMasks/FitWithMasks.py

@@ -101,7 +101,7 @@ class DrawObserver(IObserver):
             pylab.colorbar(im)
             pylab.title('Simulated data')
             # plotting difference map
-            #diff_map = (real_data - simulated_data)/(real_data + 1)
+            # diff_map = (real_data - simulated_data)/(real_data + 1)
             diff_map= fit_suite.getFitObjects().getChiSquaredMap().getArray()
             pylab.subplot(2, 2, 3)
             im = pylab.imshow(diff_map, norm=matplotlib.colors.LogNorm(), extent=[-1.0, 1.0, 0, 2.0], vmin = 0.001, vmax = 1.0)
@@ -133,7 +133,7 @@ def run_fitting():
 
     fit_suite = FitSuite()
     # fit_suite.setMinimizer("GSLLMA")
-    fit_suite.setMinimizer("Minuit2", "Fumili")
+    # fit_suite.setMinimizer("Minuit2", "Fumili")
 
     # Here we are settings masks to the detector plane to simulate image which looks like a Pac-Man
     # from ancient arcade game

Fit/FitKernel/inc/FitObject.h

@@ -52,7 +52,7 @@ class BA_CORE_API_ FitObject : public IParameterized
 
     //! Returns simulated data
     const OutputData<double> *getSimulationData() const {
-        return m_chi2_module->getSimulationData(); }
+        return m_simulation_data.get(); }
 
 
     //! Returns chi2 module
@@ -79,7 +79,11 @@ class BA_CORE_API_ FitObject : public IParameterized
     //! Returns size of data
     size_t getSizeOfData() const;
 
-    std::vector<FitElement> calculateFitElements();
+    void calculateFitElements(std::vector<FitElement> &fit_elements);
+
+    OutputData<double> *getChiSquaredMap(std::vector<FitElement>::const_iterator first,
+                                         std::vector<FitElement>::const_iterator last) const;
+
 
  protected:
     //! Registers some class members for later access via parameter pool
@@ -92,6 +96,8 @@ class BA_CORE_API_ FitObject : public IParameterized
     GISASSimulation* m_simulation;       //!< external simulation (not owned by this)
     OutputData<double>* m_real_data;  //!< real data
     IChiSquaredModule* m_chi2_module; //!< chi2 module
+    std::auto_ptr<OutputData<double> > m_simulation_data;
+
     double m_weight;                //!< weight of data set in chi2 calculations
 };
 

Fit/FitKernel/inc/FitSuite.h

@@ -118,6 +118,14 @@ class BA_CORE_API_ FitSuite : public IObservable
     //! Returns total wall time in seconds which was spend for run fit
     double getRunTime() const;
 
+
+    const OutputData<double> * getRealData(size_t i_item = 0) const { return m_fit_objects.getRealData(i_item); }
+
+    const OutputData<double> * getSimulationData(size_t i_item = 0) const { return m_fit_objects.getSimulationData(i_item); }
+
+    const OutputData<double> * getChiSquaredMap(size_t i_item = 0) const { return m_fit_objects.getChiSquaredMap(i_item); }
+
+
  private:
     //! disabled copy constructor and assignment operator
     FitSuite& operator=(const FitSuite& );

Fit/FitKernel/inc/FitSuiteObjects.h

@@ -35,7 +35,7 @@ class BA_CORE_API_  FitSuiteObjects : public IParameterized
     typedef SafePointerVector<FitObject > FitObjects_t;
 
     FitSuiteObjects();
-    virtual ~FitSuiteObjects(){}
+    virtual ~FitSuiteObjects();
 
     //! clear all data
     void clear();
@@ -105,8 +105,9 @@ class BA_CORE_API_  FitSuiteObjects : public IParameterized
         m_nfree_parameters = nfree_parameters; }
 
     //! Returns chi-squared map
-    OutputData<double> * getChiSquaredMap(size_t i_item = 0);
+    const OutputData<double> * getChiSquaredMap(size_t i_item = 0) const;
 
+    void setChiSquaredModule(const IChiSquaredModule &chi2_module);
 
  protected:
     //! Registers some class members for later access via parameter pool
@@ -145,6 +146,8 @@ class BA_CORE_API_  FitSuiteObjects : public IParameterized
     double m_chi_squared_value;
 
     std::vector<FitElement> m_fit_elements;
+    std::auto_ptr<IChiSquaredModule> m_chi2_module;
+
 };
 
 #endif // FITSUITEKIT_H

Fit/FitKernel/src/FitObject.cpp

@@ -107,24 +107,33 @@ size_t FitObject::getSizeOfData() const
     return result;
 }
 
-std::vector<FitElement> FitObject::calculateFitElements()
+void FitObject::calculateFitElements(std::vector<FitElement> &fit_elements)
 {
-    std::vector<FitElement> result;
-
     m_simulation->runSimulation();
-    boost::scoped_ptr<OutputData<double> > sim_data(m_simulation->getIntensityData());
+    m_simulation_data.reset(m_simulation->getIntensityData());
 
     const OutputData<bool> *masks(0);
     if(m_simulation->getInstrument().getDetector()->hasMasks()) {
         masks = m_simulation->getInstrument().getDetector()->getDetectorMask()->getMaskData();
     }
 
-    for(size_t index=0; index<sim_data->getAllocatedSize(); ++index) {
+    for(size_t index=0; index<m_simulation_data->getAllocatedSize(); ++index) {
         if(masks && (*masks)[index]) continue;
-        FitElement element((*sim_data)[index], (*m_real_data)[index]);
-        result.push_back(element);
+        FitElement element(index, (*m_simulation_data)[index], (*m_real_data)[index]);
+        fit_elements.push_back(element);
+    }
+}
+
+OutputData<double> *FitObject::getChiSquaredMap(std::vector<FitElement>::const_iterator first,
+                                                std::vector<FitElement>::const_iterator last) const
+{
+    OutputData<double> *result = new OutputData<double>;
+    result->copyShapeFrom(*m_simulation_data);
+
+    for(std::vector<FitElement>::const_iterator it=first; it!=last; ++it) {
+        (*result)[it->getIndex()] = it->getSquaredDifference();
+
     }
 
-    m_chi2_module->processFitElements(result.begin(), result.end());
     return result;
 }

Fit/FitKernel/src/FitSuite.cpp

@@ -142,7 +142,6 @@ void FitSuite::minimize()
     IMinimizer::function_chi2_t fun_chi2 = boost::bind(&FitSuiteChiSquaredFunction::evaluate, &m_function_chi2, _1);
     m_minimizer->setChiSquaredFunction( fun_chi2, m_fit_parameters.size());
 
-    std::cout << "m_fit_objects.getSizeOfDataSet() " << m_fit_objects.getSizeOfDataSet() << std::endl;
     IMinimizer::function_gradient_t fun_gradient = boost::bind(&FitSuiteGradientFunction::evaluate, &m_function_gradient, _1, _2, _3);
     m_minimizer->setGradientFunction( fun_gradient, m_fit_parameters.size(), m_fit_objects.getSizeOfDataSet() );
 

Fit/FitKernel/src/FitSuiteObjects.cpp

@@ -21,11 +21,17 @@ FitSuiteObjects::FitSuiteObjects()
 //  , m_simulation_normalize(false),
     ,m_nfree_parameters(0)
   , m_chi_squared_value(0)
+  , m_chi2_module(new ChiSquaredModule())
 {
     setName("FitSuiteObjects");
     init_parameters();
 }
 
+FitSuiteObjects::~FitSuiteObjects()
+{
+
+}
+
 //! clear all data
 void FitSuiteObjects::clear()
 {
@@ -50,19 +56,29 @@ void FitSuiteObjects::add(
 //! loop through all defined simulations and run them
 void FitSuiteObjects::runSimulations()
 {
+//    for(FitObjects_t::iterator it =
+//            m_fit_objects.begin(); it!= m_fit_objects.end(); ++it) {
+//        (*it)->getSimulation()->runSimulation();
+////        if(m_simulation_normalize) {
+////            (*it)->getSimulation()->normalize();
+////        }
+//    }
+//    m_chi_squared_value = calculateChiSquaredValue();
+
+    m_fit_elements.clear();
+    m_fit_elements.reserve(getSizeOfDataSet());
+
     for(FitObjects_t::iterator it =
             m_fit_objects.begin(); it!= m_fit_objects.end(); ++it) {
-        (*it)->getSimulation()->runSimulation();
-//        if(m_simulation_normalize) {
-//            (*it)->getSimulation()->normalize();
-//        }
+        (*it)->calculateFitElements(m_fit_elements);
     }
-    m_chi_squared_value = calculateChiSquaredValue();
-    std::cout << "aaa " << m_chi_squared_value;
 
-    for(FitObjects_t::iterator it =
-            m_fit_objects.begin(); it!= m_fit_objects.end(); ++it) {
-        m_fit_elements = (*it)->calculateFitElements();
+    if(m_fit_elements.size() != getSizeOfDataSet()) {
+        std::ostringstream message;
+        message << "FitSuiteObjects::runSimulations() -> Error. Dataset size mismatch. "
+                << " m_fit_elements.size():" << m_fit_elements.size()
+                << " getSizeOfDataset():" << getSizeOfDataSet() << std::endl;
+        throw LogicErrorException(message.str());
     }
 
     m_chi_squared_value = calculateChiSquaredValueNew();
@@ -78,7 +94,6 @@ size_t FitSuiteObjects::getSizeOfDataSet() const
             m_fit_objects.begin(); it!= m_fit_objects.end(); ++it) {
         result += (*it)->getSizeOfData();
     }
-    std::cout << "XXX " << result << std::endl;
     if(result == 0) {
         throw LogicErrorException("Panic, zero dataset size");
     }
@@ -131,6 +146,8 @@ double FitSuiteObjects::calculateChiSquaredValue()
 
 double FitSuiteObjects::calculateChiSquaredValueNew()
 {
+    m_chi2_module->processFitElements(m_fit_elements.begin(), m_fit_elements.end());
+
     double result(0);
     for(std::vector<FitElement>::iterator it=m_fit_elements.begin(); it!=m_fit_elements.end(); ++it) {
         result += it->getSquaredDifference();
@@ -146,8 +163,8 @@ double FitSuiteObjects::calculateChiSquaredValueNew()
 
 double FitSuiteObjects::getResidualValue(size_t global_index)
 {
-    if(global_index >= getSizeOfDataSet()) {
-        throw LogicErrorException(" FitSuiteObjects::getResidualValue() -> Error. Wrong size of dataset");
+    if(global_index >= m_fit_elements.size()) {
+        throw LogicErrorException(" FitSuiteObjects::getResidualValue() -> Error. Index exceeds size of dataset.");
     }
 //    size_t index(0);
 //    const FitObject *fitObject =
@@ -195,7 +212,21 @@ std::string FitSuiteObjects::addParametersToExternalPool(
     return new_path;
 }
 
-OutputData<double> *FitSuiteObjects::getChiSquaredMap(size_t i_item)
+const OutputData<double> *FitSuiteObjects::getChiSquaredMap(size_t i_item) const
+{
+    check_index(i_item);
+    size_t istart(0);
+    for(size_t i=0; i<i_item; ++i) {
+        std::cout << "FIXME HERE" << std::endl;
+        assert(0);
+        istart += m_fit_objects[i]->getSizeOfData();
+    }
+    std::vector<FitElement>::const_iterator start = m_fit_elements.begin() + istart;
+    std::vector<FitElement>::const_iterator end = start + m_fit_objects[i_item]->getSizeOfData();
+    return m_fit_objects[check_index(i_item)]->getChiSquaredMap(start, end);
+}
+
+void FitSuiteObjects::setChiSquaredModule(const IChiSquaredModule &chi2_module)
 {
-    return m_fit_objects[check_index(i_item)]->getChiSquaredModule()->createChi2DifferenceMap();
+    m_chi2_module.reset(chi2_module.clone());
 }

Tests/UnitTests/TestCore/DetectorMaskTest.h

@@ -129,6 +129,7 @@ TEST_F(DetectorMaskTest, AssignmentOperator)
             EXPECT_FALSE(mask.getMask(index));
         }
     }
+    EXPECT_EQ(mask.getNumberOfMaskedChannels(), 32);
 
 }