ReadTetGen.cpp

Go to the documentation of this file.

#include "ReadTetGen.hpp"
#include "moab/Interface.hpp"
#include "moab/Range.hpp"
#include "moab/ReadUtilIface.hpp"
#include "moab/FileOptions.hpp"
#include "MBTagConventions.hpp"
#include <iostream>
#include <fstream>
#include <sstream>
#include <cctype>
#include <map>
 
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