Homology.h

// Gmsh - Copyright (C) 1997-2012 C. Geuzaine, J.-F. Remacle
//
// See the LICENSE.txt file for license information. Please report all
// bugs and problems to <gmsh@geuz.org>.
//
// Contributed by Matti Pellikka <matti.pellikka@tut.fi>.

#ifndef _HOMOLOGY_H_
#define _HOMOLOGY_H_

#include <sstream>
#include "CellComplex.h"
#include "ChainComplex.h"
#include "Chain.h"
#include "OS.h"
#include "GModel.h"
#include "Options.h"

#if defined(HAVE_KBIPACK)

// Interface class for homology computation in Gmsh
class Homology
{
 private:

  // the Gmsh model for homology computation
  GModel* _model;

  // domain and the relative subdomain of the homology computation
  // physical group IDs
  std::vector<int> _domain;
  std::vector<int> _subdomain;
  std::vector<int> _imdomain;
  // corresponding geometrical entities
  std::vector<GEntity*> _domainEntities;
  std::vector<GEntity*> _subdomainEntities;
  std::vector<GEntity*> _immuneEntities;

  // save original cell complex
  bool _saveOrig;

  // use cell combining
  bool _combine;
  // use cell omit
  bool _omit;
  // use chain smoothning
  bool _smoothen;

  // file name to store the results
  std::string _fileName;

  // cell complex of the domain
  CellComplex* _cellComplex;

  bool _homologyComputed;
  bool _cohomologyComputed;

  // resulting chains
  std::vector<Chain<int>*> _chains[4];
  std::vector<Chain<int>*> _cochains[4];

  typedef std::map<Cell*, int, Less_Cell>::iterator citer;

  // create a string describing the generator
  std::string _getDomainString(const std::vector<int>& domain,
                               const std::vector<int>& subdomain);

  // construct the cell complex
  void _createCellComplex();

  // create and store a chain from homology solver result
  void _createChain(std::map<Cell*, int, Less_Cell>& preChain,
                    std::string name, bool co);

  void _deleteChains();
  void _deleteCochains();

 public:

  // Determine domain and relative subdomain of (co)homology computation
  Homology(GModel* model, std::vector<int> physicalDomain,
	   std::vector<int> physicalSubdomain,
           bool saveOrig=true,
	   bool combine=true, bool omit=true, bool smoothen=true);
  ~Homology();

  GModel* getModel() const { return _model; }
  void setFileName(std::string fileName) { _fileName = fileName; }

  // find the bases of (co)homology spaces
  void findHomologyBasis();
  void findCohomologyBasis();

  // add chains to Gmsh model
  // dim: only add dim-chains if dim != -1
  // post: create a post-processing view
  void addChainsToModel(int dim=-1, bool post=true);
  void addCochainsToModel(int dim=-1, bool post=true);

  // get representative chains of a (co)homology space basis
  void getHomologyBasis(int dim, std::vector<Chain<int> >& hom);
  void getCohomologyBasis(int dim, std::vector<Chain<int> >& coh);

  // get Betti number
  int betti(int dim);

  // get Euler characteristic
  int eulerCharacteristic();

  // write the generators to a file
  bool writeBasisMSH(bool binary=false);

  // store dim-dimensional cells of cellComplex as a physical group
  // in _model, for debugging
  void storeCells(CellComplex* cellComplex, int dim);
};

#endif

#endif