Part of email fomr Peter:

I'm still trying to figure out what the code is doing and what exactly is obsolete. Any details along these lines would be much appreciated.

Response:

I added some overview documentation on what the optics is doing to #66.

So the job is to delete the following member data:-
HepMatrix _firstOrderMap;
Tensor3 _secondOrderMap;
std::vector<Tensor*> _higherOrderMaps;
OpticsModel* _optics;
static int _order;
bool _canonicalMap;

The fundamental functionality that I really want to keep alive:-
CovarianceMatrix operator*(const CovarianceMatrix& aCovMatrix) const;
PhaseSpaceVector operator*(const PhaseSpaceVector& aPhaseSpaceVector) const;

Mark any functions that get broken as deprecated (anything that talks to Tensor, Tensor3, HepMatrix); they should raise an exception if they are called:-
TransferMap(HepMatrix firstOrderMap, PhaseSpaceVector referenceIn, PhaseSpaceVector referenceOut, OpticsModel* Optics);
TransferMap(HepMatrix transverseMap, HepMatrix longitudinalMap, PhaseSpaceVector referenceIn, PhaseSpaceVector referenceOut, OpticsModel* Optics);
TransferMap(PhaseSpaceVector referenceIn, OpticsModel* Optics);

void SetFirstOrderMap(const HepMatrix transverseMap, const HepMatrix longitudinalMap);
    void SetFirstOrderMap(const HepMatrix firstOrderMap);
    void SetSecondOrderMap(Tensor3 secondOrderMap)            {_secondOrderMap = secondOrderMap;}
    void SetReferenceOutZ(double z)                           {_referenceTrajectoryOut.setZ(z);}
    void IncrementReferenceOutZ(double dz)                    {SetReferenceOutZ(_referenceTrajectoryOut.z()+dz);}
    void SetOpticsModel(OpticsModel* optics)                  {_optics = optics;}

HepMatrix GetTransverseMap()   const {return _firstOrderMap.sub(3,6,3,6);}
    HepMatrix GetLongitudinalMap() const {return _firstOrderMap.sub(1,2,1,2);}
    //Accessor for second and higher order maps
    Tensor3   GetSecondOrderMap()  const {return _secondOrderMap;}
    Tensor    GetMap(int order)    const;
    bool              IsCanonical()         {return _canonicalMap;}
    bool              IsCanonical(bool can) {_canonicalMap = can; return _canonicalMap;}
    //order
    static void      SetOrder(int order) {_order = order;}
    static int       GetOrder()          {return _order;}

You probably want to keep the function for now, so that you don't have to go into any other stuff. Then make sure it is possible to do cpplint and get no errors. Then add tests for any functions that survive the cull and are not marked as deprecated (so, add tests in tests/cpp_unit/Optics).

I made all of the deprecation changes and had it compiling at one point. I don't understand how TransferMap is supposed to operate on CovarianceMatrix or PhaseSpaceVector without using GetFirstOrderMap (which uses HepMatrix and, as I understand, should be deprecated). Feedback would be appreciated.

I am fixing up CovarianceMatrix right now (issue #477) since part of the essential functionality of TransferMap uses CovarianceMatrix and I'm stuck on TransferMap.

I think I've figured out the data card stuff and found the Optics.cc test app in tests/integration/test_optics/. That means I at least should be able to create a valid CovarianceMatrix soon for testing with TransferMap.

I'm still not sure how to create a valid TransferMap with appropriate reference trajectories. I'm also not sure how to tell if TransferMap is working correctly (i.e. what valid output would be from TransferMap operating on a CovarianceMatrix or PhaseSpaceVector).

Chris R., you said not to test matrix multiplication, but I don't see how I can test anything without doing some sort of multiplication. After all, that's basically all TransferMap is supposed to do now. Comments?

I moved the new vector and matrix classes to common_cpp/Maths. I moved the new CovarianceMatrix, PhaseSpaceVector, and TransferMap classes in common_cpp/Optics. I resolved all of the cpplint errors for these classes except some which aren't valid. I removed MVector and MMatrix and updated all classes that used these to use the new classes.

I also moved PolynomialVector into Maths, but I largely left this unchanged and did not attempt to fix any cpplint errors. I should probably do that at some point, but I'll shift that off onto issue #66. I suppose some supporting files such Interpolator should have been moved as well (more #66 tasks I guess).