From a6944e8a83d9a34b1e79475352fbca4a5719a244 Mon Sep 17 00:00:00 2001
From: ageay <ageay>
Date: Thu, 4 Apr 2013 10:41:42 +0000
Subject: [PATCH] MEDMEM suppression

---
 src/RENUMBER/CMakeLists.txt         |   5 +-
 src/RENUMBER/Makefile.am            |   8 +-
 src/RENUMBER/RenumberingFactory.hxx |   7 +-
 src/RENUMBER/renumbering.cxx        | 352 ++++------------------------
 4 files changed, 58 insertions(+), 314 deletions(-)

diff --git a/src/RENUMBER/CMakeLists.txt b/src/RENUMBER/CMakeLists.txt
index fc48b2695..befd5a395 100644
--- a/src/RENUMBER/CMakeLists.txt
+++ b/src/RENUMBER/CMakeLists.txt
@@ -22,7 +22,8 @@ INCLUDE_DIRECTORIES(
   ${METIS_INCLUDE_DIRS}
   ${MED3_INCLUDE_DIRS}
   ${HDF5_INCLUDE_DIRS}
-  ${CMAKE_CURRENT_SOURCE_DIR}/../MEDMEM
+  ${CMAKE_CURRENT_SOURCE_DIR}/../MEDLoader
+  ${CMAKE_CURRENT_SOURCE_DIR}/../MEDCoupling
   ${CMAKE_CURRENT_SOURCE_DIR}/../INTERP_KERNEL
   ${CMAKE_CURRENT_SOURCE_DIR}/../INTERP_KERNEL/Bases
   ${CMAKE_CURRENT_SOURCE_DIR}/../INTERP_KERNEL/Geometric2D
@@ -45,7 +46,7 @@ SET(renumber_SOURCES
   renumbering.cxx
   )
 
-SET(renumbercpp_LDFLAGS medmem)
+SET(renumbercpp_LDFLAGS medloader)
 SET(renumber_DEFINITIONS "${HDF5_DEFINITIONS} ${MED3_DEFINITIONS} ${BOOST_DEFINITIONS} ${PLATFORM_DEFINITIONS}")
 
 IF(MED_ENABLE_METIS)
diff --git a/src/RENUMBER/Makefile.am b/src/RENUMBER/Makefile.am
index d6eaefb04..ce20cfd8c 100644
--- a/src/RENUMBER/Makefile.am
+++ b/src/RENUMBER/Makefile.am
@@ -16,8 +16,6 @@
 #
 # See http://www.salome-platform.org/ or email : webmaster.salome@opencascade.com
 
-#  MED MEDMEM : MED files in memory
-
 include $(top_srcdir)/adm_local/unix/make_common_starter.am
 
 # this directory must be recompiled before Test folder
@@ -53,13 +51,13 @@ endif
 
 librenumber_la_CPPFLAGS= $(MED3_INCLUDES) $(HDF5_INCLUDES) @CXXTMPDPTHFLAGS@ \
 	$(BOOST_CPPFLAGS) \
-	-I$(srcdir)/../MEDMEM -I$(srcdir)/../INTERP_KERNEL/Bases \
+	-I$(srcdir)/../MEDLoader -I$(srcdir)/../MEDCoupling -I$(srcdir)/../INTERP_KERNEL/Bases \
 	-I$(srcdir)/../INTERP_KERNEL/GaussPoints \
 	-I$(srcdir)/../INTERP_KERNEL
 
 librenumber_la_LDFLAGS= 
 #libmedsplitter_la_LDFLAGS= $(MED3_LIBS_C_ONLY) $(HDF5_LIBS) $(STDLIB) \
-#	../MEDMEM/libmedmem.la
+#	../MEDLoader/libmedloader.la
 
 if MED_ENABLE_METIS
   librenumber_la_CPPFLAGS+= $(METIS_CPPFLAGS)
@@ -75,7 +73,7 @@ if MED_ENABLE_KERNEL
 endif
 
 librenumber_la_LDFLAGS+= $(MED3_LIBS_C_ONLY) $(HDF5_LIBS) $(STDLIB) \
-	../MEDMEM/libmedmem.la ../INTERP_KERNEL/libinterpkernel.la
+	../MEDLoader/libmedloader.la ../MEDCoupling/libmedcoupling.la ../INTERP_KERNEL/libinterpkernel.la
 
 # Executables targets
 bin_PROGRAMS= renumber
diff --git a/src/RENUMBER/RenumberingFactory.hxx b/src/RENUMBER/RenumberingFactory.hxx
index 7006d730a..1e1bde8f9 100644
--- a/src/RENUMBER/RenumberingFactory.hxx
+++ b/src/RENUMBER/RenumberingFactory.hxx
@@ -17,13 +17,14 @@
 // See http://www.salome-platform.org/ or email : webmaster.salome@opencascade.com
 //
 
-#ifndef RENUMBERINGFACTORY_HXX_
-#define RENUMBERINGFACTORY_HXX_
+#ifndef __RENUMBERINGFACTORY_HXX__
+#define __RENUMBERINGFACTORY_HXX__
 
-#include <string>
 #include "RENUMBERDefines.hxx"
 #include "RENUMBER_Renumbering.hxx"
 
+#include <string>
+
 namespace MED_RENUMBER
 {
   RENUMBER_EXPORT Renumbering* RenumberingFactory(const std::string& s);
diff --git a/src/RENUMBER/renumbering.cxx b/src/RENUMBER/renumbering.cxx
index d520f4db6..765fb7f8f 100644
--- a/src/RENUMBER/renumbering.cxx
+++ b/src/RENUMBER/renumbering.cxx
@@ -17,180 +17,27 @@
 // See http://www.salome-platform.org/ or email : webmaster.salome@opencascade.com
 //
 
-#include <string>
-#include <stdlib.h>
-#include <iostream>
-#include <fstream>
+#include "MEDFileData.hxx"
+#include "MEDFileMesh.hxx"
+#include "MEDFileField.hxx"
 
-#include "MEDMEM_Family.hxx"
-#include "MEDMEM_Mesh.hxx"
-#include "MEDMEM_Meshing.hxx"
-#include "MEDMEM_MedMeshDriver.hxx"
-#include "MEDMEM_Connectivity.hxx"
-#include "MEDMEM_Field.hxx"
-#include "MEDMEM_DriversDef.hxx"
-#include "MEDMEM_MedFileBrowser.hxx"
-#include "MEDMEM_MedMeshDriver.hxx"
+#include "MEDCouplingUMesh.hxx"
 
 #include "RenumberingFactory.hxx"
 
 #include <time.h>
-using namespace MEDMEM;
+#include <string>
+#include <cstdlib>
+#include <fstream>
+#include <iostream>
+
 using namespace std;
-using namespace MED_EN;
+using namespace ParaMEDMEM;
 using namespace MED_RENUMBER;
 
-void computeNeighbour(const MESH* mesh,const medGeometryElement& Type, vector<list<int> >& neighbour, int& ntot,int& nb_cell)
-{
-  CONNECTIVITY* conn = (CONNECTIVITY*)mesh->getConnectivityptr();
-  conn->calculateFullDescendingConnectivity(MED_CELL);
-  const int* rev_conn=mesh->getReverseConnectivity(MED_EN::MED_DESCENDING, MED_EN::MED_CELL);
-  const int* rev_conn_index=mesh->getReverseConnectivityIndex(MED_EN::MED_DESCENDING, MED_EN::MED_CELL);
-  int nb_face= mesh->getNumberOfElements(MED_FACE,MED_ALL_ELEMENTS);
-  int nb_edge = mesh->getNumberOfElements(MED_EDGE,MED_ALL_ELEMENTS);
-  nb_cell= mesh->getNumberOfElements(MED_CELL,Type);
-
-  int nb_constituent;
-  if(mesh->getMeshDimension()==2)
-    nb_constituent = nb_edge;
-  else if (mesh->getMeshDimension()==3)
-    nb_constituent = nb_face;
-  else
-    throw MEDEXCEPTION("Wrong dimension");
-
-  neighbour.resize(nb_cell,(list<int>)0);
-  ntot=0;
-  for(int i=0;i<nb_constituent;++i)
-    {
-      for(int j=rev_conn_index[i]-1;j<rev_conn_index[i+1]-1;++j)
-        {
-          for(int k=j+1;k<rev_conn_index[i+1]-1;++k)
-            {
-              if(rev_conn[j]!=0 && rev_conn[k]!=0)
-                {
-                  ntot+=2;
-                  neighbour[rev_conn[j]-1].push_back(rev_conn[k]);
-                  neighbour[rev_conn[k]-1].push_back(rev_conn[j]);
-                }
-            }
-        }
-    }
-}
-
-void changeConnectivity(MESH& mesh, const medGeometryElement& Type, const int& nb_cell, const vector<int>& iperm)
-{
-  /*if(Type==MED_POLYHEDRA)
-    {
-      int *conn_face_index_init=(int*)mesh.getPolyhedronFacesIndex();
-      int *conn_index_init=(int*)mesh.getPolyhedronIndex(MED_FULL_INTERLACE);
-      int *conn_init=(int*)mesh.getPolyhedronConnectivity(MED_FULL_INTERLACE);
-
-      int *conn_index_renum=new int[nb_cell+1];
-      int *conn_face_index_renum=new int[conn_index_init[nb_cell]];
-      int *conn_renum=new int[conn_face_index_init[conn_index_init[nb_cell]-1]-1];
-
-      int i_cell,i_face,i_conn;
-      int iter_face=0;
-      int iter_conn=0;
-      int i2;
-      conn_index_renum[0]=1;
-      conn_face_index_renum[0]=1;
-      for(i_cell=0;i_cell<nb_cell;++i_cell)
-        {
-          i2=iperm[i_cell]-1;
-          for(i_face=conn_index_init[i2]-1;i_face<conn_index_init[i2+1]-1;++i_face)
-            {
-              for(i_conn=conn_face_index_init[i_face]-1;i_conn<conn_face_index_init[i_face+1]-1;++i_conn)
-                {
-                  conn_renum[iter_conn]=conn_init[i_conn];
-                  ++iter_conn;
-                }
-              conn_face_index_renum[iter_face+1]=iter_conn+1;
-              ++iter_face;
-            }
-          conn_index_renum[i_cell+1]=iter_face+1;
-        }
-      memcpy(conn_face_index_init,conn_face_index_renum,sizeof(int)*conn_index_init[nb_cell]);
-      memcpy(conn_index_init,conn_index_renum,sizeof(int)*(nb_cell+1));
-      memcpy(conn_init,conn_renum, sizeof(int)*(conn_face_index_init[conn_index_init[nb_cell]-1]-1));
-
-      delete[] conn_index_renum;
-      delete[] conn_face_index_renum;
-      delete[] conn_renum;
-    }
-  else if (Type==MED_POLYGON)
-    {
-      int *conn_init=(int*)mesh.getPolygonsConnectivity(MED_FULL_INTERLACE,MED_CELL);
-      int *conn_index_init=(int*)mesh.getPolygonsConnectivityIndex(MED_FULL_INTERLACE,MED_CELL);
-      int *conn_index_renum=new int[nb_cell+1];
-      int *conn_renum=new int[conn_index_init[nb_cell]-1];
-
-      int iter=0;
-      int i2;
-      conn_index_renum[0]=1;
-      for(int i=0;i<nb_cell;++i)
-        {
-          i2=iperm[i]-1;
-          for(int k=conn_index_init[i2];k<conn_index_init[i2+1];++k)
-            {
-              conn_renum[iter]=conn_init[k-1];
-              ++iter;
-            }
-          conn_index_renum[i+1]=iter+1;
-        }
-      memcpy(conn_index_init,conn_index_renum,sizeof(int)*(nb_cell+1));
-      memcpy(conn_init,conn_renum, sizeof(int)*(conn_index_init[nb_cell]-1));
-
-      delete[] conn_renum;
-      delete[] conn_index_renum;
-    }
-    else*/
-    {
-      const int *conn_init=mesh.getConnectivity(MED_NODAL,MED_CELL,Type);
-      const int *conn_index_init=mesh.getConnectivityIndex(MED_NODAL,MED_CELL);
-      int *conn_renum=new int[conn_index_init[nb_cell]-1];
-      int *conn_index_renum=new int[nb_cell+1];
-
-      int iter=0;
-      int i2;
-      conn_index_renum[0]=1;
-      for(int i=0;i<nb_cell;++i)
-        {
-          i2=iperm[i]-1;
-          for(int k=conn_index_init[i2];k<conn_index_init[i2+1];++k)
-            {
-              conn_renum[iter]=conn_init[k-1];
-              ++iter;
-            }
-          conn_index_renum[i+1]=iter+1;
-        }
-
-      CONNECTIVITY* myConnectivity=(CONNECTIVITY*)mesh.getConnectivityptr();
-      myConnectivity->setNodal(conn_renum,MED_CELL,Type,conn_index_renum);
-      delete[] conn_renum;
-      delete[] conn_index_renum;
-    }
-}
-
-void changeFamily(MESH* mesh, const medGeometryElement& Type, const vector<int>& perm)
-{
-  int nb_families=mesh->getNumberOfFamilies(MED_CELL);
-  for (int i=0;i<nb_families;++i)
-    {
-      const FAMILY* family=mesh->getFamily(MED_CELL,i+1);
-      if (!family->isOnAllElements())
-        {
-          int nb_elem=family->getNumberOfElements(Type);
-          int *number=(int *)family->getNumber(Type);
-          for(int j=0;j<nb_elem;++j)
-            number[j]=perm[number[j]-1];
-        }
-    }
-}
-
-int main (int argc, char** argv)
+int main(int argc, char** argv)
 {
-  double t_begin,t_read_st,t_read_mesh,t_compute_graph,t_connectiv,t_family,t_field;
+  double t_begin,t_read_st,t_compute_graph,t_family,t_field;
   t_begin=clock();
   if (argc <5)
     {
@@ -206,159 +53,56 @@ int main (int argc, char** argv)
   if(type_renum!="METIS" && type_renum!="BOOST")
     {
       cout << "The method has to be METIS or BOOST!" << endl;
-      exit(-1);
-    }
-
-  string s="rm "+filename_out;
-  system(s.c_str());
-
-  // Reading file structure
-  const MEDFILEBROWSER med_struct(filename_in);
-  int nb_mesh, nb_fields;
-  vector<string> mesh_names,f_names;
-  nb_mesh=med_struct.getNumberOfMeshes();
-  nb_fields=med_struct.getNumberOfFields();
-  mesh_names=med_struct.getMeshNames();
-  f_names=med_struct.getFieldNames();
-  if(nb_mesh!=1)
-    {
-      cout << "There are many meshes in the file" << endl;
       return -1;
     }
-  if(mesh_names[0].c_str()!=meshname)
-    {
-      cout << "Mesh name does not match" << endl;
-      return -1;
-    }
-  vector<string> field_names;
-  vector<int> iternumber;
-  vector<int> ordernumber;
-  vector<int> types;
-  int nb_fields_tot=0;
-  for (int ifield = 0; ifield < nb_fields; ifield++)
+  // Reading file structure
+  cout << "Reading : " << flush;
+  MEDCouplingAutoRefCountObjectPtr<MEDFileData> fd=MEDFileData::New(filename_in);
+  MEDFileMesh *m=fd->getMeshes()->getMeshWithName(meshname.c_str());
+  MEDFileUMesh *mc=dynamic_cast<MEDFileUMesh *>(m);
+  if(!mc)
     {
-      vector<DT_IT_> dtit=med_struct.getFieldIteration(f_names[ifield]);
-      for (vector<DT_IT_>::const_iterator iter =dtit.begin(); iter!=dtit.end(); iter++)
-        {
-          field_names.push_back(f_names[ifield]);
-          iternumber.push_back(iter->dt);
-          ordernumber.push_back(iter->it);
-          ++nb_fields_tot;
-          if(med_struct.getFieldType(f_names[ifield])==MED_EN::MED_REEL64)
-            types.push_back(1);
-          else
-            types.push_back(0);
-
-        }
+      std::ostringstream oss; oss << "In file \"" << filename_in << "\" the mesh name \"" << meshname<< "\" exists but is not unstructured !";
+      throw INTERP_KERNEL::Exception(oss.str().c_str());
     }
   t_read_st=clock();
-
+  cout << (t_read_st-t_begin)/(double) CLOCKS_PER_SEC << "s" << endl << flush;
   // Reading mesh
-  MESH myMesh;
-  myMesh.setName(meshname);
-  MED_MESH_RDONLY_DRIVER *drv22=new MED_MESH_RDONLY_DRIVER(filename_in,&myMesh);
-  drv22->desactivateFacesComputation();
-  int newDrv=myMesh.addDriver(*drv22);
-  delete drv22;
-  myMesh.read(newDrv);
-  int nb_type=myMesh.getNumberOfTypes(MED_CELL);
-  if (nb_type!=1)
-    {
-      cout << "Mesh must have only one type of cell" << endl;
-      return -1;
-    }
-  const medGeometryElement *Types = myMesh.getTypes(MED_CELL);
-  medGeometryElement Type=Types[0];
-
-  t_read_mesh=clock();
-  MESH* workMesh=new MESH(myMesh);
-  cout << "Building the graph    ";
-  cout.flush();
-  int ntot,nb_cell;
-  vector<list<int> > neighbour;
-  computeNeighbour(workMesh,Type,neighbour,ntot,nb_cell);
-  int* graph=new int[ntot];
-  int* graph_index=new int[nb_cell+1];
-  graph_index[0]=1;
-  int count=0;
-  for(int i=0;i<nb_cell;++i)
-    {
-      for (list<int>::const_iterator it=neighbour[i].begin();it!=neighbour[i].end();++it)
-        {
-          graph[count]=*it;
-          ++count;
-        }
-      graph_index[i+1]=count+1;
-    }
-
-
-  // Compute permutation
+  MEDCouplingAutoRefCountObjectPtr<MEDCouplingUMesh> workMesh=mc->getMeshAtLevel(0);
+  std::vector<int> code=workMesh->getDistributionOfTypes();
+  cout << "Building the graph : " << flush;
+  DataArrayInt *neighb=0,*neighbI=0;
+  workMesh->computeNeighborsOfCells(neighb,neighbI);
+  MEDCouplingAutoRefCountObjectPtr<DataArrayInt> neighbSafe(neighb),neighbISafe(neighbI);
+  const int *graph=neighbSafe->begin();
+  const int *graph_index=neighbISafe->begin();
+  // Compute permutation iperm->new2old perm->old2new
   vector<int> iperm,perm;
-  Renumbering* renumb= RenumberingFactory(type_renum);
+  Renumbering *renumb=RenumberingFactory(type_renum);
   renumb->renumber(graph,graph_index,nb_cell,iperm,perm);
   delete renumb;
-  delete workMesh;
   t_compute_graph=clock();
-  cout << " : " << (t_compute_graph-t_read_mesh)/(double) CLOCKS_PER_SEC << "s" << endl;
+  cout << " : " << (t_compute_graph-t_read_st)/(double) CLOCKS_PER_SEC << "s" << endl;
   cout.flush();
-
   // Connectivity
-  cout << "Computing connectivity";
-  cout.flush();
-  MESH meshRenum(myMesh);
-  changeConnectivity(meshRenum,Type,nb_cell,iperm);
-  t_connectiv=clock();
-  cout << " : " << (t_connectiv-t_compute_graph)/(double) CLOCKS_PER_SEC << "s" << endl;
-  cout.flush();
-
-  // Familles
-  cout << "Computing families    ";
-  cout.flush();
-  changeFamily(&meshRenum,Type,perm);
-  int drv3=meshRenum.addDriver(MED_DRIVER,filename_out,meshRenum.getName());
-  meshRenum.write(drv3);
-  t_family=clock();
-  cout << " : " << (t_family-t_connectiv)/(double) CLOCKS_PER_SEC << "s" << endl;
-  cout.flush();
-
-  // Fields
-  cout << "Computing fields      ";
-  cout.flush();
-  bool exist_type;
-  for(int ifield=0;ifield<nb_fields_tot;++ifield)
+  cout << "Reordering connectivity & families and writing : " << flush;
+  workMesh->renumberCells(&perm[0],false);
+  mc->setMeshAtLevel(0,workMesh);
+  const DataArrayInt *famField=mc->getFamilyFieldAtLevel(0);
+  if(famField)
     {
-      exist_type=false;
-      FIELD<double> myField(MED_DRIVER,filename_in,field_names[ifield],iternumber[ifield],ordernumber[ifield]);
-      FIELD<double> newField(myField);
-      const SUPPORT* mySupport=newField.getSupport();
-      const medGeometryElement *typesOfSupport = mySupport->getTypes();
-      for(int t=0;t<mySupport->getNumberOfTypes();++t)
-        {
-          if(typesOfSupport[t]==Type)
-            {
-              exist_type=true;
-              break;
-            }
-        }
-      if(exist_type)
-        {
-          for(int i=0;i<mySupport->getNumberOfElements(Type);++i)
-            {
-              for(int j=0;j<newField.getNumberOfComponents();++j)
-                {
-                  newField.setValueIJ(i+1,j+1,myField.getValueIJ(iperm[i],j+1));
-                }
-            }
-        }
-      int drv=newField.addDriver(MED_DRIVER,filename_out,field_names[ifield]);
-      newField.write(drv);
+      MEDCouplingAutoRefCountObjectPtr<DataArrayInt> famField2=famField->renumber(&perm[0]);
+      mc->setFamilyFieldArr(0,famField2);
     }
+  mc->write(filename_out.c_str(),2);
+  t_family=clock();
+  cout << " : " << (t_family-t_compute_graph)/(double) CLOCKS_PER_SEC << "s" << endl << flush;
+  // Fields
+  cout << "Reordering fields and writing : " << flush;
+  MEDFileFields *fs=fd->getFields();
+  fs->renumberEntitiesLyingOnMesh(meshname.c_str(),code,code,&perm[0]);
+  fs->write();
   t_field=clock();
-  cout << " : " << (t_field-t_family)/(double) CLOCKS_PER_SEC << "s" << endl;
-  cout.flush();
-
-  delete[] graph_index;
-  delete[] graph;
-
+  cout << " : " << (t_field-t_family)/(double) CLOCKS_PER_SEC << "s" << endl << flush;
   return 0;
 }
-- 
2.39.2