Work towards full forward modelling support

examples/ForwardFID.cpp

         std::cout << "./ForwardFID Kernel.yaml TxString RxString  vtkoutput<true/false> \n";
     //    return(EXIT_FAILURE);
     }
+    auto Kernel = KernelV0::DeSerialize(YAML::LoadFile(argv[1]));
+    //    std::cout << *Kernel;
 
     auto Model = LayeredEarthMR::NewSP();
-        Model->SetNumberOfLayers(20);
+        Model->AlignWithKernel(Kernel);
         Model->SetT2StarBins(10, 500, 20);
         std::cout << *Model << std::endl;
 
+/*
     auto Forward = ForwardFID::NewSP();
         //Forward->SetWindowEdges( VectorXr::LinSpaced(10,0,1) );
         Forward->SetLogSpacedWindows(10,1000,30);
         //auto FID =  Forward->ForwardModel(Model);
     //std::cout << *Forward << std::endl;
-
+*/
     return EXIT_SUCCESS;
 }

include/LayeredEarthMR.h

 #pragma once
 #include "LayeredEarth.h"
 #include "MerlinConfig.h"
+#include "KernelV0.h"
 
 namespace Lemma {
 
          */
         virtual YAML::Node Serialize() const;
 
-        /*
+        /**
          *  Factory method for generating concrete class.
          *  @return a std::shared_ptr of type LayeredEarthMR
          */
         // ====================  ACCESS        =======================
 
 
-        void SetNumberOfLayers(const int& nlay);
 
+        /**
+         *  Sets the T2StarBins to solve for, these are log spaced
+         *  @param[in] first is the beginning of the bins
+         *  @param[in] last is the end of the bins
+         *  @param[in] nT2 is the number of bins
+         */
         void SetT2StarBins(const Real& first, const Real& last, const int& nT2);
 
+        /**
+         *  Convenience method, that aligns model with a Kernel
+         *  @param[in] Kern input kernel to align with
+         */
+        void AlignWithKernel( std::shared_ptr<KernelV0> Kern );
+
         // ====================  INQUIRY       =======================
         /**
          *  Returns the name of the underlying class, similiar to Python's type
         /** ASCII string representation of the class name */
         static constexpr auto CName = "LayeredEarthMR";
 
+        /**
+         * Sets the number of layers
+         */
+        void SetNumberOfLayers(const int& nlay);
+
+        /** Initializes the model matrix */
+        void InitModelMat();
+
         VectorXr T2StarBins;
         VectorXr T2StarBinEdges;  // Convenience for pcolor
+        MatrixXr ModelMat;
 
     }; // -----  end of class  LayeredEarthMR  -----
 }  // -----  end of namespace Lemma ----

src/LayeredEarthMR.cpp

         node["Merlin_VERSION"] = MERLIN_VERSION;
         node["T2StarBins"] = T2StarBins;
         node["T2StarBinEdges"] = T2StarBinEdges;
+        node["ModelMat"] = ModelMat;
         return node;
     }		// -----  end of method LayeredEarthMR::Serialize  -----
 
     //      Method:  SetNumberOfLayers
     //--------------------------------------------------------------------------------------
     void LayeredEarthMR::SetNumberOfLayers ( const int& nlay  ) {
+        NumberOfLayers = nlay;
+        NumberOfInterfaces = nlay+1;
         return ;
     }		// -----  end of method LayeredEarthMR::SetNumberOfLayers  -----
 
+    //--------------------------------------------------------------------------------------
+    //       Class:  LayeredEarthMR
+    //      Method:  AlignWithKernel
+    //--------------------------------------------------------------------------------------
+    void LayeredEarthMR::AlignWithKernel ( std::shared_ptr<KernelV0> Kern ) {
+        int nlay = Kern->GetInterfaces().size()-1;
+        SetNumberOfLayers( nlay );
+        LayerThickness = Kern->GetInterfaces().tail(nlay) - Kern->GetInterfaces().head(nlay) ;
+        SetMagneticFieldComponents( Kern->GetSigmaModel()->GetMagneticField(), TESLA);
+        return ;
+    }		// -----  end of method LayeredEarthMR::AlignWithKernel  -----
 
     //--------------------------------------------------------------------------------------
     //       Class:  LayeredEarthMR
             T2StarBinEdges[i] = T2StarBinEdges[i-1]*quotient;
         }
         T2StarBins = (T2StarBinEdges.head(nT2) + T2StarBinEdges.tail(nT2)) / 2;
+        InitModelMat();
         return;
     }		// -----  end of method LayeredEarthMR::SetNumberOfT2StarBins  -----
 
 
-} // ----  end of namespace Lemma  ----
-
-
-
+    //--------------------------------------------------------------------------------------
+    //       Class:  LayeredEarthMR
+    //      Method:  InitModelMat
+    //--------------------------------------------------------------------------------------
+    void LayeredEarthMR::InitModelMat (  ) {
+        ModelMat = MatrixXr::Zero( T2StarBins.size(), NumberOfLayers );
+        return ;
+    }		// -----  end of method LayeredEarthMR::InitModelMat  -----
 
+} // ----  end of namespace Lemma  ----
 
 /* vim: set tabstop=4 expandtab: */
 /* vim: set filetype=cpp: */