Cppcheck report - MOAB: src/MergeMesh.cpp

#include "moab/MergeMesh.hpp"

#include "moab/Skinner.hpp"
#include "moab/AdaptiveKDTree.hpp"
#include "moab/Range.hpp"
#include "moab/CartVect.hpp"

#include "Internals.hpp"
#include <vector>
#include <algorithm>
#include <string>
#include <vector>
#include <cassert>
#include <iostream>
#include <iomanip>

#include <cstdlib>

namespace moab
{

MergeMesh::MergeMesh( Interface* impl, bool printErrorIn )
    : mbImpl( impl ), mbMergeTag( 0 ), mergeTol( 0.001 ), mergeTolSq( 0.000001 ), printError( printErrorIn )
{
}

MergeMesh::~MergeMesh()
{
    if( mbMergeTag ) mbImpl->tag_delete( mbMergeTag );
    mbMergeTag = NULL;
}

ErrorCode MergeMesh::merge_entities( EntityHandle* elems,
                                     int elems_size,
                                     const double merge_tol,
                                     const int do_merge,
                                     const int update_sets,
                                     Tag merge_tag,
                                     bool do_higher_dim )
{
    mergeTol   = merge_tol;
    mergeTolSq = merge_tol * merge_tol;
    Range tmp_elems;
    tmp_elems.insert( elems, elems + elems_size );
    ErrorCode result = merge_entities( tmp_elems, merge_tol, do_merge, update_sets, (Tag)merge_tag, do_higher_dim );

    return result;
}

/*  This function appears to be not necessary after MOAB conversion

 void MergeMesh::perform_merge(iBase_TagHandle merge_tag)
 {
 // put into a range
 ErrorCode result = perform_merge((Tag) merge_tag);
 if (result != MB_SUCCESS)
 throw MKException(iBase_FAILURE, "");
 }*/

ErrorCode MergeMesh::merge_entities( Range& elems,
                                     const double merge_tol,
                                     const int do_merge,
                                     const int,
                                     Tag merge_tag,
                                     bool merge_higher_dim )
{
    // If merge_higher_dim is true, do_merge must also be true
    if( merge_higher_dim && !do_merge )
    {
        return MB_FAILURE;
    }

    mergeTol   = merge_tol;
    mergeTolSq = merge_tol * merge_tol;

    // get the skin of the entities
    Skinner skinner( mbImpl );
    Range skin_range;
    ErrorCode result = skinner.find_skin( 0, elems, 0, skin_range, false, false );
    if( MB_SUCCESS != result ) return result;

    // create a tag to mark merged-to entity; reuse tree_root
    EntityHandle tree_root = 0;
    if( 0 == merge_tag )
    {
        result = mbImpl->tag_get_handle( "__merge_tag", 1, MB_TYPE_HANDLE, mbMergeTag, MB_TAG_DENSE | MB_TAG_EXCL,
                                         &tree_root );
        if( MB_SUCCESS != result ) return result;
    }
    else
        mbMergeTag = merge_tag;

    // build a kd tree with the vertices
    AdaptiveKDTree kd( mbImpl );
    result = kd.build_tree( skin_range, &tree_root );
    if( MB_SUCCESS != result ) return result;

    // find matching vertices, mark them
    result = find_merged_to( tree_root, kd, mbMergeTag );
    if( MB_SUCCESS != result ) return result;

    // merge them if requested
    if( do_merge )
    {
        result = perform_merge( mbMergeTag );
        if( MB_SUCCESS != result ) return result;
    }

    if( merge_higher_dim && deadEnts.size() != 0 )
    {
        result = merge_higher_dimensions( elems );
        if( MB_SUCCESS != result ) return result;
    }

    return MB_SUCCESS;
}

ErrorCode MergeMesh::merge_all( EntityHandle meshset, const double merge_tol )
{
    ErrorCode rval;
    if( 0 == mbMergeTag )
    {
        EntityHandle def_val = 0;
        rval = mbImpl->tag_get_handle( "__merge_tag", 1, MB_TYPE_HANDLE, mbMergeTag, MB_TAG_DENSE | MB_TAG_EXCL,
                                       &def_val );MB_CHK_ERR( rval );
    }
    // get all entities;
    // get all vertices connected
    // build a kdtree
    // find merged to
    mergeTol   = merge_tol;
    mergeTolSq = merge_tol * merge_tol;

    // get all vertices
    Range entities;
    rval = mbImpl->get_entities_by_handle( meshset, entities, /*recursive*/ true );MB_CHK_ERR( rval );
    Range sets = entities.subset_by_type( MBENTITYSET );
    entities   = subtract( entities, sets );
    Range verts;
    rval = mbImpl->get_connectivity( entities, verts );MB_CHK_ERR( rval );

    // build a kd tree with the vertices
    AdaptiveKDTree kd( mbImpl );
    EntityHandle tree_root;
    rval = kd.build_tree( verts, &tree_root );MB_CHK_ERR( rval );
    // find matching vertices, mark them
    rval = find_merged_to( tree_root, kd, mbMergeTag );MB_CHK_ERR( rval );

    rval = perform_merge( mbMergeTag );MB_CHK_ERR( rval );

    if( deadEnts.size() != 0 )
    {
        rval = merge_higher_dimensions( entities );MB_CHK_ERR( rval );
    }
    return MB_SUCCESS;
}
ErrorCode MergeMesh::perform_merge( Tag merge_tag )
{
    // we start with an empty range of vertices that are "merged to"
    // they are used (eventually) for higher dim entities
    mergedToVertices.clear();
    ErrorCode result;
    if( deadEnts.size() == 0 )
    {
        if( printError ) std::cout << "\nWarning: Geometries don't have a common face; Nothing to merge" << std::endl;
        return MB_SUCCESS;  // nothing to merge carry on with the program
    }
    if( mbImpl->type_from_handle( *deadEnts.begin() ) != MBVERTEX ) return MB_FAILURE;
    std::vector< EntityHandle > merge_tag_val( deadEnts.size() );
    Range deadEntsRange;
    std::copy( deadEnts.rbegin(), deadEnts.rend(), range_inserter( deadEntsRange ) );
    result = mbImpl->tag_get_data( merge_tag, deadEntsRange, &merge_tag_val[0] );
    if( MB_SUCCESS != result ) return result;

    std::set< EntityHandle >::iterator rit;
    unsigned int i;
    for( rit = deadEnts.begin(), i = 0; rit != deadEnts.end(); ++rit, i++ )
    {
        assert( merge_tag_val[i] );
        if( MBVERTEX == TYPE_FROM_HANDLE( merge_tag_val[i] ) ) mergedToVertices.insert( merge_tag_val[i] );
        result = mbImpl->merge_entities( merge_tag_val[i], *rit, false, false );
        if( MB_SUCCESS != result )
        {
            return result;
        }
    }
    result = mbImpl->delete_entities( deadEntsRange );
    return result;
}
// merge vertices according to an input tag
// merge them if the tags are equal
struct handle_id
{
    EntityHandle eh;
    int val;
};

// handle structure comparison function for qsort
// if the id is the same , compare the handle.
int compare_handle_id( const void* a, const void* b )
{

    handle_id* ia = (handle_id*)a;
<--- C-style pointer casting [+]
C-style pointer casting detected. C++ offers four different kinds of casts as replacements: static_cast, const_cast, dynamic_cast and reinterpret_cast. A C-style cast could evaluate to any of those automatically, thus it is considered safer if the programmer explicitly states which kind of cast is expected. See also: https://www.securecoding.cert.org/confluence/display/cplusplus/EXP05-CPP.+Do+not+use+C-style+casts.
    handle_id* ib = (handle_id*)b;
<--- C-style pointer casting [+]
C-style pointer casting detected. C++ offers four different kinds of casts as replacements: static_cast, const_cast, dynamic_cast and reinterpret_cast. A C-style cast could evaluate to any of those automatically, thus it is considered safer if the programmer explicitly states which kind of cast is expected. See also: https://www.securecoding.cert.org/confluence/display/cplusplus/EXP05-CPP.+Do+not+use+C-style+casts.
    if( ia->val == ib->val )
    {
        return ( ia->eh < ib->eh ) ? -1 : 1;
    }
    else
    {
        return ( ia->val - ib->val );
    }
}

ErrorCode MergeMesh::merge_using_integer_tag( Range& verts, Tag user_tag, Tag merge_tag )
{
    ErrorCode rval;
    DataType tag_type;
    rval = mbImpl->tag_get_data_type( user_tag, tag_type );
    if( rval != MB_SUCCESS || tag_type != MB_TYPE_INTEGER ) return MB_FAILURE;

    std::vector< int > vals( verts.size() );
    rval = mbImpl->tag_get_data( user_tag, verts, &vals[0] );
    if( rval != MB_SUCCESS ) return rval;

    if( 0 == merge_tag )
    {
        EntityHandle def_val = 0;
        rval = mbImpl->tag_get_handle( "__merge_tag", 1, MB_TYPE_HANDLE, mbMergeTag, MB_TAG_DENSE | MB_TAG_EXCL,
                                       &def_val );
        if( MB_SUCCESS != rval ) return rval;
    }
    else
        mbMergeTag = merge_tag;

    std::vector< handle_id > handles( verts.size() );
    int i = 0;
    for( Range::iterator vit = verts.begin(); vit != verts.end(); ++vit )
    {
        handles[i].eh  = *vit;
        handles[i].val = vals[i];
        i++;
    }
    // std::sort(handles.begin(), handles.end(), compare_handle_id);
    qsort( &handles[0], handles.size(), sizeof( handle_id ), compare_handle_id );
    i = 0;
    while( i < (int)verts.size() - 1 )
    {
        handle_id first = handles[i];
        int j           = i + 1;
        while( j < (int)verts.size() && handles[j].val == first.val )
        {
            rval = mbImpl->tag_set_data( mbMergeTag, &( handles[j].eh ), 1, &( first.eh ) );
            if( rval != MB_SUCCESS ) return rval;
            deadEnts.insert( handles[j].eh );
            j++;
        }
        i = j;
    }

    rval = perform_merge( mbMergeTag );

    return rval;
}
ErrorCode MergeMesh::find_merged_to( EntityHandle& tree_root, AdaptiveKDTree& tree, Tag merge_tag )
{
    AdaptiveKDTreeIter iter;

    // evaluate vertices in this leaf
    Range leaf_range, leaf_range2;
    std::vector< EntityHandle > sorted_leaves;
    std::vector< double > coords;
    std::vector< EntityHandle > merge_tag_val, leaves_out;

    ErrorCode result = tree.get_tree_iterator( tree_root, iter );
    if( MB_SUCCESS != result ) return result;
    while( result == MB_SUCCESS )
    {
        sorted_leaves.push_back( iter.handle() );
        result = iter.step();
    }
    if( result != MB_ENTITY_NOT_FOUND ) return result;
    std::sort( sorted_leaves.begin(), sorted_leaves.end() );

    std::vector< EntityHandle >::iterator it;
    for( it = sorted_leaves.begin(); it != sorted_leaves.end(); ++it )
    {

        leaf_range.clear();
        result = mbImpl->get_entities_by_handle( *it, leaf_range );
        if( MB_SUCCESS != result ) return result;
        coords.resize( 3 * leaf_range.size() );
        merge_tag_val.resize( leaf_range.size() );
        result = mbImpl->get_coords( leaf_range, &coords[0] );
        if( MB_SUCCESS != result ) return result;
        result = mbImpl->tag_get_data( merge_tag, leaf_range, &merge_tag_val[0] );
        if( MB_SUCCESS != result ) return result;
        Range::iterator rit;
        unsigned int i;
        bool inleaf_merged, outleaf_merged = false;
        unsigned int lr_size = leaf_range.size();

        for( i = 0, rit = leaf_range.begin(); i != lr_size; ++rit, i++ )
        {
            if( 0 != merge_tag_val[i] ) continue;
            CartVect from( &coords[3 * i] );
            inleaf_merged = false;

            // check close-by leaves too
            leaves_out.clear();
            result =
                tree.distance_search( from.array(), mergeTol, leaves_out, mergeTol, 1.0e-6, NULL, NULL, &tree_root );
            leaf_range2.clear();
            for( std::vector< EntityHandle >::iterator vit = leaves_out.begin(); vit != leaves_out.end(); ++vit )
            {
                if( *vit > *it )
                {  // if we haven't visited this leaf yet in the outer loop
                    result = mbImpl->get_entities_by_handle( *vit, leaf_range2, Interface::UNION );
                    if( MB_SUCCESS != result ) return result;
                }
            }
            if( !leaf_range2.empty() )
            {
                coords.resize( 3 * ( lr_size + leaf_range2.size() ) );
                merge_tag_val.resize( lr_size + leaf_range2.size() );
                result = mbImpl->get_coords( leaf_range2, &coords[3 * lr_size] );
                if( MB_SUCCESS != result ) return result;
                result = mbImpl->tag_get_data( merge_tag, leaf_range2, &merge_tag_val[lr_size] );
                if( MB_SUCCESS != result ) return result;
                outleaf_merged = false;
            }

            // check other verts in this leaf
            for( unsigned int j = i + 1; j < merge_tag_val.size(); j++ )
            {
                EntityHandle to_ent = j >= lr_size ? leaf_range2[j - lr_size] : leaf_range[j];

                if( *rit == to_ent ) continue;

                if( ( from - CartVect( &coords[3 * j] ) ).length_squared() < mergeTolSq )
                {
                    merge_tag_val[j] = *rit;
                    if( j < lr_size )
                    {
                        inleaf_merged = true;
                    }
                    else
                    {
                        outleaf_merged = true;
                    }
                    deadEnts.insert( to_ent );
                }
            }
            if( outleaf_merged )
            {
                result = mbImpl->tag_set_data( merge_tag, leaf_range2, &merge_tag_val[leaf_range.size()] );
                if( MB_SUCCESS != result ) return result;
                outleaf_merged = false;
            }
            if( inleaf_merged )
            {
                result = mbImpl->tag_set_data( merge_tag, leaf_range, &merge_tag_val[0] );
                if( MB_SUCCESS != result ) return result;
            }
        }
    }
    return MB_SUCCESS;
}

// Determine which higher dimensional entities should be merged
ErrorCode MergeMesh::merge_higher_dimensions( Range& elems )
{
    // apply a different strategy
    // look at the vertices that were merged to, earlier, and find all entities adjacent to them
    // elems (input) are used just for initial connectivity
    ErrorCode result;
    Range verts;
    result = mbImpl->get_connectivity( elems, verts );
    if( MB_SUCCESS != result ) return result;

    // all higher dim entities that will be merged will be connected to the vertices that were
    // merged earlier; we will look at these vertices only
    Range mergedToVertsRange;
    std::copy( mergedToVertices.rbegin(), mergedToVertices.rend(), range_inserter( mergedToVertsRange ) );
    Range vertsOfInterest = intersect( mergedToVertsRange, verts );
    // Go through each dimension
    Range possibleEntsToMerge, conn, matches, moreDeadEnts;

    for( int dim = 1; dim < 3; dim++ )
    {
        moreDeadEnts.clear();
        possibleEntsToMerge.clear();
        result = mbImpl->get_adjacencies( vertsOfInterest, dim, false, possibleEntsToMerge, Interface::UNION );
        if( MB_SUCCESS != result ) return result;
        // Go through each possible entity and see if it shares vertices with another entity of same
        // dimension
        for( Range::iterator pit = possibleEntsToMerge.begin(); pit != possibleEntsToMerge.end(); ++pit )
        {
            EntityHandle eh = *pit;  // possible entity to be matched
            conn.clear();
            // Get the vertices connected to it in a range

            result = mbImpl->get_connectivity( &eh, 1, conn );
            if( MB_SUCCESS != result ) return result;
            matches.clear();
            // now retrieve all entities connected to all conn vertices
            result = mbImpl->get_adjacencies( conn, dim, false, matches, Interface::INTERSECT );
            if( MB_SUCCESS != result ) return result;
            if( matches.size() > 1 )
            {
                for( Range::iterator matchIt = matches.begin(); matchIt != matches.end(); ++matchIt )
                {
                    EntityHandle to_remove = *matchIt;
                    if( to_remove != eh )
                    {
                        moreDeadEnts.insert( to_remove );
                        result = mbImpl->merge_entities( eh, to_remove, false, false );
                        if( result != MB_SUCCESS ) return result;
                        possibleEntsToMerge.erase( to_remove );
                    }
                }
            }
        }
        // Delete the entities of dimension dim
        result = mbImpl->delete_entities( moreDeadEnts );
        if( result != MB_SUCCESS ) return result;
    }
    return MB_SUCCESS;
#if 0
  Range skinEnts, adj, matches, moreDeadEnts;
  ErrorCode result;
  Skinner skinner(mbImpl);
  //Go through each dimension
  for (int dim = 1; dim < 3; dim++)
  {
    skinEnts.clear();
    moreDeadEnts.clear();
    result = skinner.find_skin(0, elems, dim, skinEnts, false, false);
    //Go through each skin entity and see if it shares adjacancies with another entity
    for (Range::iterator skinIt = skinEnts.begin();
        skinIt != skinEnts.end(); ++skinIt)
    {
      adj.clear();
      //Get the adjacencies 1 dimension lower
      result = mbImpl->get_adjacencies(&(*skinIt), 1, dim - 1, false, adj);
      if (result != MB_SUCCESS)
        return result;
      //See what other entities share these adjacencies
      matches.clear();
      result = mbImpl->get_adjacencies(adj, dim, false, matches,
          Interface::INTERSECT);
      if (result != MB_SUCCESS)
        return result;
      //If there is more than one entity, then we have some to merge and erase
      if (matches.size() > 1)
      {
        for (Range::iterator matchIt = matches.begin();
            matchIt != matches.end(); ++matchIt)
        {
          if (*matchIt != *skinIt)
          {
            moreDeadEnts.insert(*matchIt);
            result = mbImpl->merge_entities(*skinIt, *matchIt, false, false);
            if (result != MB_SUCCESS)
              return result;
            skinEnts.erase(*matchIt);
          }
        }
      }
    }
    //Delete the entities
    result = mbImpl->delete_entities(moreDeadEnts);
    if (result != MB_SUCCESS)
      return result;
  }
  return MB_SUCCESS;
#endif
}

}  // End namespace moab