ReorderTool.cpp

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/** \file   ReorderTool.cpp
 *  \author Jason Kraftcheck
 *  \date   2011-05-23
 */

#include "moab/ReorderTool.hpp"
#include "moab/Core.hpp"
#include "moab/Range.hpp"

#include "SequenceManager.hpp"
#include "TypeSequenceManager.hpp"
#include "EntitySequence.hpp"

#include 
#include 
#include 
#include 

namespace moab
{

// no-op function as a convenient spot to set a breakpoint
static inline ErrorCode error( ErrorCode val )
{
    return val;
}

#define CHKERR \
    if( MB_SUCCESS != rval ) return error( rval )

#define UNRECOVERABLE( ERRCODE )                                                                             \
    do                                                                                                       \
    {                                                                                                        \
        if( MB_SUCCESS != ( ERRCODE ) )                                                                      \
        {                                                                                                    \
            error( ( ERRCODE ) );                                                                            \
            std::cerr << "Unreconverable error during mesh reorder." << std::endl                            \
                      << "Error Code " << ( ERRCODE ) << " at " << __FILE__ << ":" << __LINE__ << std::endl; \
            std::cerr.flush();                                                                               \
            abort();                                                                                         \
        }                                                                                                    \
    } while( false )

static ErrorCode check_tag_type( Interface* moab, Tag tag, DataType exp_type, int exp_size )
{
    ErrorCode rval;
    DataType act_type;
    int act_size;

    rval = moab->tag_get_data_type( tag, act_type );CHKERR;

    rval = moab->tag_get_bytes( tag, act_size );CHKERR;

    if( act_type != exp_type || act_size != exp_size ) return MB_TYPE_OUT_OF_RANGE;

    return MB_SUCCESS;
}

ErrorCode ReorderTool::handle_order_from_int_tag( Tag tag, int skip_value, Tag& new_handles )
{
    ErrorCode rval;

    // check that input tag handles are what we expect
    rval = check_tag_type( mMB, tag, MB_TYPE_INTEGER, sizeof( int ) );CHKERR;
    EntityHandle zero = 0;
    rval = mMB->tag_get_handle( 0, 1, MB_TYPE_HANDLE, new_handles, MB_TAG_DENSE | MB_TAG_CREAT | MB_TAG_EXCL, &zero );CHKERR;

    // Can only reorder within same type/connectivity (or vertex/num_coords)
    // groupings.  Call helper function for each such grouping.
    for( EntityType t = MBVERTEX; t < MBENTITYSET; ++t )
    {
        // Get list of all connectivity lengths (or vertex dimensions)
        // that exist for type t.
        TypeSequenceManager& seqs = mMB->sequence_manager()->entity_map( t );
        TypeSequenceManager::iterator i;
        std::set< int > values;
        for( i = seqs.begin(); i != seqs.end(); ++i )
        {
            EntitySequence* seq = *i;
            // 0 values per entity implies structured data, which
            // we cannot reorder.  Skip those.
            if( t == MBVERTEX || 0 < seq->values_per_entity() ) values.insert( seq->values_per_entity() );
        }

        // Call helper function for each (type,size) tuple.
        std::set< int >::iterator j;
        for( j = values.begin(); j != values.end(); ++j )
        {
            rval = handle_order_from_int_tag( t, *j, tag, skip_value, new_handles );
            if( MB_SUCCESS != rval )
            {
                mMB->tag_delete( new_handles );
                return error( rval );
            }
        }
    }

    return MB_SUCCESS;
}

void ReorderTool::get_entities( EntityType t, int vals_per_ent, Range& entities )
{
    Range::iterator hint = entities.begin();
    ;
    TypeSequenceManager& seqs = mMB->sequence_manager()->entity_map( t );
    TypeSequenceManager::iterator s;
    for( s = seqs.begin(); s != seqs.end(); ++s )
    {
        EntitySequence* seq = *s;
        if( seq->values_per_entity() == vals_per_ent )
            hint = entities.insert( hint, seq->start_handle(), seq->end_handle() );
    }
}

ErrorCode ReorderTool::handle_order_from_int_tag( EntityType t,
                                                  int vals_per_ent,
                                                  Tag tag,
                                                  int skip_value,
                                                  Tag new_handles )
{
    ErrorCode rval;

    // check that input tag handles are what we expect
    rval = check_tag_type( mMB, tag, MB_TYPE_INTEGER, sizeof( int ) );CHKERR;
    rval = check_tag_type( mMB, new_handles, MB_TYPE_HANDLE, sizeof( EntityHandle ) );CHKERR;

    // get entities to re-order
    Range entities;
    get_entities( t, vals_per_ent, entities );

    // get entity order values
    std::vector< int > sortvals( entities.size() );
    rval = mMB->tag_get_data( tag, entities, &sortvals[0] );CHKERR;

    // remove any entities for which value is skip_value
    size_t r = 0, w = 0;
    for( Range::iterator i = entities.begin(); i != entities.end(); ++r )
    {
        if( sortvals[r] == skip_value )
            i = entities.erase( i );
        else
        {
            sortvals[w++] = sortvals[r];
            ++i;
        }
    }
    sortvals.resize( w );

    // sort
    std::sort( sortvals.begin(), sortvals.end() );
    // Convert to unique list and offsets for each value
    // When done, sortvals will contain unique, sortvals and
    // offsets will contain, for each unique value in sortvals,
    // the number of values that occured in the non-unique list
    // before the first instance of that value.
    std::vector< size_t > offsets;
    offsets.push_back( 0 );
    offsets.push_back( 1 );
    for( w = 0, r = 1; r < sortvals.size(); ++r )
    {
        if( sortvals[r] == sortvals[w] )
        {
            ++offsets.back();
        }
        else
        {
            ++w;
            sortvals[w] = sortvals[r];
            offsets.push_back( offsets.back() + 1 );
        }
    }
    ++w;
    assert( w + 1 == offsets.size() );
    sortvals.resize( w );

    // Tag each entity with its new handle
    for( Range::iterator i = entities.begin(); i != entities.end(); ++i )
    {
        int val;
        rval = mMB->tag_get_data( tag, &*i, 1, &val );CHKERR;
        w = std::lower_bound( sortvals.begin(), sortvals.end(), val ) - sortvals.begin();
        assert( w < sortvals.size() );
        size_t offset = offsets[w];
        ++offsets[w];
        // should maybe copy range into array to avoid possibly n^2 behavior here
        EntityHandle h = *( entities.begin() + offset );
        rval           = mMB->tag_set_data( new_handles, &*i, 1, &h );CHKERR;
    }

    return MB_SUCCESS;
}

ErrorCode ReorderTool::handle_order_from_sets_and_adj( const Range& sets, Tag& handle_tag )
{
    ErrorCode rval;

    if( !sets.all_of_type( MBENTITYSET ) ) return MB_TYPE_OUT_OF_RANGE;

    Tag order_tag;
    const int negone = -1;
    rval = mMB->tag_get_handle( 0, 1, MB_TYPE_INTEGER, order_tag, MB_TAG_DENSE | MB_TAG_CREAT | MB_TAG_EXCL, &negone );
    if( MB_SUCCESS != rval )
    {
        mMB->tag_delete( handle_tag );
        handle_tag = 0;
        return error( rval );
    }

    std::vector< std::vector< EntityHandle >* > data;
    rval = int_order_from_sets_and_adj( sets, order_tag, negone, data );
    for( size_t i = 0; i < data.size(); ++i )
        delete data[i];
    if( MB_SUCCESS != rval )
    {
        mMB->tag_delete( order_tag );
        return error( rval );
    }

    rval = handle_order_from_int_tag( order_tag, negone, handle_tag );
    if( MB_SUCCESS != rval )
    {
        mMB->tag_delete( order_tag );
        return error( rval );
    }

    rval = mMB->tag_delete( order_tag );
    if( MB_SUCCESS != rval ) return error( rval );

    return MB_SUCCESS;
}

// Compare function to use for a map keyed on pointers to sorted vectors
struct CompSortedVect
{
    bool operator()( const std::vector< EntityHandle >* v1, const std::vector< EntityHandle >* v2 ) const
    {
        std::vector< EntityHandle >::const_iterator i1, i2;
        for( i1 = v1->begin(), i2 = v2->begin(); i1 != v1->end(); ++i1, ++i2 )
        {
            if( i2 == v2->end() || *i1 > *i2 )
                return false;
            else if( *i1 < *i2 )
                return true;
        }
        return i2 != v2->end();
    }
};

ErrorCode ReorderTool::int_order_from_sets_and_adj( const Range& sets,
                                                    Tag order_tag,
                                                    int skip_val,
                                                    std::vector< std::vector< EntityHandle >* >& revMap )
{
    ErrorCode rval;

    if( !sets.all_of_type( MBENTITYSET ) ) return MB_TYPE_OUT_OF_RANGE;

    rval = check_tag_type( mMB, order_tag, MB_TYPE_INTEGER, sizeof( int ) );CHKERR;

    // Compare function to use for a map keyed on pointers to sorted vectors
    CompSortedVect lessthan;
    // Map from sorted list of handles to index
    std::map< std::vector< EntityHandle >*, int, CompSortedVect > forMap;
    std::map< std::vector< EntityHandle >*, int, CompSortedVect >::iterator fiter, fiter2;
    std::vector< EntityHandle > sharing;  // tmp storage for entity

    // for each set
    for( Range::iterator s = sets.begin(); s != sets.end(); ++s )
    {

        // gather up all entities and adjacencies
        Range tmp, ents, adj[4];  // indexed by dimension
        for( int dim = 0; dim < 4; ++dim )
        {
            rval = mMB->get_entities_by_dimension( *s, dim, tmp );CHKERR;
            for( int ldim = 0; ldim < dim; ++ldim )
            {
                rval = mMB->get_adjacencies( tmp, ldim, false, adj[ldim], Interface::UNION );CHKERR;
            }
            for( int udim = dim + 1; udim <= 3; ++udim )
            {
                rval = mMB->get_adjacencies( tmp, udim, false, adj[udim], Interface::UNION );CHKERR;
            }
            ents.merge( tmp );
            tmp.clear();
        }
        for( int dim = 0; dim < 4; ++dim )
        {
            ents.merge( adj[dim] );
            adj[dim].clear();
        }

        // process each entity
        for( Range::iterator e = ents.begin(); e != ents.end(); ++e )
        {
            int val;
            rval = mMB->tag_get_data( order_tag, &*e, 1, &val );CHKERR;

            // If this entity is already in one or more of the sets (either
            // directly or through adjacency) then get the existing list of
            // sets and append this set handle (we are iterating over sets
            // in sorted order, so appending should aways maintain a sorted
            // list.)
            sharing.clear();
            if( val != skip_val )
            {
                sharing = *revMap[val];
                assert( std::lower_bound( sharing.begin(), sharing.end(), *s ) == sharing.end() );
            }
            sharing.push_back( *s );

            // Check if new sharing list already exists in forward map
            fiter = forMap.lower_bound( &sharing );
            if( fiter == forMap.end() || lessthan( fiter->first, &sharing ) )
            {
                // Add new sharing list to forward and reverse maps.
                std::vector< EntityHandle >* newvec = new std::vector< EntityHandle >;
                newvec->swap( sharing );
                if( (int)revMap.size() == skip_val ) revMap.push_back( 0 );
                fiter2 =
                    forMap.insert( fiter, std::pair< std::vector< EntityHandle >*, int >( newvec, revMap.size() ) );
                assert( fiter2 != fiter );
                fiter = fiter2;
                revMap.push_back( newvec );
            }

            // Update index on entity
            val  = fiter->second;
            rval = mMB->tag_set_data( order_tag, &*e, 1, &val );CHKERR;
        }
    }

    return MB_SUCCESS;
}

ErrorCode ReorderTool::get_reordered_handles( Tag tag,
                                              const Range& old_handles,
                                              std::vector< EntityHandle >& new_handles )
{
    new_handles.resize( old_handles.size() );
    ErrorCode rval = mMB->tag_get_data( tag, old_handles, ( new_handles.empty() ) ? NULL : &new_handles[0] );CHKERR;

    Range::const_iterator it1                 = old_handles.begin();
    std::vector< EntityHandle >::iterator it2 = new_handles.begin();
    for( ; it1 != old_handles.end(); ++it1, ++it2 )
        if( 0 == *it2 ) *it2 = *it1;

    return MB_SUCCESS;
}

ErrorCode ReorderTool::get_reordered_handles( Tag tag,
                                              const std::vector< EntityHandle >& old_handles,
                                              std::vector< EntityHandle >& new_handles )
{
    new_handles.resize( old_handles.size() );
    return get_reordered_handles( tag, &old_handles[0], &new_handles[0], old_handles.size() );
}

ErrorCode ReorderTool::get_reordered_handles( Tag tag,
                                              const EntityHandle* old_handles,
                                              EntityHandle* new_handles,
                                              size_t num_handles )
{
    ErrorCode rval = mMB->tag_get_data( tag, old_handles, num_handles, new_handles );CHKERR;

    for( size_t i = 0; i < num_handles; ++i )
        if( 0 == new_handles[i] ) new_handles[i] = old_handles[i];

    return MB_SUCCESS;
}

ErrorCode ReorderTool::get_new_handles( Tag tag, Range& old_handles, std::vector< EntityHandle >& newhandles )
{
    // get new handles for tagged entities
    newhandles.resize( old_handles.size() );
    ErrorCode rval = mMB->tag_get_data( tag, old_handles, ( newhandles.empty() ) ? NULL : &newhandles[0] );CHKERR;

    // remove entities that were not reordered
    Range::iterator i = old_handles.begin();
    size_t w          = 0;
    for( size_t r = 0; r < newhandles.size(); ++r )
    {
        if( 0 != newhandles[r] )
        {
            newhandles[w] = newhandles[r];
            ++w;
            ++i;
        }
        else
        {
            i = old_handles.erase( i );
        }
    }
    newhandles.resize( w );
    assert( newhandles.size() == old_handles.size() );
    return MB_SUCCESS;
}

ErrorCode ReorderTool::reorder_entities( Tag new_handles )
{
    ErrorCode rval;

    rval = check_tag_type( mMB, new_handles, MB_TYPE_HANDLE, sizeof( EntityHandle ) );CHKERR;
    EntityHandle defval;
    rval = mMB->tag_get_default_value( new_handles, &defval );CHKERR;
    if( 0 != defval ) return error( MB_INDEX_OUT_OF_RANGE );

    // Can only reorder within same type/connectivity (or vertex/num_coords)
    // groupings.
    for( EntityType t = MBVERTEX; t < MBENTITYSET; ++t )
    {
        // Get list of all connectivity lengths (or vertex dimensions)
        // that exist for type t.
        TypeSequenceManager& seqs = mMB->sequence_manager()->entity_map( t );
        TypeSequenceManager::iterator i;
        std::set< int > values;
        for( i = seqs.begin(); i != seqs.end(); ++i )
        {
            EntitySequence* seq = *i;
            // 0 values per entity implies structured data, which
            // we cannot reorder.  Skip those.
            if( t == MBVERTEX || 0 < seq->values_per_entity() ) values.insert( seq->values_per_entity() );
        }

        // reorder primary data for each (type,size) tuple.
        std::set< int >::iterator j;
        for( j = values.begin(); j != values.end(); ++j )
        {
            Range entities;
            get_entities( t, *j, entities );
            std::vector< EntityHandle > handles;
            rval = get_reordered_handles( new_handles, entities, handles );
            UNRECOVERABLE( rval );

            if( t == MBVERTEX )
            {
                std::vector< double > coords( entities.size() * 3 );
                rval = mMB->get_coords( entities, &coords[0] );
                UNRECOVERABLE( rval );
                rval = mMB->set_coords( &handles[0], handles.size(), &coords[0] );
                UNRECOVERABLE( rval );
            }
            else
            {
                std::vector< EntityHandle > conn;
                conn.reserve( entities.size() * *j );
                std::vector< EntityHandle > old_handles;
                old_handles.resize( entities.size() );
                std::copy( entities.begin(), entities.end(), old_handles.begin() );
                rval = mMB->get_connectivity( &old_handles[0], old_handles.size(), conn, false );
                UNRECOVERABLE( rval );
                old_handles.clear();
                old_handles = conn;
                rval        = get_reordered_handles( new_handles, old_handles, conn );
                UNRECOVERABLE( rval );
                for( unsigned int h = 0; h < handles.size(); ++h )
                {
                    rval = mMB->set_connectivity( handles[h], &conn[h * *j], *j );
                    UNRECOVERABLE( rval );
                }
            }
        }
    }

    // now update tag data
    std::vector< Tag > tag_handles;
    mMB->tag_get_tags( tag_handles );
    for( size_t i = 0; i < tag_handles.size(); ++i )
    {
        Tag tag = tag_handles[i];
        if( tag == new_handles )  // don't mess up mapping from old to new handles
            continue;

        for( EntityType t = MBVERTEX; t <= MBENTITYSET; ++t )
        {
            rval = reorder_tag_data( t, new_handles, tag );
            UNRECOVERABLE( rval );
        }
    }

    rval = update_set_contents( new_handles );
    UNRECOVERABLE( rval );

    return MB_SUCCESS;
}

ErrorCode ReorderTool::reorder_tag_data( EntityType etype, Tag new_handles, Tag tag )
{
    ErrorCode rval;

    int tagsize;
    DataType tagtype;
    rval = mMB->tag_get_data_type( tag, tagtype );
    if( MB_SUCCESS != rval ) return error( rval );
    if( MB_TYPE_BIT == tagtype )
        tagsize = 1;
    else
    {
        rval = mMB->tag_get_bytes( tag, tagsize );
        if( MB_VARIABLE_DATA_LENGTH == rval )
            tagsize = -1;
        else if( MB_SUCCESS != rval )
            return error( rval );
    }

    // we don't re-order set handles, so we don't care about sets
    // unless the tag contains handles that need to be updated
    if( MBENTITYSET == etype && MB_TYPE_HANDLE != tagtype ) return MB_SUCCESS;

    // get tagged entities
    Range old_tagged;
    rval = mMB->get_entities_by_type_and_tag( 0, etype, &tag, 0, 1, old_tagged );
    if( MB_SUCCESS != rval && old_tagged.empty() ) return error( rval );

    // remove entities that were not reordered, unless the tag
    // is handle type in which case we need to update the data
    // for all entities, regardless of reordering.
    std::vector< EntityHandle > newhandles;
    if( MB_TYPE_HANDLE == tagtype )
        rval = get_reordered_handles( new_handles, old_tagged, newhandles );
    else
        rval = get_new_handles( new_handles, old_tagged, newhandles );CHKERR;

    if( old_tagged.empty() ) return MB_SUCCESS;

    // get copy of all tag data
    std::vector< unsigned char > buffer;
    std::vector< const void* > pointers;
    std::vector< int > sizes;
    // if variable-length tag
    if( -1 == tagsize )
    {
        pointers.resize( old_tagged.size() );
        sizes.resize( pointers.size() );
        rval = mMB->tag_get_by_ptr( tag, old_tagged, &pointers[0], &sizes[0] );CHKERR;
        int total = std::accumulate( sizes.begin(), sizes.end(), 0 );
        DataType dtype;
        mMB->tag_get_data_type( tag, dtype );
        int type_size;
        switch( dtype )
        {
            case MB_TYPE_INTEGER:
                type_size = sizeof( int );
                break;
            case MB_TYPE_DOUBLE:
                type_size = sizeof( double );
                break;
            case MB_TYPE_HANDLE:
                type_size = sizeof( EntityHandle );
                break;
            case MB_TYPE_BIT:
                type_size = 1;
                break;
            case MB_TYPE_OPAQUE:
                type_size = 1;
                break;
            default:
                return MB_TYPE_OUT_OF_RANGE;
        }
        buffer.resize( total * type_size );
        size_t off = 0;
        for( size_t j = 0; j < pointers.size(); ++j )
        {
            memcpy( &buffer[off], pointers[j], type_size * sizes[j] );
            pointers[j] = &buffer[off];
            off += sizes[j] * type_size;
        }
    }
    // if fixed-length tag
    else
    {
        buffer.resize( old_tagged.size() * tagsize );
        rval = mMB->tag_get_data( tag, old_tagged, &buffer[0] );CHKERR;
    }

    // if handle tag, update tag values for reordered handles
    if( MB_TYPE_HANDLE == tagtype )
    {
        assert( !( buffer.size() % sizeof( EntityHandle ) ) );
        std::vector< unsigned char > buffer2( buffer.size() );
        rval = get_reordered_handles( new_handles, reinterpret_cast< const EntityHandle* >( &buffer[0] ),
                                      reinterpret_cast< EntityHandle* >( &buffer2[0] ),
                                      buffer.size() / sizeof( EntityHandle ) );CHKERR;
        // if var-length tag then do not do swap because pointers[] contains pointers
        // into old buffer
        if( -1 == tagsize )
            memcpy( &buffer[0], &buffer2[0], buffer.size() );
        else
            buffer.swap( buffer2 );
    }

    // store re-ordered tag data
    if( -1 == tagsize )
    {
        rval = mMB->tag_set_by_ptr( tag, &newhandles[0], newhandles.size(), &pointers[0], &sizes[0] );
        pointers.clear();
        sizes.clear();
        buffer.clear();
    }
    else
    {
        rval = mMB->tag_set_data( tag, &newhandles[0], newhandles.size(), &buffer[0] );
        buffer.clear();
    }
    CHKERR;

    // all permutations should be cyclical, but not all permuted
    // entities necessarily had tag values, so we might need to delete
    // tags for some entities
    std::sort( newhandles.begin(), newhandles.end() );
    std::vector< EntityHandle >::iterator k = newhandles.begin();
    Range::iterator i                       = old_tagged.begin();
    while( i != old_tagged.end() )
    {
        while( k != newhandles.end() && *k < *i )
            ++k;
        if( k == newhandles.end() ) break;

        if( *i == *k )  // what old_tagged -= newhandles
            i = old_tagged.erase( i );
        else
            ++i;
    }

    if( !old_tagged.empty() )
    {
        rval = mMB->tag_delete_data( tag, old_tagged );CHKERR;
    }

    return MB_SUCCESS;
}

ErrorCode ReorderTool::update_set_contents( Tag nh_tag )
{
    Range sets;
    ErrorCode rval = mMB->get_entities_by_type( 0, MBENTITYSET, sets );CHKERR;

    std::vector< EntityHandle > old_handles, new_handles;
    for( Range::iterator i = sets.begin(); i != sets.end(); ++i )
    {
        // If set is un-ordered...
        unsigned opts = 0;
        mMB->get_meshset_options( *i, opts );
        if( !( opts & MESHSET_ORDERED ) )
        {
            Range contents;
            rval = mMB->get_entities_by_handle( *i, contents );CHKERR;

            rval = get_new_handles( nh_tag, contents, new_handles );CHKERR;

            Range replace;
            std::sort( new_handles.begin(), new_handles.end() );
            Range::iterator hint = replace.begin();
            for( size_t j = 0; j < new_handles.size(); ++j )
                hint = replace.insert( hint, new_handles[j] );
            Range common = intersect( contents, replace );
            contents -= common;
            replace -= common;
            assert( contents.size() == replace.size() );
            if( !contents.empty() )
            {
                rval = mMB->remove_entities( *i, contents );CHKERR;
                rval = mMB->add_entities( *i, replace );
            }
        }

        // If set is ordered...
        else
        {
            // get set contents
            old_handles.clear();
            rval = mMB->get_entities_by_handle( *i, old_handles );CHKERR;

            // get new handles from old contained handles
            rval = get_reordered_handles( nh_tag, old_handles, new_handles );CHKERR;

            rval = mMB->clear_meshset( &*i, 1 );CHKERR;

            rval = mMB->add_entities( *i, &new_handles[0], new_handles.size() );CHKERR;
        }
    }  // for each set

    return MB_SUCCESS;
}

}  // namespace moab