Merge branch 'polarized_meso' into develop

App/inc/DrawHelper.h

 // ************************************************************************** //
-//                                                                         
+//
 //  BornAgain: simulate and fit scattering at grazing incidence
 //
 //! @file      App/inc/DrawHelper.h
@@ -31,7 +31,7 @@ class TPad;
 //!
 class DrawHelper :public TObject
 {
- public:
+public:
     //! Sets own drawing style
     static void SetStyle();
 
@@ -57,7 +57,7 @@ class DrawHelper :public TObject
     //! attempt to draw meso crystal lattice in 3d
     static void DrawMesoCrystal(const MultiLayer *sample);
 
- private:
+private:
     static int m_default_canvas_xsize;
     static int m_default_canvas_ysize;
     static std::vector<TCanvas *> m_registered_canvases;

App/inc/FitSuiteObserverFactory.h

 // ************************************************************************** //
-//                                                                         
+//
 //  BornAgain: simulate and fit scattering at grazing incidence
 //
 //! @file      App/inc/FitSuiteObserverFactory.h
@@ -24,7 +24,7 @@
 //! factory to create observers for FitSuite
 class FitSuiteObserverFactory
 {
- public:
+public:
     typedef boost::shared_ptr<FitSuitePrintObserver> observer_print_t;
     typedef boost::shared_ptr<FitSuiteDrawObserver> observer_draw_t;
     typedef boost::shared_ptr<FitSuiteWriteTreeObserver> observer_tree_t;

App/inc/FunctionalTestFactory.h

@@ -27,7 +27,7 @@ class ProgramOptions;
 
 class FunctionalTestFactory : public IFactory<std::string, IFunctionalTest>
 {
-  public:
+public:
     FunctionalTestFactory();
     virtual ~FunctionalTestFactory();
 
@@ -49,7 +49,7 @@ class FunctionalTestFactory : public IFactory<std::string, IFunctionalTest>
     iterator begin() { return m_descriptions.begin(); }
     iterator end() { return m_descriptions.end(); }
 
-  private:
+private:
     TBenchmark *m_benchmark;
 };
 

App/inc/IFunctionalTest.h

 // ************************************************************************** //
-//                                                                         
+//
 //  BornAgain: simulate and fit scattering at grazing incidence
 //
 //! @file      App/inc/IFunctionalTest.h
@@ -27,7 +27,7 @@ class ProgramOptions;
 //!
 class IFunctionalTest : public INamed
 {
- public:
+public:
     IFunctionalTest() : mp_options(0) {}
     IFunctionalTest(const std::string& name) : INamed(name), mp_options(0) {}
     virtual ~IFunctionalTest(){}
@@ -39,7 +39,7 @@ class IFunctionalTest : public INamed
     std::string getOutputPath() const { return m_output_path; }
     void setOutputPath(const std::string& output_path)
     { m_output_path = output_path; }
- protected:
+protected:
     ProgramOptions *mp_options;
     std::string m_output_path;
 };

App/inc/IsGISAXSData.h

 // ************************************************************************** //
-//                                                                         
+//
 //  BornAgain: simulate and fit scattering at grazing incidence
 //
 //! @file      App/inc/IsGISAXSData.h
@@ -25,7 +25,7 @@
 
 class IsGISAXSData
 {
- public:
+public:
     typedef SafePointerVector<OutputData<double> >  DataSet_t;
     enum ItemToRead { kSin_twotheta, kSin_alphaf, kQx, kQy, kQz,
                       kSimResult, kData2fit, kErrorbar, kIobs_Icalc, kFitted };
@@ -46,7 +46,7 @@ class IsGISAXSData
     //! Read special isgisaxs *.out file with isgisaxs fit results.
     static void read_outfile(const std::string& filename, DataSet_t& dataset, ItemToRead item = kData2fit);
 
- private:
+private:
     //! Convert isgisaxs 1d scan to output data 2d object.
     static OutputData<double> *convert_isgi_scan(
         std::vector<IsgiData >& isgi_data);

App/inc/IsGISAXSTools.h

@@ -163,7 +163,7 @@ public:
         double hmax = -1.,
         double hdiff=0.0001 );
 
- private:
+private:
     //! selects specific matrix elements from polarized output data and puts
     //! these in a non-polarized output data structure
     static void copyElementsWithPosition(

App/inc/SampleFactory.h

 // ************************************************************************** //
-//                                                                         
+//
 //  BornAgain: simulate and fit scattering at grazing incidence
 //
 //! @file      App/inc/SampleFactory.h
@@ -27,7 +27,7 @@
 class SampleFactory : public ISingleton<SampleFactory>,
                       public IFactory<std::string, ISample>
 {
- public:
+public:
     SampleFactory();
 
     static ISample *createSample(const std::string& sample_name)

App/inc/TestConvolution.h

 // ************************************************************************** //
-//                                                                         
+//
 //  BornAgain: simulate and fit scattering at grazing incidence
 //
 //! @file      App/inc/TestConvolution.h
@@ -25,7 +25,7 @@
 
 class TestConvolution : public IFunctionalTest
 {
- public:
+public:
     TestConvolution();
 
     void execute();
@@ -36,7 +36,7 @@ class TestConvolution : public IFunctionalTest
     //! testing convolution in 2d
     void test_convolve2d();
 
- private:
+private:
     //! test function with many gaus'es on top of flat background for convolution studies
     double fpeaks(double *x, double *par);
 

App/inc/TestDetectorResolution.h

@@ -25,7 +25,7 @@
 
 class TestDetectorResolution : public IFunctionalTest
 {
- public:
+public:
     TestDetectorResolution() : mp_intensity_output(0), mp_sample(0) {}
     virtual ~TestDetectorResolution()
     {
@@ -34,7 +34,7 @@ class TestDetectorResolution : public IFunctionalTest
     }
     virtual void execute();
 
- private:
+private:
     void initializeSample();
     OutputData<double> *mp_intensity_output;
     ISample *mp_sample;

App/inc/TestDiffuseReflection.h

@@ -26,14 +26,14 @@ class MultiLayer;
 
 class TestDiffuseReflection : public IFunctionalTest
 {
- public:
+public:
     TestDiffuseReflection();
 
     void execute();
 
     void draw();
 
- private:
+private:
     MultiLayer *m_sample; //!< pointer to multilayer sample
 //    OutputData<double  > *m_data_spec; //!< specular reflectivity
     OutputData<double  > *m_data_offspec; //!< off-specular reflectivity

App/inc/TestFittingBenchmark.h

@@ -22,7 +22,7 @@
 
 class TestFittingBenchmark : public IFunctionalTest
 {
- public:
+public:
     TestFittingBenchmark() {}
     virtual ~TestFittingBenchmark() {}
     virtual void execute();

App/inc/TestFittingModule1.h

@@ -28,12 +28,12 @@ class FitSuite;
 
 class TestFittingModule1 : public IFunctionalTest
 {
- public:
+public:
     TestFittingModule1();
     virtual ~TestFittingModule1();
     virtual void execute();
 
- private:
+private:
     //! Initializes sample: layer + nanoparticles, 2 parameters
     void initializeSample1();
     //! Initializes sample: layer + substrate + nanoparticles, 4 parameters

App/inc/TestFittingModule2.h

 // ************************************************************************** //
-//                                                                         
+//
 //  BornAgain: simulate and fit scattering at grazing incidence
 //
 //! @file      App/inc/TestFittingModule2.h
@@ -34,7 +34,7 @@ class FitSuite;
 //!
 class TestFittingModule2 : public IFunctionalTest
 {
- public:
+public:
     TestFittingModule2();
     virtual ~TestFittingModule2();
     virtual void execute();
@@ -42,13 +42,13 @@ class TestFittingModule2 : public IFunctionalTest
     //! builds sample for fitter testing
     class SampleBuilder : public ISampleBuilder
     {
-      public:
+    public:
         SampleBuilder();
         virtual ~SampleBuilder(){}
         virtual ISample *buildSample() const;
-      protected:
+    protected:
         virtual void init_parameters();
-      private:
+    private:
         double m_cylinder_height;
         double m_cylinder_radius;
         double m_prism3_half_side;
@@ -68,7 +68,7 @@ class TestFittingModule2 : public IFunctionalTest
     //! fit example with data masking
     void fit_example_mask();
 
- private:
+private:
     void initializeSimulation();
     void initializeRealData();
 

App/inc/TestFittingModule3.h

@@ -32,14 +32,14 @@ class FitSuite;
 //!
 class TestFittingModule3 : public IFunctionalTest
 {
- public:
+public:
     typedef SafePointerVector<OutputData<double> >  DataScan_t;
 
     TestFittingModule3();
     virtual ~TestFittingModule3();
     virtual void execute();
 
- private:
+private:
     void initializeSample();
     void initializeSimulation();
     void initializeRealData();

App/inc/TestFormFactor.h

@@ -22,13 +22,13 @@
 
 class TestFormFactor : public IFunctionalTest
 {
- public:
+public:
     TestFormFactor();
     ~TestFormFactor();
     virtual void execute();
     void draw(), draw4();
 
- private:
+private:
     OutputData<double> *mp_intensity_output;
     FormFactorCylinder m_ff;
 };

App/inc/TestFormFactors.h

@@ -24,13 +24,13 @@
 
 class TestFormFactors : public IFunctionalTest
 {
- public:
+public:
     TestFormFactors(){}
     virtual ~TestFormFactors(){}
 
     virtual void execute();
     virtual void finalise();
- private:
+private:
     std::string m_data_path;
 };
 

App/inc/TestFourier.h

@@ -22,12 +22,12 @@
 
 class TestFourier : public IFunctionalTest
 {
- public:
+public:
     TestFourier();
     virtual ~TestFourier();
     virtual void execute();
 
- private:
+private:
     void initializeSample();
     OutputData<double> *mp_intensity_output;
     ISample *mp_sample;

App/inc/TestFumiliLMA.h

@@ -36,7 +36,7 @@ class TCanvas;
 
 class TestFumiliLMA : public IFunctionalTest
 {
- public:
+public:
     friend class MyChi2Function;
 
     TestFumiliLMA();
@@ -45,7 +45,7 @@ class TestFumiliLMA : public IFunctionalTest
 
     double functionToMinimize(const double *pars);
 
- private:
+private:
     void FillOutputDataFromFunction(
         OutputData<double>& data, TF2 *fun, int nbinsx=100, int nbinsy=100);
 
@@ -63,7 +63,7 @@ class TestFumiliLMA : public IFunctionalTest
 
 class IFunctionObject
 {
- public:
+public:
     virtual ~IFunctionObject(){}
     virtual double operator()(const double *xx, const double *pars ) = 0;
 };
@@ -71,7 +71,7 @@ class IFunctionObject
 
 class RosenBrockFunctionObject : public IFunctionObject
 {
- public:
+public:
     double operator()(const double *xx, const double *pars )
     {
         const double x = xx[0];
@@ -87,7 +87,7 @@ class RosenBrockFunctionObject : public IFunctionObject
 
 class SincXSincYFunctionObject : public IFunctionObject
 {
- public:
+public:
     double operator()(const double *xx, const double *pars )
     {
         const double x = xx[0];
@@ -103,7 +103,7 @@ class SincXSincYFunctionObject : public IFunctionObject
 
 class MyChi2Function : public ROOT::Math::FitMethodFunction
 {
- public:
+public:
     typedef ROOT::Math::BasicFitMethodFunction<ROOT::Math::IMultiGenFunction>::Type_t  Type_t;
 
     MyChi2Function(TestFumiliLMA *test)

App/inc/TestIsGISAXS1.h

@@ -22,7 +22,7 @@
 
 class TestIsGISAXS1 : public IFunctionalTest
 {
- public:
+public:
     TestIsGISAXS1();
     virtual ~TestIsGISAXS1() { }
 

App/inc/TestIsGISAXS10.h

@@ -22,7 +22,7 @@
 
 class TestIsGISAXS10 : public IFunctionalTest
 {
- public:
+public:
     TestIsGISAXS10();
     virtual ~TestIsGISAXS10(){}