Added placeholder for homology computation plugin.

Geo/CellComplex.cpp

@@ -7,6 +7,7 @@
 
 #include "CellComplex.h"
 
+
 CellComplex::CellComplex( std::vector<GEntity*> domain, std::vector<GEntity*> subdomain ){
   
   _domain = domain;

Geo/CellComplex.h

@@ -26,7 +26,6 @@
 #include "GVertex.h"
 
 
-
 // Abstract class representing an elemtary cell of a cell complex.
 class Cell
 {  
@@ -498,7 +497,7 @@ class CombinedCell : public Cell{
 // A class representing a cell complex made out of a finite element mesh.
 class CellComplex
 {
- protected:
+ private:
    
    // the domain in the model which this cell complex covers
    std::vector<GEntity*> _domain;
@@ -527,14 +526,14 @@ class CellComplex
    
   protected: 
    // enqueue cells in queue if they are not there already
-   virtual void enqueueCells(std::list<Cell*>& cells, 
+   void enqueueCells(std::list<Cell*>& cells, 
                              std::queue<Cell*>& Q, std::set<Cell*, Less_Cell>& Qset);
    // remove cell from the queue set
-   virtual void removeCellQset(Cell*& cell, std::set<Cell*, Less_Cell>& Qset);
+   void removeCellQset(Cell*& cell, std::set<Cell*, Less_Cell>& Qset);
       
    // insert cells into this cell complex
    //virtual void insert_cells(bool subdomain, bool boundary);
-   virtual void insert_cells(bool subdomain, bool boundary);
+   void insert_cells(bool subdomain, bool boundary);
    
   public: 
    CellComplex(  std::vector<GEntity*> domain, std::vector<GEntity*> subdomain, std::set<Cell*, Less_Cell> cells ) {
@@ -571,68 +570,68 @@ class CellComplex
    
    CellComplex( std::vector<GEntity*> domain, std::vector<GEntity*> subdomain );
    CellComplex(){}
-   virtual ~CellComplex(){}
+   ~CellComplex(){}
 
    
    // get the number of certain dimensional cells
-   virtual int getSize(int dim){ return _cells[dim].size(); }
+   int getSize(int dim){ return _cells[dim].size(); }
    
-   virtual int getDim() {return _dim; } 
+   int getDim() {return _dim; } 
    
-   virtual std::set<Cell*, Less_Cell> getCells(int dim){ return _cells[dim]; }
+   std::set<Cell*, Less_Cell> getCells(int dim){ return _cells[dim]; }
       
    // iterators to the first and last cells of certain dimension
-   virtual citer firstCell(int dim) {return _cells[dim].begin(); }
-   virtual citer lastCell(int dim) {return _cells[dim].end(); }
+    citer firstCell(int dim) {return _cells[dim].begin(); }
+    citer lastCell(int dim) {return _cells[dim].end(); }
   
    // kappa for two cells of this cell complex
    // implementation will vary depending on cell type
-   virtual inline int kappa(Cell* sigma, Cell* tau) const { return sigma->kappa(tau); }
+   inline int kappa(Cell* sigma, Cell* tau) const { return sigma->kappa(tau); }
    
    // remove a cell from this cell complex
-   virtual void removeCell(Cell* cell);
-   virtual void replaceCells(Cell* c1, Cell* c2, Cell* newCell, bool orMatch, bool co=false);
+   void removeCell(Cell* cell);
+   void replaceCells(Cell* c1, Cell* c2, Cell* newCell, bool orMatch, bool co=false);
    
    
-   virtual void insertCell(Cell* cell);
+   void insertCell(Cell* cell);
    
    // check whether two cells both belong to subdomain or if neither one does
-   virtual bool inSameDomain(Cell* c1, Cell* c2) const { return 
+   bool inSameDomain(Cell* c1, Cell* c2) const { return 
        ( (!c1->inSubdomain() && !c2->inSubdomain()) || (c1->inSubdomain() && c2->inSubdomain()) ); }
    
    
    // reduction of this cell complex
    // removes reduction pairs of cell of dimension dim and dim-1
-   virtual int reduction(int dim);
+   int reduction(int dim);
    
    
    // useful functions for (co)reduction of cell complex
-   virtual void reduceComplex(bool omitHighdim = false);
-   virtual void coreduceComplex(bool omitlowDim = false);
+   void reduceComplex(bool omitHighdim = false);
+   void coreduceComplex(bool omitlowDim = false);
    
    // queued coreduction presented in Mrozek's paper
-   virtual int coreduction(Cell* generator);
-      
+   int coreduction(Cell* generator);
+   
    // add every volume, face and edge its missing boundary cells
-   //virtual void repairComplex(int i=3);
+   // void repairComplex(int i=3);
    // change non-subdomain cells to be in subdomain, subdomain cells to not to be in subdomain
-   virtual void swapSubdomain();
-   virtual void removeSubdomain();
+   void swapSubdomain();
+   void removeSubdomain();
    
    
    // print the vertices of cells of certain dimension
-   virtual void printComplex(int dim);
+   void printComplex(int dim);
    
    // write this cell complex in 2.0 MSH ASCII format
-   virtual int writeComplexMSH(const std::string &name); 
+   int writeComplexMSH(const std::string &name); 
    
-   virtual int combine(int dim);
-   virtual int cocombine(int dim);
+   int combine(int dim);
+   int cocombine(int dim);
    
-   virtual void computeBettiNumbers();
-   virtual int getBettiNumber(int i) { if(i > -1 && i < 4) return _betti[i]; else return 0; }
+   void computeBettiNumbers();
+   int getBettiNumber(int i) { if(i > -1 && i < 4) return _betti[i]; else return 0; }
    
-   virtual void makeDualComplex(){
+   void makeDualComplex(){
      std::set<Cell*, Less_Cell> temp = _cells[0];
      _cells[0] = _cells[3];
      _cells[3] = temp;

Plugin/HomologyComputation.cpp

+// Gmsh - Copyright (C) 1997-2009 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
+
+#include <stdlib.h>
+#include "GmshConfig.h"
+#include "GModel.h"
+#include "CellComplex.h"
+#include "HomologyComputation.h"
+
+
+StringXNumber HomologyComputationOptions_Number[] = {
+  {GMSH_FULLRC, "test number", NULL, 1.},
+};
+
+StringXString HomologyComputationOptions_String[] = {
+  {GMSH_FULLRC, "test string", NULL, "test string"},
+};
+
+extern "C"
+{
+  GMSH_Plugin *GMSH_RegisterHomologyComputationPlugin()
+  {
+    return new GMSH_HomologyComputationPlugin();
+  }
+}
+
+void GMSH_HomologyComputationPlugin::getName(char *name) const
+{
+  strcpy(name, "Homology Computation");
+}
+
+void GMSH_HomologyComputationPlugin::getInfos(char *author, char *copyright,
+                                   char *help_text) const
+{
+  strcpy(author, "Matti Pellikka");
+  strcpy(copyright, "C. Geuzaine, J.-F. Remacle");
+  strcpy(help_text,
+         "Plugin(HomologyComputation) is here!\n"
+         "\n"
+         "Plugin(HomologyComputation) creates a new view.\n");
+}
+
+int GMSH_HomologyComputationPlugin::getNbOptions() const
+{
+  return sizeof(HomologyComputationOptions_Number) / sizeof(StringXNumber);
+}
+
+StringXNumber *GMSH_HomologyComputationPlugin::getOption(int iopt)
+{
+  return &HomologyComputationOptions_Number[iopt];
+}
+
+int GMSH_HomologyComputationPlugin::getNbOptionsStr() const
+{
+  return sizeof(HomologyComputationOptions_String) / sizeof(StringXString);
+}
+
+StringXString *GMSH_HomologyComputationPlugin::getOptionStr(int iopt)
+{
+  return &HomologyComputationOptions_String[iopt];
+}
+
+void GMSH_HomologyComputationPlugin::catchErrorMessage(char *errorMessage) const
+{
+  strcpy(errorMessage, "Homology Computation failed...");
+}
+
+
+PView *GMSH_HomologyComputationPlugin::execute(PView *v)
+{
+  std::string testString = HomologyComputationOptions_String[0].def;
+  int testInt = (int)HomologyComputationOptions_Number[0].def;
+
+  GModel *m = GModel::current();
+  std::map<int, std::vector<GEntity*> > groups[4];
+  m->getPhysicalGroups(groups);
+
+  std::map<int, std::vector<double> > data;
+
+  std::vector<GEntity*> domain;
+  std::vector<GEntity*> subdomain;
+
+  // Here's the problem, linker cannot find the method for the constructor of 
+  // CellComplex class, or any other methods coded in Geo/CellComplex.cpp
+  
+  //CellComplex* testComplex = new CellComplex(domain, subdomain);
+  
+  // insert homology fun here
+  
+  PView *pv = new PView("homology", "ElementData", m, data, 0.);
+  
+  Msg::Error("test.");
+  
+  return 0;
+}

Plugin/HomologyComputation.h

+// Gmsh - Copyright (C) 1997-2009 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
+
+#ifndef _HOMOLOGY_COMPUTATION_H_
+#define _HOMOLOGY_COMPUTATION_H_
+
+#include <string>
+#include "Plugin.h"
+
+extern "C"
+{
+  GMSH_Plugin *GMSH_RegisterHomologyComputationPlugin();
+}
+
+class GMSH_HomologyComputationPlugin : public GMSH_PostPlugin
+{
+public:
+  GMSH_HomologyComputationPlugin(){}
+  void getName(char *name) const;
+  void getInfos(char *author, char *copyright, char *helpText) const;
+  void catchErrorMessage(char *errorMessage) const;
+  int getNbOptions() const;
+  StringXNumber *getOption(int iopt);  
+  int getNbOptionsStr() const;
+  StringXString *getOptionStr(int iopt);  
+  PView *execute(PView *);
+};
+
+#endif

Plugin/Makefile

@@ -33,7 +33,8 @@ SRC = Plugin.cpp PluginManager.cpp\
         Annotate.cpp Remove.cpp\
         Probe.cpp\
         HarmonicToTime.cpp ModulusPhase.cpp\
-        FiniteElement.cpp
+        FiniteElement.cpp\
+        HomologyComputation.cpp
 
 OBJ = ${SRC:.cpp=${OBJEXT}}
 
@@ -339,3 +340,6 @@ FiniteElement${OBJEXT}: FiniteElement.cpp ../Common/GmshConfig.h ../Geo/GModel.h
   ../Numeric/gmshTermOfFormulation.h ../Numeric/gmshFunction.h \
   ../Numeric/GmshMatrix.h ../Numeric/gmshLinearSystemGmm.h \
   ../Numeric/gmshLinearSystem.h
+HomologyComputation${OBJEXT}: HomologyComputation.cpp Plugin.h \
+  ../Geo/GModel.h ../Geo/GEntity.h ../Geo/CellComplex.h \
+  ../Post/PView.h HomologyComputation.h

Plugin/PluginManager.cpp

@@ -43,6 +43,7 @@
 #include "GSHHS.h"
 #include "FiniteElement.h"
 #include "Context.h"
+#include "HomologyComputation.h"
 
 #if !defined(HAVE_NO_DLL)
 #include <dlfcn.h>
@@ -228,6 +229,8 @@ void PluginManager::registerDefaultPlugins()
 #endif
     allPlugins.insert(std::pair<const char*, GMSH_Plugin*>
                       ("FiniteElement", GMSH_RegisterFiniteElementPlugin()));
+    allPlugins.insert(std::pair<const char*, GMSH_Plugin*>
+                      ("HomologyComputation", GMSH_RegisterHomologyComputationPlugin()));
   }
 
 #if defined(HAVE_FLTK)