Added Abragam Fit Function and Unit Test re #4956

also corrected comment in StaticKuboToyabe.h

Signed-off-by: Karl Palmen <karl.palmen@stfc.ac.uk>

Code/Mantid/Framework/CurveFitting/CMakeLists.txt

@@ -1,4 +1,5 @@
 set ( SRC_FILES
+  src/Abragam.cpp
 	src/BFGS_Minimizer.cpp
 	src/BackToBackExponential.cpp
 	src/BackgroundFunction.cpp
@@ -54,6 +55,7 @@ set ( SRC_FILES
 set ( SRC_UNITY_IGNORE_FILES src/Fit1D.cpp src/GSLFunctions.cpp )
 
 set ( INC_FILES
+  inc/MantidCurveFitting/Abragam.h
 	inc/MantidCurveFitting/BFGS_Minimizer.h
 	inc/MantidCurveFitting/BackToBackExponential.h
 	inc/MantidCurveFitting/BackgroundFunction.h
@@ -109,6 +111,7 @@ set ( INC_FILES
 )
 
 set ( TEST_FILES
+  test/AbragamTest.h
 	test/BackToBackExponentialTest.h
 	test/BivariateNormalTest.h
 	test/BoundaryConstraintTest.h

Code/Mantid/Framework/CurveFitting/inc/MantidCurveFitting/Abragam.h

@@ -0,0 +1,68 @@
+#ifndef MANTID_CURVEFITTING_ABRAGAM_H_
+#define MANTID_CURVEFITTING_ABRAGAM_H_
+
+//----------------------------------------------------------------------
+// Includes
+//----------------------------------------------------------------------
+#include "MantidAPI/ParamFunction.h"
+//#include "MantidAPI/IPeakFunction.h"
+
+#include "MantidAPI/IFunctionMW.h"
+
+namespace Mantid
+{
+  namespace CurveFitting
+  {
+    /** 
+    Provide Abragam fitting function for muon scientists
+   
+     @author Karl Palmen, ISIS, RAL 
+     @date 21/03/2012 
+  
+     Copyright © 2007-2012 ISIS Rutherford Appleton Laboratory & NScD Oak Ridge National Laboratory 
+  
+     This file is part of Mantid. 
+  
+     Mantid is free software; you can redistribute it and/or modify 
+     it under the terms of the GNU General Public License as published by 
+     the Free Software Foundation; either version 3 of the License, or 
+     (at your option) any later version. 
+  
+     Mantid is distributed in the hope that it will be useful, 
+     but WITHOUT ANY WARRANTY; without even the implied warranty of 
+     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the 
+     GNU General Public License for more details. 
+  
+     You should have received a copy of the GNU General Public License 
+     along with this program.  If not, see <http://www.gnu.org/licenses/>. 
+  
+     File change history is stored at: <https://svn.mantidproject.org/mantid/trunk/Code/Mantid> 
+     Code Documentation is available at: <http://doxygen.mantidproject.org> 
+     */ 
+
+    class DLLExport Abragam : public API::ParamFunction, public API::IFunctionMW
+    {
+    public:
+
+      /// Destructor
+      virtual ~Abragam() {}
+
+      /// overwrite IFunction base class methods
+      std::string name()const{return "Abragam";}
+
+      /// overwrite IFunction base class methods
+      virtual const std::string category() const { return "Muon";}
+    protected:
+      virtual void functionMW(double* out, const double* xValues, const size_t nData)const;
+      virtual void functionDerivMW(API::Jacobian* out, const double* xValues, const size_t nData);
+      virtual void setActiveParameter(size_t i,double value);
+
+      /// overwrite IFunction base class method that declares function parameters 
+      virtual void init(); 
+
+    };
+
+  } // namespace CurveFitting
+} // namespace Mantid
+
+#endif /*MANTID_CURVEFITTING_ABRAGAM_H_*/

Code/Mantid/Framework/CurveFitting/inc/MantidCurveFitting/StaticKuboToyabe.h

@@ -15,7 +15,7 @@ namespace Mantid
     Provide static Kubo Toyabe fitting function
    
      @author Karl Palmen, ISIS, RAL 
-     @date 20/01/2012 
+     @date 20/03/2012 
   
      Copyright © 2007-2012 ISIS Rutherford Appleton Laboratory & NScD Oak Ridge National Laboratory 
   

Code/Mantid/Framework/CurveFitting/src/Abragam.cpp

@@ -0,0 +1,69 @@
+//----------------------------------------------------------------------
+// Includes
+//----------------------------------------------------------------------
+#include "MantidCurveFitting/Abragam.h"
+#include <cmath>
+
+
+namespace Mantid
+{
+namespace CurveFitting
+{
+
+using namespace Kernel;
+using namespace API;
+
+DECLARE_FUNCTION(Abragam)
+
+void Abragam::init()
+{
+  declareParameter("A", 0.2); 
+  declareParameter("Omega", 0.5); 
+  declareParameter("Phi", 0); 
+  declareParameter("Sigma", 1); 
+  declareParameter("Tau",1); 
+}
+
+
+void Abragam::functionMW(double* out, const double* xValues, const size_t nData)const
+{
+  const double& A = getParameter("A"); 
+  const double& w = getParameter("Omega"); 
+  const double& phi = getParameter("Phi"); 
+  const double& sig = getParameter("Sigma");   
+  const double& t = getParameter("Tau"); 
+
+  for (int i = 0; i < nData; i++) { 
+    double A1=A*cos(w*xValues[i]+phi); 
+    double A2=-(sig*sig*t*t)*(exp(-xValues[i]/t)-1+(xValues[i]/t)); 
+    double A3=exp(A2); 
+
+    out[i] = A1*A3; 
+  } 
+
+}
+
+void Abragam::functionDerivMW(Jacobian* out, const double* xValues, const size_t nData)
+{
+  calNumericalDeriv(out, xValues, nData);
+}
+
+void Abragam::setActiveParameter(size_t i,double value)
+{
+  size_t j = indexOfActive(i);
+
+  if (parameterName(j) == "Sigma"  ) 
+    setParameter(j,fabs(value),false);  // Make sigma positive
+  else if (parameterName(j) == "Phi")
+  {
+    double a = fmod(value, 2*M_PI); // Put angle in range of 0 to 360 degrees
+    if( a<0 ) a += 2*M_PI; 
+    setParameter(j,a,false);
+  }
+  else
+    setParameter(j,value,false);
+}
+
+
+} // namespace CurveFitting
+} // namespace Mantid

Code/Mantid/Framework/CurveFitting/test/AbragamTest.h

@@ -0,0 +1,129 @@
+#ifndef ABRAGAMTEST_H_
+#define ABRAGAMTEST_H_
+
+#include <cxxtest/TestSuite.h>
+
+#include "MantidCurveFitting/Abragam.h"
+#include "MantidAPI/CompositeFunction.h"
+#include "MantidCurveFitting/LinearBackground.h"
+#include "MantidCurveFitting/BoundaryConstraint.h"
+#include "MantidCurveFitting/Fit.h"
+#include "MantidKernel/UnitFactory.h"
+#include "MantidAPI/AnalysisDataService.h"
+#include "MantidAPI/WorkspaceFactory.h"
+#include "MantidAPI/Algorithm.h"
+#include "MantidDataObjects/Workspace2D.h"
+#include "MantidDataHandling/LoadRaw.h"
+#include "MantidKernel/Exception.h"
+#include "MantidAPI/FunctionFactory.h"
+
+using namespace Mantid::Kernel;
+using namespace Mantid::API;
+using namespace Mantid::CurveFitting;
+using namespace Mantid::DataObjects;
+using namespace Mantid::DataHandling;
+
+
+class AbragamTest : public CxxTest::TestSuite
+{
+public:
+
+  void getMockData(Mantid::MantidVec& y, Mantid::MantidVec& e)
+  {
+    // Data got from the Abragam function on Excel spreadsheet with
+    // A = 0.3, Omega = 0.4, Phi = PI/4, Sigma = 0.2, Tau = 2.0
+    y[0] = 0.212132034;
+    y[1] = 0.110872429;
+    y[2] = -0.004130004;
+    y[3] = -0.107644046;
+    y[4] = -0.181984622;
+    y[5] = -0.218289678;
+    y[6] = -0.215908947;
+    y[7] = -0.180739307;
+    y[8] = -0.123016506;
+    y[9] = -0.054943061;
+    y[10] = 0.011526466;
+    y[11] = 0.066481012;
+    y[12] = 0.103250678;
+    y[13] = 0.118929645;
+    y[14] = 0.114251678;
+    y[15] = 0.092934753;
+    y[16] = 0.060672555;
+    y[17] = 0.023977227;
+    y[18] = -0.010929869;
+    y[19] = -0.039018774;
+    y[20] = -0.057037526;
+
+    for (int i = 0; i <=20; i++)
+    {
+      e[i] = 0.01;
+    }
+
+  }
+
+  void testAgainstMockData()
+  {
+    Fit alg2;
+    TS_ASSERT_THROWS_NOTHING(alg2.initialize());
+    TS_ASSERT( alg2.isInitialized() );
+
+    // create mock data to test against
+    std::string wsName = "AbragamMockData";
+    int histogramNumber = 1;
+    int timechannels = 21;
+    Workspace_sptr ws = WorkspaceFactory::Instance().create("Workspace2D",histogramNumber,timechannels,timechannels);
+    Workspace2D_sptr ws2D = boost::dynamic_pointer_cast<Workspace2D>(ws);
+    for (int i = 0; i < 21; i++) ws2D->dataX(0)[i] = i;
+    Mantid::MantidVec& y = ws2D->dataY(0); // y-values (counts)
+    Mantid::MantidVec& e = ws2D->dataE(0); // error values of counts
+    getMockData(y, e);
+
+    //put this workspace in the data service
+    TS_ASSERT_THROWS_NOTHING(AnalysisDataService::Instance().addOrReplace(wsName, ws2D));
+
+    // set up Lorentzian fitting function
+    Abragam fn;
+    fn.initialize();
+
+    //alg2.setFunction(fn);
+    alg2.setPropertyValue("Function",fn.asString());
+
+
+    // Set which spectrum to fit against and initial starting values
+    alg2.setPropertyValue("InputWorkspace", wsName);
+    alg2.setPropertyValue("WorkspaceIndex","0");
+    alg2.setPropertyValue("StartX","0");
+    alg2.setPropertyValue("EndX","20");
+
+    // execute fit
+   TS_ASSERT_THROWS_NOTHING(
+      TS_ASSERT( alg2.execute() )
+    )
+
+    TS_ASSERT( alg2.isExecuted() );
+
+    // test the output from fit is what you expect
+    double dummy = alg2.getProperty("OutputChi2overDoF");
+    TS_ASSERT_DELTA( dummy, 0.000001,0.000001);
+
+    // test the output from fit is what you expect
+    IFitFunction *out = FunctionFactory::Instance().createInitialized(alg2.getPropertyValue("Function"));
+    TS_ASSERT_DELTA( out->getParameter("A"), 0.3 ,0.001);
+    TS_ASSERT_DELTA( out->getParameter("Omega"), 0.4 ,0.001);
+    TS_ASSERT_DELTA( out->getParameter("Phi"), M_PI/4.0 ,0.01);  // 45 degrees
+    TS_ASSERT_DELTA( out->getParameter("Sigma"), 0.2 ,0.001);
+    TS_ASSERT_DELTA( out->getParameter("Tau"), 2.0 ,0.01); 
+
+    // check it categories
+    const std::vector<std::string> categories = out->categories();
+    TS_ASSERT( categories.size() == 1 );
+    TS_ASSERT( categories[0] == "Muon" );
+
+    AnalysisDataService::Instance().remove(wsName);
+
+  }
+
+
+};
+
+#endif /*ABRAGAMTEST_H_*/