Merge pull request #12 from lsst/tickets/DM-5297

jointcal running on test data (DM-5297)

Review complete, code builds, tests run.

include/lsst/jointcal/Associations.h

@@ -34,6 +34,17 @@ class Associations {
   RefStarList photRefStarList; // the (e.g) Landolt stars
   FittedStarList fittedStarList; //  the std::list of stars that are going to be fitted
 
+
+  // TODO: NOTE: these only exist because those lists can't be swig'd because
+  // swig doesn't like boost::intrusive_ptr (which the lists contain).
+  // Once DM-4043 is solved, delete these.
+  size_t refStarListSize()
+  { return refStarList.size(); }
+  size_t photRefStarListSize()
+  { return photRefStarList.size(); }
+  size_t fittedStarListSize()
+  { return fittedStarList.size(); }
+
     // fit cuts and stuff:
   Point commonTangentPoint;
 
@@ -76,13 +87,13 @@ class Associations {
 
   //! Collect stars form an external reference catalog (USNO-A by default) that match the FittedStarList. Optionally project these RefStar s on the tangent plane defined by the CommonTangentPoint().
   void CollectRefStars(const bool ProjectOnTP=true);
-  
+
   //! Collect stars from an external reference catalog using the LSST stack mechanism
   void CollectLSSTRefStars(lsst::afw::table::SortedCatalogT< lsst::afw::table::SimpleRecord > &Ref, std::string filter);
 
 
 
-    
+
 #ifdef STORAGE
   //! This is Monte-Carlo stuff -- to remove this from associations
   //! the Association class should provide us w/ iterators and acceptors
@@ -111,21 +122,21 @@ class Associations {
 			   const double &MatchCutArcSec);
 #endif
   //    void SetRefPhotFactor(int chip, double photfact);
-  
+
   //! apply cuts (mainly number of measurements) on potential FittedStars
   void SelectFittedStars();
-  
+
   const CcdImageList& TheCcdImageList() const {return ccdImageList;}
-  
+
   unsigned int NShoots() const { return nshoots_; }
 
   //! Number of different bands in the input image list. Not implemented so far
   unsigned NBands() const {return 1;}
-  
+
   // Return the bounding box in (ra, dec) coordinates containing the whole catalog
   const lsst::afw::geom::Box2D GetRaDecBBox();
 
-  
+
 private:
   void AssociateRefStars(const double &MatchCutInArcSec, const Gtransfo *T);
   unsigned int nshoots_;

include/lsst/jointcal/AstromFit.h

@@ -77,12 +77,12 @@ class AstromFit {
   unsigned int _nParTot;
   unsigned _nMeasuredStars;
   double _posError;  // constant term on error on position (in pixel unit)
-  
+
  public :
 
   //! this is the only constructor
   AstromFit (Associations &A, DistortionModel *D, double PosError);
-  
+
   //! Does a 1 step minimization, assuming a linear model.
   /*! It calls AssignIndices, LSDerivatives, solves the linear system
     and calls OffsetParams. No line search. Relies on sparse linear
@@ -176,7 +176,7 @@ class AstromFit {
   template <class Accum>
     void AccumulateStatRefStars(Accum &Accu) const;
 
-  
+
   //! only for outlier removal
   void GetMeasuredStarIndices(const MeasuredStar &Ms,
 			      std::vector<unsigned> &Indices) const;

include/lsst/jointcal/CcdImage.h

@@ -33,7 +33,7 @@ class CcdImage : public RefCount
   Frame imageFrame; // in pixels
   // wholeCatalog is just store the catalog of selected sources
   //  lsst::afw::table::SortedCatalogT<lsst::afw::table::SourceRecord> wholeCatalog;
-  
+
   MeasuredStarList wholeCatalog; // the catalog of measured objets
   MeasuredStarList catalogForFit;
 
@@ -48,16 +48,16 @@ class CcdImage : public RefCount
   CountedRef<Gtransfo> TP2CTP; // reverse one
   CountedRef<Gtransfo> pix2CommonTangentPlane;// pixels -> CTP
   CountedRef<Gtransfo> pix2TP;
-  
+
   CountedRef<Gtransfo> sky2TP;
-  
+
   std::string riName;
   std::string riDir;
   std::string instrument;
   int chip; // CCD number
   ShootIdType shoot; // Same value for all CcdImages from the same exposure
   unsigned bandRank; // some incremental band indicator.
-  
+
 
   double expTime; // seconds
   double airMass; // airmass value.
@@ -75,7 +75,7 @@ class CcdImage : public RefCount
   std::string dateObs;
   // refraction
   double sineta,coseta,tgz,hourAngle;  // eta : parallactic angle, z: zenithal angle (X = 1/cos(z))
-  
+
   std::string band;
   std::string flatName;
   //  std::string flat; // full flat name
@@ -86,7 +86,7 @@ class CcdImage : public RefCount
   int    bandIndex;
   int    index;
   int    expindex;
-  
+
   Point  commonTangentPoint;
 
   void LoadCatalog(const lsst::afw::table::SortedCatalogT<lsst::afw::table::SourceRecord> &Cat, const std::string &fluxField);
@@ -99,15 +99,15 @@ class CcdImage : public RefCount
     const int &visit, const int &ccd, const std::string &ccdImage, const std::string &fluxField );
 
 
-    
+
 #ifdef TO_BE_FIXED
   //!
   CcdImage(const ReducedImage &Ri, const Point &CommonTangentPoint, const CatalogLoader * LoadIt);
 #endif
 
   //!
   std::string Name() const { return riName;}
-  
+
   //!
   std::string Dir() const { return riDir; }
 
@@ -127,19 +127,19 @@ class CcdImage : public RefCount
   //!
   const Gtransfo* CommonTangentPlane2TP() const
   { return CTP2TP.get();}
-  
+
   //!
   const Gtransfo* TP2CommonTangentPlane() const
   { return TP2CTP.get();}
-  
+
   //!
   const Gtransfo* Pix2TangentPlane() const
   { return pix2TP.get();}
 
   //!
   const Gtransfo* Sky2TP() const
   { return sky2TP.get();}
-  
+
   //! returns chip ID
   int Chip() const { return chip;}
 
@@ -151,29 +151,29 @@ class CcdImage : public RefCount
 
   //! returns seeing
   //  double Seeing() const { return seeing;}
-  
+
   //! returns gfseeing
   //  double GFSeeing() const { return gfseeing;}
-  
+
   //! returns sigma back
   //  double SigmaBack() const { return sigmaback;}
-  
+
   //! returns shoot ID
   ShootIdType Shoot() const { return shoot;}
-  
+
   //! Exposure time (s)
   double ExpTime() const { return expTime;}
-  
+
   //!  Airmass
   double AirMass() const {return airMass;}
-  
+
   //! Date Obs
   std::string DateObs() const { return dateObs; }
 
   //! Julian Date
   double JD() const { return jd; }
 
-  
+
   //!Elixir ZP (applies to fluxes in ADU/sec at airmass 1).
   double ElixirZP() const { return elixirZP;}
 
@@ -182,10 +182,10 @@ class CcdImage : public RefCount
 
   //!zp from the psf zp file, returns 0 if not present
   double PSFZP() const { return psfzp;}
-  
+
   //! absorption term
   double PhotK() const { return photk; }
-  
+
   //! original ZP
   double PhotC() const { return photc; }
 
@@ -206,58 +206,58 @@ class CcdImage : public RefCount
 
   //!conversion from ADU to ADU/sec at airmass=1
   double FluxCoeff() const { return fluxCoeff;}
-  
+
   //! return the CcdImage band name
   std::string Band() const { return band;}
-  
+
   //! return the CcdImage band index. This is a static index that mostly turns a letter (e.g. 'g') into a number (e.g. 2). Different from BandRank()
   int BandIndex() const { return bandIndex; }
-  
+
   //! Flat used to flatfield
   std::string FlatName() const { return flatName;}
 
   //! Full path of the scatter corrections
   std::string CFHTScatter() const { return cfhtscatter; }
-  
+
   //! SNLS grid
   std::string SNLSGrid() const { return snlsgrid; }
-  
+
   //! correction map to convert from one set of fluxes to another
   std::string FlatCVMap() const { return flatcvmap; }
-  
+
   //void SetPix2TangentPlane(const Gtransfo *);
-  
+
   //! the wcs read in the header. NOT updated when fitting.
   const Gtransfo *ReadWCS() const {return readWcs.get();}
-  
+
   //! the inverse of the one above.
   const Gtransfo *InverseReadWCS() const {return inverseReadWcs.get();}
-  
+
   //! Frame in pixels
   const Frame& ImageFrame() const { return imageFrame;}
-  
+
   //! Frame on sky
   //Frame RaDecFrame() const;
-  
+
   //! Fitted Ccd object (contain the refscale parameters)
   //  void             SetFittedCcd(FittedCcd* ccd) { if(ccd) fittedccd=ccd; }
   //  FittedCcd*       GetFittedCcd() { return fittedccd; }
   //  FittedCcd const* GetFittedCcd() const { return fittedccd; }
-  
+
   //! returns wether "this" overlaps with Other.
   //  bool Overlaps(const CcdImage &Other) const;
-  
+
   //! CcdImage index
   int     Index() const { return index; }
   void    SetIndex(int idx) { index = idx; }
-  
+
   //! Exposure Index
   int     ExpIndex() const { return expindex; }
   void    SetExpIndex(int idx) { expindex = idx; }
-  
+
   //! Common Tangent Point
   Point const&       CommonTangentPoint() const { return commonTangentPoint; }
-  
+
  private:
   CcdImage(const CcdImage &); // forbid copies
 
@@ -270,19 +270,19 @@ class CcdImage : public RefCount
 
 //! a  list of CcdImage. Usually produced by Associations
 //class CcdImageList : public std::list<CountedRef<CcdImage> >
-class CcdImageList : public std::list<boost::shared_ptr<CcdImage> >
+class CcdImageList : public std::list<std::shared_ptr<CcdImage> >
 {
   public:
-  
+
   //!
   //std::list<std::string> DateObs() const;
-  
+
   //!
   //std::list<std::string> Bands() const;
-  
+
   //!
   //double       MeanAirmass() const;
-  
+
   //!
   template<class Accept> CcdImageList SubList(const Accept &OP) const
     {
@@ -291,7 +291,7 @@ class CcdImageList : public std::list<boost::shared_ptr<CcdImage> >
 	if (OP(**i)) out.push_back(*i);
       return out;
     }
-  
+
   // find the matching image. Chip==-1 means any chip
 //  double AirMass(const int Shoot, const int Chip = -1) const;
 };

include/lsst/jointcal/ConstrainedPolyModel.h

@@ -70,7 +70,7 @@ public :
 
   //! Access to array of shoots involved in the solution.
   std::vector<ShootIdType> GetShoots() const;
-   
+
   /*! the mapping of sky coordinates (i.e. the coordinate system
   in which fitted stars are reported) onto the Tangent plane
   (into which the pixel coordinates are transformed) */
@@ -86,7 +86,7 @@ public :
   poloka-core */
   //  bool WriteChipArrangement(const std::string &FileName) const;
 
- 
+
 };
 
 }} // end of namespaces

include/lsst/jointcal/FastFinder.h

@@ -11,7 +11,7 @@ namespace jointcal {
 /*! \file
     \brief Fast locator in starlists.
 */
- 
+
 /*!  This is an auxillary class for matching objects from
   starlists. It allows to locate rapidly the closest objects from a
   given position. The very simple strategy is to sort objects