ReadTetGen.cpp

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#include "ReadTetGen.hpp"
#include "moab/Interface.hpp"
#include "moab/Range.hpp"
#include "moab/ReadUtilIface.hpp"
#include "moab/FileOptions.hpp"
#include "MBTagConventions.hpp"
#include 
#include 
#include 
#include 
#include 

namespace moab
{

ReaderIface* ReadTetGen::factory( Interface* moab )
{
    return new ReadTetGen( moab );
}

ReadTetGen::ReadTetGen( Interface* moab ) : mbIface( moab ), readTool( 0 )
{
    moab->query_interface( readTool );
}

ReadTetGen::~ReadTetGen()
{
    if( mbIface && readTool ) mbIface->release_interface( readTool );
}

ErrorCode ReadTetGen::open_file( const std::string& filename,
                                 const std::string& basename,
                                 const std::string& suffix,
                                 const char* exp_suffix,
                                 const char* opt_name,
                                 const FileOptions& opts,
                                 std::ifstream& file_stream,
                                 bool file_required )
{
    std::string real_file_name;
    ErrorCode rval = opts.get_option( opt_name, real_file_name );
    if( MB_ENTITY_NOT_FOUND == rval || real_file_name.empty() )
    {
        if( MB_SUCCESS == rval ) file_required = true;
        if( suffix == exp_suffix )
        {
            real_file_name = filename;
        }
        else
        {
            real_file_name = basename;
            real_file_name += ".";
            real_file_name += exp_suffix;
        }
    }

    if( !real_file_name.empty() ) file_stream.open( real_file_name.c_str(), std::ios::in );
    if( file_required && !file_stream.is_open() )
    {
        MB_SET_ERR( MB_FILE_DOES_NOT_EXIST, real_file_name << ": cannot read file" );
    }

    return MB_SUCCESS;
}

ErrorCode ReadTetGen::read_tag_values( const char* /* file_name */,
                                       const char* /* tag_name */,
                                       const FileOptions& /* opts */,
                                       std::vector< int >& /* tag_values_out */,
                                       const SubsetList* /* subset_list */ )
{
    return MB_NOT_IMPLEMENTED;
}

ErrorCode ReadTetGen::load_file( const char* file_name_c,
                                 const EntityHandle* /* file_set */,
                                 const FileOptions& opts,
                                 const ReaderIface::SubsetList* subset_list,
                                 const Tag* file_id_tag )
{
    std::ifstream node_file, ele_file, face_file, edge_file;
    ErrorCode rval;

    if( subset_list )
    {
        MB_SET_ERR( MB_UNSUPPORTED_OPERATION, "Reading subset of files not supported for TetGen" );
    }

    std::string suffix, base, filename( file_name_c );
    size_t dot_idx = filename.find_last_of( '.' );
    if( dot_idx == std::string::npos )
    {
        base = filename;
    }
    else
    {
        suffix = filename.substr( dot_idx + 1 );
        for( size_t i = 0; i < suffix.length(); ++i )
            suffix[i] = (char)tolower( suffix[i] );
        if( suffix == "node" || suffix == "ele" || suffix == "face" || suffix == "edge" )
        {
            base = filename.substr( 0, dot_idx );
        }
        else
        {
            base = filename;
            suffix.clear();
        }
    }

    rval = open_file( filename, base, suffix, "node", "NODE_FILE", opts, node_file, true );
    if( MB_SUCCESS != rval ) return rval;
    rval = open_file( filename, base, suffix, "ele", "ELE_FILE", opts, ele_file );
    if( MB_SUCCESS != rval ) return rval;
    rval = open_file( filename, base, suffix, "face", "FACE_FILE", opts, face_file );
    if( MB_SUCCESS != rval ) return rval;
    rval = open_file( filename, base, suffix, "edge", "EDGE_FILE", opts, edge_file );
    if( MB_SUCCESS != rval ) return rval;

    std::vector< Tag > attr_tags[4];
    std::vector< int > attr_idx[4];
    const char* option_names[4] = { "NODE_ATTR_LIST", "EDGE_ATTR_LIST", "TRI_ATTR_LIST", "TET_ATTR_LIST" };
    const char* group_names[4]  = { 0, "CURVE_ID", "SURFACE_ID", "VOLUME_ID" };
    for( int i = 0; i < 4; ++i )
    {
        std::string opt_str;
        rval = opts.get_str_option( option_names[i], opt_str );
        if( MB_SUCCESS != rval ) continue;
        rval = parse_attr_list( opt_str, attr_tags[i], attr_idx[i], group_names[i] );
        if( MB_SUCCESS != rval )
        {
            MB_SET_ERR( MB_TYPE_OUT_OF_RANGE, option_names[i] << ": invalid option value" );
        }
    }

    Range tets, tris, edges;
    std::vector< EntityHandle > nodes;
    rval = read_node_file( node_file, &attr_tags[0][0], &attr_idx[0][0], attr_tags[0].size(), nodes );
    if( MB_SUCCESS == rval && ele_file.is_open() ) rval = read_elem_file( MBTET, ele_file, nodes, tets );
    if( MB_SUCCESS == rval && face_file.is_open() ) rval = read_elem_file( MBTRI, face_file, nodes, tris );
    if( MB_SUCCESS == rval && edge_file.is_open() ) rval = read_elem_file( MBEDGE, edge_file, nodes, edges );

    if( file_id_tag && MB_SUCCESS == rval ) rval = readTool->assign_ids( *file_id_tag, &nodes[0], nodes.size() );
    if( file_id_tag && MB_SUCCESS == rval ) rval = readTool->assign_ids( *file_id_tag, edges );
    if( file_id_tag && MB_SUCCESS == rval ) rval = readTool->assign_ids( *file_id_tag, tris );
    if( file_id_tag && MB_SUCCESS == rval ) rval = readTool->assign_ids( *file_id_tag, tets );

    return rval;
}

ErrorCode ReadTetGen::parse_attr_list( const std::string& option_str,
                                       std::vector< Tag >& tag_list,
                                       std::vector< int >& index_list,
                                       const char* group_designator )
{
    std::vector< std::string > name_list;
    size_t prev_pos = 0;
    while( prev_pos != std::string::npos )
    {
        size_t pos = option_str.find_first_of( ',', prev_pos );
        name_list.push_back( option_str.substr( prev_pos, pos ) );
        prev_pos = pos + 1;
    }

    index_list.resize( name_list.size() );
    std::map< std::string, int > name_count;
    for( size_t i = 0; i < name_list.size(); ++i )
        index_list[i] = name_count[name_list[i]]++;

    for( size_t i = 0; i < name_list.size(); ++i )
    {
        if( group_designator && name_list[i] == group_designator )
        {
            tag_list[i]   = 0;
            index_list[i] = -1;
        }
        else if( name_list.empty() )
        {
            tag_list[i]   = 0;
            index_list[i] = 0;
        }
        else
        {
            ErrorCode rval = mbIface->tag_get_handle( name_list[i].c_str(), name_count[name_list[i]], MB_TYPE_DOUBLE,
                                                      tag_list[i], MB_TAG_DENSE | MB_TAG_CREAT );
            if( MB_SUCCESS != rval ) return rval;
        }
    }

    return MB_SUCCESS;
}

ErrorCode ReadTetGen::read_line( std::istream& file, std::string& line, int& lineno )
{
    // Loop until we find a non-empty line
    do
    {
        // Read a line
        line.clear();
        if( !getline( file, line ) ) return MB_FILE_WRITE_ERROR;
        ++lineno;
        // Strip comments from line
        size_t pos = line.find_first_of( '#' );
        if( pos != std::string::npos ) line = line.substr( 0, pos );
        // Strip leading whitespace from line
        for( pos = 0; pos < line.length() && isspace( line[pos] ); ++pos )
            ;
        if( pos == line.length() )
            line.clear();
        else if( pos != 0 )
            line = line.substr( pos );
    } while( line.empty() );

    return MB_SUCCESS;
}

ErrorCode ReadTetGen::read_line( std::istream& file, double* values_out, int num_values, int& lineno )
{
    // Get a line of text
    std::string line;
    ErrorCode rval = read_line( file, line, lineno );
    if( MB_SUCCESS != rval ) return rval;

    // Tokenize line as doubles
    std::stringstream str( line );
    for( int i = 0; i < num_values; ++i )
    {
        double v;
        if( !( str >> v ) )
        {
            MB_SET_ERR( MB_FAILURE, "Error reading node data at line " << lineno );
        }
        values_out[i] = v;
    }

    // Check that we're at the end of the line
    int junk;
    if( ( str >> junk ) || !str.eof() )
    {
        MB_SET_ERR( MB_FAILURE, "Unexpected trailing data for line " << lineno << " of node data" );
    }

    return MB_SUCCESS;
}

ErrorCode ReadTetGen::read_node_file( std::istream& file,
                                      const Tag* attr_tag_list,
                                      const int* attr_tag_index,
                                      int attr_tag_list_len,
                                      std::vector< EntityHandle >& nodes )
{
    int lineno = 0;
    ErrorCode rval;

    double header_vals[4];
    rval = read_line( file, header_vals, 4, lineno );
    if( MB_SUCCESS != rval ) return rval;

    const int num_vtx   = (int)header_vals[0];
    const int dim       = (int)header_vals[1];
    const int num_attr  = (int)header_vals[2];
    const int bdry_flag = (int)header_vals[3];
    if( num_vtx < 1 || dim < 2 || dim > 3 || num_attr < 0 || bdry_flag < 0 || bdry_flag > 1 )
    {
        MB_SET_ERR( MB_FAILURE, "Invalid header line for node data" );
    }
    if( attr_tag_list_len > num_attr ) attr_tag_list_len = num_attr;

    // Allocate space for tag data
    std::map< Tag, int > tag_size;
    std::map< Tag, std::vector< double > > tag_data;
    for( int i = 0; i < attr_tag_list_len; ++i )
    {
        if( !attr_tag_list[i] || attr_tag_index[i] < 0 ) continue;
        std::vector< double >& data = tag_data[attr_tag_list[i]];
        // Increase tag size by one value per vertex for each time
        // we encounter it in the list.
        data.resize( data.size() + num_vtx );
        ++tag_size[attr_tag_list[i]];
    }
    std::vector< double* > attr_data( attr_tag_list_len );
    std::vector< int > attr_size( attr_tag_list_len );
    for( int i = 0; i < attr_tag_list_len; ++i )
    {
        if( !attr_tag_list[i] || attr_tag_index[i] < 0 )
        {
            attr_data[i] = 0;
            attr_size[i] = 0;
        }
        else
        {
            attr_data[i] = &( tag_data[attr_tag_list[i]] )[0];
            attr_size[i] = tag_size[attr_tag_list[i]];
        }
    }

    // Allocate vertices
    std::vector< double* > coords;
    EntityHandle start_handle;
    rval = readTool->get_node_coords( dim, num_vtx, 1, start_handle, coords );
    if( MB_SUCCESS != rval ) return rval;

    // Read data line for each node
    nodes.reserve( num_vtx );
    std::vector< double > data( 1 + dim + num_attr + bdry_flag );
    std::vector< int > ids( num_vtx );
    for( int i = 0; i < num_vtx; ++i )
    {
        rval = read_line( file, &data[0], data.size(), lineno );
        if( MB_SUCCESS != rval ) return rval;

        // Get ID
        ids[i] = (int)data[0];
        if( ids[i] >= (int)nodes.size() ) nodes.resize( ids[i] + 1 );
        nodes[ids[i]] = start_handle + i;

        // Get coordinates
        // Cppcheck warning (false positive): variable coords is assigned a value that is never used
        for( int j = 0; j < dim; ++j )
            coords[j][i] = data[j + 1];

        // Get attribute data
        for( int j = 0; j < attr_tag_list_len; ++j )
            if( attr_data[j] ) attr_data[j][i * attr_size[j] + attr_tag_index[j]] = data[j + 1 + dim];

        // Discard boundary bit
    }

    // Store tag data
    Range node_range;
    node_range.insert( start_handle, start_handle + num_vtx - 1 );
    for( std::map< Tag, std::vector< double > >::iterator i = tag_data.begin(); i != tag_data.end(); ++i )
    {
        rval = mbIface->tag_set_data( i->first, node_range, &i->second[0] );
        if( MB_SUCCESS != rval ) return rval;
    }
    Tag idtag = mbIface->globalId_tag();

    rval = mbIface->tag_set_data( idtag, node_range, &ids[0] );
    if( MB_SUCCESS != rval ) return rval;

    return MB_SUCCESS;
}

ErrorCode ReadTetGen::read_elem_file( EntityType type,
                                      std::istream& file,
                                      const std::vector< EntityHandle >& nodes,
                                      Range& elems )
{
    int lineno = 0;
    ErrorCode rval;

    int node_per_elem, have_group_id, dim;
    double header_vals[3];
    switch( type )
    {
        case MBTET:
            rval          = read_line( file, header_vals, 3, lineno );
            node_per_elem = (int)header_vals[1];
            have_group_id = (int)header_vals[2];
            dim           = 3;
            break;
        case MBTRI:
            rval          = read_line( file, header_vals, 2, lineno );
            node_per_elem = 3;
            have_group_id = (int)header_vals[1];
            dim           = 2;
            break;
        case MBEDGE:
            rval          = read_line( file, header_vals, 1, lineno );
            node_per_elem = 2;
            have_group_id = 0;
            dim           = 1;
            break;
        default:
            rval = MB_FAILURE;
            break;
    }
    if( MB_SUCCESS != rval ) return rval;
    const int num_elem = (int)header_vals[0];
    if( num_elem < 1 || node_per_elem < 2 || have_group_id < 0 || have_group_id > 1 )
    {
        MB_SET_ERR( MB_FAILURE, "Invalid header line for element data" );
    }

    // Create group map
    std::map< double, EntityHandle > groups;
    Tag dim_tag, id_tag;
    id_tag = mbIface->globalId_tag();

    const int negone = -1;
    rval = mbIface->tag_get_handle( GEOM_DIMENSION_TAG_NAME, 1, MB_TYPE_INTEGER, dim_tag, MB_TAG_SPARSE | MB_TAG_CREAT,
                                    &negone );
    if( MB_SUCCESS != rval ) return rval;

    // Allocate elements
    EntityHandle start_handle, *conn_array;
    rval = readTool->get_element_connect( num_elem, node_per_elem, type, 1, start_handle, conn_array );
    if( MB_SUCCESS != rval ) return rval;
    elems.insert( start_handle, start_handle + num_elem - 1 );

    // Read data line for each node
    std::vector< double > data( 1 + node_per_elem + have_group_id );
    std::vector< int > ids( num_elem );
    for( int i = 0; i < num_elem; ++i )
    {
        rval = read_line( file, &data[0], data.size(), lineno );
        if( MB_SUCCESS != rval ) return rval;

        // Get ID
        ids[i] = (int)data[0];

        // Get connectivity
        for( int j = 0; j < node_per_elem; ++j )
            conn_array[node_per_elem * i + j] = nodes[(int)data[j + 1]];

        // Grouping
        if( have_group_id && 0.0 != data[node_per_elem + 1] )
        {
            double id        = data[node_per_elem + 1];
            EntityHandle grp = groups[id];
            if( 0 == grp )
            {
                rval = mbIface->create_meshset( MESHSET_SET, grp );
                if( MB_SUCCESS != rval ) return rval;
                elems.insert( grp );
                rval = mbIface->tag_set_data( dim_tag, &grp, 1, &dim );
                if( MB_SUCCESS != rval ) return rval;
                int iid = (int)id;
                rval    = mbIface->tag_set_data( id_tag, &grp, 1, &iid );
                if( MB_SUCCESS != rval ) return rval;
                groups[id] = grp;
            }
            EntityHandle handle = start_handle + i;
            rval                = mbIface->add_entities( grp, &handle, 1 );
            if( MB_SUCCESS != rval ) return rval;
        }
    }

    // Store id data
    Range elems2;
    elems2.insert( start_handle, start_handle + num_elem - 1 );
    rval = mbIface->tag_set_data( id_tag, elems2, &ids[0] );
    if( MB_SUCCESS != rval ) return rval;

    return MB_SUCCESS;
}

}  // namespace moab